RESIDUES

RESIDUES will put a label on each atom in a protein. The label is a short description of the atom, and is useful in identifying the atoms in a protein. The general form of the label for an atom is '(nnnnn TYPfrrr)' where nnnnn is the atom number (the 10th atom would have the atom number 10), TYP is a three letter symbol for each amino acid (the allowed symbols are shown in the Table). If a residue is not recognized, then the symbol 'UNK' (unknown) will be used. Backbone atoms are indicated by an asterisk (*) after the residue symbol, i.e., `f'=*; for all other atoms, 'f' is a space; rrr is the residue number. A modified residue can still be recognized if XENO=text is used. The residue nearest to the NH₂ end of the protein is No. 1, the next is 2, and so on.

When RESIDUES is present, the net charge on each residue will be printed in the normal output; this is useful in identifying ionized residues. If gradients are printed, then gradient norms for each residue are also printed.

Table: Abbreviations for the 20 Amino Acids

Amino Acid	Formula of Residue $^{dag }$	Three-Letter Abbreviation	One-Letter Abbreviation
Glycine	C₂NOH₃	GLY	G
Alanine	C₃NOH₅	ALA	A
Valine	C₅NOH₉	VAL	V
Leucine	C₆NOH₁₁	LEU	L
Isoleucine	C₆NOH₁₁	ILE	I
Serine	C₃NO₂H₅	SER	S
Threonine	C₄NO₂H₇	THR	T
Aspartic acid	C₄NO₃H₅ (4)	ASP	D
Asparagine	C₄N₂O₂H₆	ASN	N
Lysine	C₆N₂OH₁₂ (13)	LYS	K
Glutamic acid	C₅NO₃H₇ (6)	GLU	E
Glutamine	C₅N₂O₂H₈	GLN	Q
Arginine	C₆N₄OH₁₂ (13)	ARG	R
Histidine	C₆N₃OH₇(8)	HIS	H
Phenylalanine	C₉NOH₉	PHE	F
Cysteine	C₃NOSH₅ (4)	CYS	C
Tryptophan	C₁₁N₂OH₁₀	TRP	W
Tyrosine	C₉NO₂H₉(8)	TYR	Y
Methionine	C₅NOSH₉	MET	M
Proline	C₅NOH₇	PRO	P

: The number of hydrogen atoms in the ionized residue is given in parenthesis after the formula. Cysteine may exist in the neutral, ionized or reduced form.