Contacts of the helix formed by residues 42 - 71 (chain L) in PDB entry 3A68
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 42 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 3.5 1.6 - - - +
40L LYS* 4.0 5.1 + - - +
41L TYR* 1.3 80.6 - - - +
43L ASP* 1.3 65.8 + - - +
44L GLU* 3.6 18.4 - - - +
45L SER* 3.0 31.6 + - - +
46L GLU* 3.0 12.5 + - - +
157L ASN* 3.6 35.9 - - + +
159L ASP* 4.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 3.0 25.7 + - - +
42L VAL* 1.3 73.1 - - - +
44L GLU* 1.3 65.3 + - + +
46L GLU* 3.3 12.3 + - - +
47L SER* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 3.6 11.2 - - - +
43L ASP* 1.3 89.7 + - + +
45L SER* 1.3 57.5 + - - +
47L SER* 3.6 6.1 + - - -
48L ALA* 3.0 28.1 + - - +
153L VAL* 3.7 8.8 - - + +
157L ASN* 3.0 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L TYR* 4.0 16.6 - - - -
42L VAL* 3.0 23.7 + - - +
44L GLU* 1.3 76.2 - - - +
46L GLU* 1.3 66.2 + - - +
48L ALA* 3.2 2.7 + - - +
49L VAL* 2.9 28.1 + - - +
153L VAL* 4.2 11.4 + - - +
154L ALA* 4.6 0.2 - - - -
157L ASN* 4.2 13.5 + - - +
159L ASP* 4.1 8.8 + - - +
162L LEU* 3.8 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 3.7 24.8 + - - +
41L TYR* 3.7 21.2 - - + -
42L VAL 3.0 12.3 + - - +
43L ASP* 3.6 17.5 - - - +
45L SER* 1.3 77.5 - - - +
47L SER* 1.3 63.4 + - - +
49L VAL 3.4 0.2 + - - -
50L ASN* 3.1 16.2 + - - +
102L GLN* 3.0 37.0 + - - +
107L GLY* 3.4 4.8 - - - -
108L LYS* 2.7 34.9 + - - +
110L LYS* 6.0 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ASP* 2.8 24.3 + - - +
44L GLU* 3.8 6.5 - - - -
46L GLU* 1.3 74.0 + - - +
48L ALA* 1.3 57.8 + - - +
50L ASN* 3.2 10.5 + - - +
51L GLU* 2.9 28.3 + - - +
112L GLN* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L GLU 3.0 18.7 + - - +
45L SER 3.2 4.0 + - - +
47L SER* 1.3 76.0 - - - +
49L VAL* 1.3 63.2 + - - +
51L GLU* 3.3 8.2 + - - +
52L GLN* 3.0 22.5 + - - +
149L ASN* 6.0 1.6 - - - +
150L LEU* 3.5 23.7 - - + +
153L VAL* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L TYR* 3.3 20.2 - - - +
45L SER 2.9 17.2 + - - +
46L GLU 3.7 4.5 - - - +
48L ALA* 1.3 75.6 - - - +
50L ASN* 1.3 63.9 + - - +
52L GLN* 3.1 6.0 + - - +
53L ILE* 2.9 25.6 + - + +
98L LEU* 3.8 32.5 - - + +
101L TYR* 4.7 4.0 - - + -
102L GLN* 3.7 20.4 - - + +
150L LEU* 4.1 11.0 - - + -
162L LEU* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L GLU* 3.1 17.4 + - - +
47L SER* 3.5 10.8 - - - +
49L VAL* 1.3 76.2 - - - +
51L GLU* 1.3 62.0 + - - +
53L ILE* 3.4 15.7 + - - +
54L ASN* 3.2 16.8 + - - +
102L GLN* 3.1 18.4 + - - +
108L LYS 3.0 21.0 + - - -
109L VAL* 3.4 4.2 - - - -
110L LYS* 3.0 47.2 + - + +
112L GLN* 3.8 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L SER 2.9 13.5 + - - +
48L ALA* 3.5 12.3 - - - +
49L VAL 3.2 0.2 - - - -
50L ASN* 1.3 75.8 - - - +
52L GLN* 1.3 60.4 + - - +
54L ASN* 3.1 4.7 + - - +
55L VAL* 3.0 35.1 + - + +
112L GLN* 3.8 22.6 + - - +
146L LYS* 3.8 18.0 + - + +
149L ASN* 6.4 0.2 - - - +
14T ILE 4.3 11.4 + - - +
15T PHE* 3.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ALA 3.0 14.1 + - - +
49L VAL 3.1 7.2 + - - +
51L GLU* 1.3 73.8 - - - +
53L ILE* 1.3 67.5 + - - +
55L VAL* 3.1 17.4 + - - +
56L GLU* 2.8 54.7 + - - +
98L LEU* 3.5 22.2 - - + -
143L THR* 4.0 5.3 + - - +
146L LYS* 3.4 30.4 - - - +
147L LEU* 3.4 29.1 - - + +
150L LEU* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L VAL* 2.9 25.1 + - + +
50L ASN* 3.6 26.7 - - - +
51L GLU 3.3 0.2 - - - -
52L GLN* 1.3 75.6 - - - +
54L ASN* 1.3 58.7 + - - +
56L GLU* 3.4 2.4 + - - +
57L TYR* 3.0 29.1 + - + +
95L ALA* 3.9 12.2 - - + +
98L LEU* 3.5 28.7 - - + +
99L MET* 3.7 39.3 - - + +
102L GLN* 4.8 0.2 - - + -
109L VAL* 4.3 9.4 - - + -
110L LYS 5.9 0.9 - - - +
111L LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASN 3.2 7.4 + - - +
51L GLU* 3.1 10.7 + - - +
53L ILE* 1.3 79.1 - - - +
55L VAL* 1.3 58.7 - - - +
57L TYR* 3.4 4.1 + - - +
58L ASN* 2.9 57.0 + - - +
111L LEU* 6.4 0.2 - - - -
112L GLN* 3.5 44.1 + - + +
113L SER 3.1 21.8 + - - +
114L ILE* 4.5 1.9 - - - +
14T ILE* 5.3 0.2 - - - +
15T PHE* 3.6 24.5 + - - +
61V TYR* 4.2 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L GLU* 3.0 34.2 + - + +
52L GLN* 3.1 27.6 + - - +
54L ASN* 1.3 76.7 - - - +
56L GLU* 1.3 63.0 + - - +
58L ASN* 3.2 3.6 + - - +
59L VAL* 3.0 23.3 + - + +
143L THR* 4.2 20.6 - - + +
146L LYS* 4.0 35.2 - - + -
15T PHE* 4.0 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLN* 2.8 39.4 + - - +
55L VAL* 1.3 74.2 - - - +
57L TYR* 1.3 57.5 - - - +
59L VAL* 3.3 4.3 + - - +
60L SER* 2.9 27.5 + - - -
91L GLU* 3.0 17.0 - - - +
94L HIS* 3.7 12.4 - - + +
95L ALA* 3.8 22.2 - - + +
98L LEU* 3.9 17.7 - - + -
143L THR* 3.5 14.1 - - - +
147L LEU* 3.9 10.4 - - - +
170L TYR* 4.4 4.2 - - - -
214L CA 2.5 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ILE* 3.0 24.3 + - + +
54L ASN* 3.8 7.2 - - - +
56L GLU* 1.3 76.2 - - - +
58L ASN* 1.3 62.0 + - - +
60L SER* 3.3 12.9 + - - -
61L TYR* 3.0 23.5 + + + +
92L ARG* 3.8 21.4 + - + -
95L ALA* 3.8 23.0 - - + +
99L MET* 4.5 7.2 - - - -
111L LEU* 4.7 2.0 - - + -
114L ILE* 3.5 25.6 - - + -
57V TYR* 5.3 13.2 - + - -
60V SER* 4.9 2.8 + - - -
61V TYR* 3.5 39.4 - + - +
64V HIS* 2.6 42.0 + + - +
88V SER* 4.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L ASN* 2.9 53.0 + - - +
55L VAL 3.6 4.5 - - - +
57L TYR* 1.3 75.5 - - - +
59L VAL* 1.3 64.7 + - - +
61L TYR* 3.1 3.5 + - - +
62L VAL* 2.9 27.8 + - - +
113L SER 4.1 6.7 + - - -
114L ILE* 3.3 26.0 - - - +
115L VAL* 3.5 23.2 + - - +
15T PHE* 3.8 16.0 + - + -
17T PRO* 3.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L VAL* 3.0 24.0 + - + +
56L GLU* 3.7 7.2 - - - +
58L ASN* 1.3 74.4 - - - +
60L SER* 1.3 63.1 + - - +
62L VAL* 3.3 7.4 + - - +
63L TYR* 2.9 51.5 + - + -
91L GLU* 3.7 17.0 - - - +
139L LEU* 4.8 22.7 - - + +
140L GLU* 4.2 4.9 - - - +
143L THR* 3.4 25.1 - - + +
15T PHE* 5.1 7.2 - - + -
17T PRO* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L GLU 2.9 14.0 + - - -
57L TYR* 3.4 16.1 - - - -
58L ASN 3.2 0.2 - - - -
59L VAL* 1.3 75.8 - - - +
61L TYR* 1.3 57.6 + - - +
63L TYR 3.3 0.5 + - - -
64L HIS 3.0 14.9 + - - -
88L SER* 2.8 52.0 + - - +
91L GLU* 3.6 13.8 - - - +
92L ARG* 3.7 18.6 - - - +
57V TYR* 5.0 2.9 + - - -
92V ARG* 4.5 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L TYR* 3.0 13.9 + + - +
58L ASN* 3.1 8.0 + - - +
60L SER* 1.3 75.7 - - - +
62L VAL* 1.3 64.6 + - + +
64L HIS* 3.1 6.7 + - - +
65L ALA* 3.0 21.3 + - - +
114L ILE* 3.6 28.3 - - + -
115L VAL 3.9 4.7 - - - -
117L PRO* 3.6 31.9 - - + -
54V ASN* 4.1 5.2 + - - -
57V TYR* 3.6 51.2 - + - +
111V LEU* 3.6 20.9 - - + +
112V GLN 2.6 36.6 + - - -
113V SER* 5.1 0.2 - - - -
114V ILE* 3.8 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ASN* 2.9 20.3 + - - +
59L VAL* 3.7 5.8 - - - +
61L TYR* 1.3 77.0 - - + +
63L TYR* 1.3 57.4 + - - +
65L ALA* 3.1 5.0 + - - +
66L MET* 2.9 40.3 + - + +
117L PRO* 4.1 12.1 - - + -
121L PHE* 5.1 0.4 - - + -
139L LEU* 3.4 30.7 - - + -
17T PRO* 4.1 21.5 - - + -
18T PHE* 3.6 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L VAL* 2.9 34.5 + - + +
60L SER 3.7 4.0 - - - +
62L VAL* 1.3 75.6 - - - +
64L HIS* 1.3 58.3 + - - +
66L MET* 3.2 13.6 + - + +
67L PHE* 2.9 25.3 + - - +
83L PHE* 5.5 1.1 - + - -
84L PHE* 3.6 43.2 - + - +
87L SER* 3.7 20.9 - - - -
88L SER 3.7 5.2 - - - +
91L GLU* 3.6 21.8 - - + -
136L ALA* 3.8 30.5 + - + +
139L LEU* 4.5 6.8 - - + +
140L GLU* 2.5 41.2 + - - +
181L ILE* 4.0 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L SER 3.0 8.2 + - - +
61L TYR* 3.1 8.7 + - - +
63L TYR* 1.3 75.8 - - - +
65L ALA* 1.3 58.7 + - - +
67L PHE* 3.3 20.2 + + + +
68L ALA* 2.9 27.5 + - - +
85L LYS* 5.1 2.2 - - - -
88L SER* 3.5 20.8 + - - +
57V TYR* 2.7 36.0 + + - +
92V ARG* 3.8 18.2 + - + -
96V GLU* 2.7 41.8 + - + +
99V MET* 3.7 23.5 - - + +
111V LEU* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L TYR 3.0 12.4 + - - +
62L VAL* 3.3 9.0 - - - +
64L HIS* 1.3 76.6 - - - +
66L MET* 1.3 60.9 + - - +
68L ALA* 3.2 7.6 + - - +
69L TYR* 3.1 18.7 + - - +
117L PRO* 3.9 16.6 - - + -
118L LEU 3.4 25.1 - - - +
119L SER* 4.5 4.5 - - - +
121L PHE* 3.8 9.5 - - + -
111V LEU* 3.7 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L VAL* 2.9 34.3 + - + +
63L TYR* 3.2 19.5 + - - +
65L ALA* 1.3 73.6 - - - +
67L PHE* 1.3 66.2 + - - +
69L TYR* 3.3 1.4 + - - +
70L PHE* 3.1 33.2 + - + -
84L PHE* 3.8 39.9 - - + -
121L PHE* 3.5 26.0 - - + -
132L ALA* 4.4 7.2 - - - +
135L LEU* 3.2 44.4 - - + -
136L ALA* 4.5 1.6 - - - +
139L LEU* 3.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L TYR 2.9 13.3 + - - +
64L HIS* 3.4 25.4 - + - +
66L MET* 1.3 76.6 - - - +
68L ALA* 1.3 69.1 + - - +
70L PHE* 3.3 1.7 + - - +
71L ASP* 3.0 47.8 + - + +
81L ALA* 3.4 28.7 - - + +
84L PHE* 3.7 7.5 - - - +
85L LYS* 3.6 39.0 - - + +
96V GLU* 4.4 14.8 - - + -
99V MET* 4.1 15.7 - - + -
100V GLU* 4.0 31.0 - - + -
103V ASN* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L HIS 2.9 14.0 + - - +
65L ALA* 3.2 11.2 + - - +
67L PHE* 1.3 84.4 - - + +
69L TYR* 1.3 60.7 + - - +
72L ARG* 3.7 5.5 + - - +
99V MET* 3.9 9.9 - - + -
103V ASN* 2.9 31.5 + - - +
109V VAL* 3.7 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L ALA 3.1 6.3 + - - +
66L MET 3.6 6.7 - - - +
68L ALA* 1.3 77.9 - - - +
70L PHE* 1.3 88.0 + + - +
72L ARG* 3.1 54.8 + - - +
75L VAL* 3.6 33.8 - - + +
119L SER 3.7 9.4 + - - +
120L ASP* 3.0 21.0 + - - -
121L PHE* 3.6 40.2 - + + -
122L ASP* 3.2 32.4 + - - +
128L ASP* 4.1 7.3 + - + +
33V GLN* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L MET* 3.1 29.9 + - + +
69L TYR* 1.3 91.6 - + + +
71L ASP* 1.3 58.9 + - - +
72L ARG 3.2 2.1 + - - -
75L VAL* 3.6 15.9 - - + -
76L ALA* 3.8 5.7 + - - -
77L LEU* 3.5 54.6 + - + +
80L LEU* 4.0 7.2 - - + -
81L ALA* 3.9 25.4 - - - +
84L PHE* 3.7 18.4 - + - -
121L PHE* 4.5 6.3 - - + -
128L ASP* 3.6 26.7 - - + -
129L ALA* 4.2 4.0 - - - -
132L ALA* 3.4 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E LYS* 3.0 34.4 + - - -
183E GLU* 4.5 2.9 - - - +
67L PHE* 3.0 45.1 + - + +
69L TYR 3.2 0.2 - - - -
70L PHE* 1.3 74.1 - - - +
72L ARG* 1.3 64.6 + - - +
76L ALA* 5.7 0.2 - - - -
81L ALA* 4.0 7.5 - - + +
100V GLU* 4.2 13.2 - - - +
103V ASN* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il