Contacts of the helix formed by residues 113 - 143 (chain Y) in PDB entry 2X17
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 ASP 113 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 TYR* 4.9 2.9 + - - -
1Y MET 5.9 2.5 - - - -
2Y LEU* 3.8 15.3 - - - +
3Y SER 5.5 0.7 + - - -
6Y MET* 4.0 10.0 - - + +
64Y ARG* 4.7 6.6 + - - -
108Y ALA* 2.8 21.0 + - - +
111Y GLU* 3.2 12.5 - - + +
112Y LYS* 1.3 73.6 - - - +
114Y TYR* 1.3 63.1 + - - +
115Y SER* 3.7 14.0 + - - -
116Y THR* 2.6 27.2 + - - +
117Y ARG* 3.2 20.4 + - - +
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Residues in contact with TYR 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 TYR* 3.6 55.0 - + + -
1052 ALA* 3.9 12.3 - - + -
1062 ALA* 3.4 19.6 - - + +
1092 GLU* 2.9 38.0 + - - -
1172 ARG* 3.7 19.6 + - - -
1242 ILE* 3.7 12.0 - - + +
112Y LYS* 3.4 35.7 + - + +
113Y ASP* 1.3 73.1 + - - +
115Y SER* 1.3 52.6 + - - +
117Y ARG* 3.6 7.8 - - + +
118Y ALA* 2.8 37.2 + - - +
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Residues in contact with SER 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 TYR* 2.6 29.0 + - - -
1242 ILE* 3.9 11.5 + - - +
1252 ASN* 5.1 1.0 - - - +
1282 VAL* 3.6 19.0 - - - +
60Y TYR* 3.1 15.8 + - - -
64Y ARG* 3.4 24.2 + - - -
113Y ASP* 3.3 5.9 + - - -
114Y TYR* 1.3 78.8 - - - +
116Y THR* 1.3 57.8 + - - +
118Y ALA* 3.8 2.5 - - - +
119Y PHE* 3.1 24.9 + - - +
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Residues in contact with THR 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Y LEU* 3.6 9.2 - - - +
6Y MET* 3.8 24.0 - - + -
10Y LEU* 3.9 22.4 - - + -
60Y TYR* 2.8 24.4 + - + -
108Y ALA* 4.3 4.5 - - + -
113Y ASP* 2.6 33.1 + - - -
114Y TYR 3.4 0.2 - - - -
115Y SER* 1.3 72.8 - - - +
117Y ARG* 1.3 60.1 + - - +
119Y PHE* 3.3 2.2 + - + +
120Y LEU* 2.9 40.5 + - + +
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Residues in contact with ARG 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ARG* 5.3 9.9 - - - +
1212 GLU* 5.6 0.4 + - - -
1143 TYR* 3.9 16.8 + - - +
1173 ARG* 5.4 8.7 - - - +
1183 ALA* 6.0 0.6 - - - +
105Y ALA* 3.6 31.6 - - - +
108Y ALA* 3.9 12.0 - - + +
109Y GLU* 3.2 28.4 + - + -
113Y ASP 3.2 14.2 + - - +
114Y TYR* 3.6 13.2 - - + +
116Y THR* 1.3 78.1 - - - +
118Y ALA* 1.3 59.8 + - - +
120Y LEU* 3.5 3.7 + - - +
121Y GLU* 2.9 37.7 + - - +
124Y ILE* 3.5 24.1 - - - +
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Residues in contact with ALA 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ARG* 5.7 1.0 - - - +
1212 GLU* 3.4 29.5 - - - +
1242 ILE* 4.0 16.8 - - + -
1252 ASN* 3.5 26.2 + - - +
114Y TYR 2.8 20.8 + - - +
115Y SER 3.8 4.0 - - - +
117Y ARG* 1.3 73.3 - - - +
119Y PHE* 1.3 61.9 + - - +
121Y GLU* 3.4 14.8 - - - +
122Y TRP* 4.4 1.7 + - - +
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Residues in contact with PHE 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252 ASN* 4.3 3.8 + - - -
10Y LEU* 4.3 1.3 - - + -
56Y ARG* 3.6 20.4 - - + -
57Y PHE* 3.5 37.7 - + - -
60Y TYR* 3.6 59.2 - + + -
115Y SER 3.1 18.6 + - - +
116Y THR* 3.5 9.2 - - + +
117Y ARG 3.3 0.2 - - - -
118Y ALA* 1.3 77.9 - - - +
120Y LEU* 1.3 67.6 + - + +
121Y GLU 3.4 0.5 + - - -
122Y TRP* 3.5 17.9 + - + +
123Y PHE* 3.5 30.1 - + - -
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Residues in contact with LEU 120 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y LEU* 5.2 0.2 - - + -
57Y PHE* 4.0 31.2 - - + -
101Y ILE* 4.3 18.8 - - + +
104Y LEU* 3.6 49.1 - - + +
105Y ALA* 3.7 12.6 - - + +
108Y ALA* 4.7 0.4 - - + -
116Y THR* 2.9 34.4 + - + +
117Y ARG* 3.5 9.4 + - - +
118Y ALA 3.4 0.2 - - - -
119Y PHE* 1.3 77.0 - - + +
121Y GLU* 1.3 61.0 + - - +
122Y TRP 3.1 2.7 - - - -
123Y PHE* 2.9 24.6 + - + +
124Y ILE* 3.1 15.6 + - + +
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Residues in contact with GLU 121 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 GLU* 4.3 15.0 - - + +
1173 ARG* 4.7 1.0 - - - +
1183 ALA* 3.5 32.4 - - - +
1213 GLU* 4.3 17.0 - - + +
117Y ARG* 2.9 43.1 + - - +
118Y ALA 3.4 15.9 - - - +
119Y PHE 3.2 0.2 - - - -
120Y LEU* 1.3 76.9 - - - +
122Y TRP* 1.3 59.7 + - - +
124Y ILE* 3.6 8.3 + - - +
125Y ASN* 3.1 37.5 + - - +
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Residues in contact with TRP 122 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G MET* 3.8 31.2 - - + -
53Y HIS* 3.4 32.3 - + - -
56Y ARG* 3.5 51.5 - - - +
118Y ALA 4.4 1.0 + - - -
119Y PHE 3.5 13.3 + - - +
120Y LEU 3.1 0.6 - - - -
121Y GLU* 1.3 80.5 - - - +
123Y PHE* 1.3 80.2 + + + +
125Y ASN* 3.6 6.1 + - - +
126Y GLU* 3.0 37.2 + - + +
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Residues in contact with PHE 123 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y GLU* 4.3 9.6 - - - -
53Y HIS* 3.7 34.8 - - + -
56Y ARG* 3.8 14.6 - - + -
57Y PHE* 3.4 33.0 - + - -
101Y ILE* 4.0 22.0 - - + -
119Y PHE* 3.5 40.8 - + - -
120Y LEU* 2.9 13.4 + - + +
122Y TRP* 1.3 99.5 - + + +
124Y ILE* 1.3 58.8 + - - +
126Y GLU* 3.7 13.0 - - - +
127Y GLN* 2.9 38.2 + - + +
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Residues in contact with ILE 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143 TYR* 3.7 43.5 - - + +
1153 SER* 3.8 12.5 + - - +
1183 ALA* 3.9 7.0 - - + -
101Y ILE* 3.8 18.2 - - + -
102Y TYR* 4.5 8.2 - - + -
105Y ALA* 4.4 10.5 - - + -
117Y ARG* 3.5 36.3 - - - +
120Y LEU 3.1 14.2 + - - +
121Y GLU* 3.8 13.2 - - - +
123Y PHE* 1.3 78.6 - - - +
125Y ASN* 1.3 60.4 + - - +
127Y GLN* 4.1 4.2 - - - +
128Y VAL* 3.3 24.8 + - - +
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Residues in contact with ASN 125 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153 SER 5.0 1.0 - - - +
1183 ALA* 3.4 38.3 + - - +
1193 PHE* 4.1 3.8 + - - -
121Y GLU* 3.1 29.4 + - - +
122Y TRP* 3.9 6.6 - - - +
123Y PHE 3.3 0.2 - - - -
124Y ILE* 1.3 76.4 - - - +
126Y GLU* 1.3 62.4 + - - +
128Y VAL* 3.7 19.1 + - - +
129Y GLU* 3.8 10.9 + - - +
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Residues in contact with GLU 126 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G MET* 3.7 13.0 - - + -
53Y HIS* 2.9 37.9 + - - +
122Y TRP* 3.0 32.2 + - + +
123Y PHE* 3.7 10.8 - - - +
124Y ILE 3.3 0.4 - - - -
125Y ASN* 1.3 76.1 - - - +
127Y GLN* 1.3 90.5 + - - +
129Y GLU* 3.2 13.3 + - + +
130Y GLU* 3.0 44.9 + - - +
1171Y AG 3.4 7.3 - - - -
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Residues in contact with GLN 127 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643 ARG* 5.4 0.7 - - - -
17Y GLU* 4.4 10.9 + - - -
50Y GLU* 5.1 4.0 + - - -
53Y HIS* 5.5 0.6 + - - -
94Y GLU* 2.8 30.5 + - - +
97Y ILE* 3.6 23.6 - - - +
98Y SER* 3.3 32.8 + - - +
101Y ILE* 4.5 9.6 - - + +
123Y PHE* 2.9 23.8 + - + +
124Y ILE* 4.1 5.6 - - - +
125Y ASN 3.4 0.2 - - - -
126Y GLU* 1.3 95.2 + - - +
128Y VAL* 1.3 59.2 + - - +
130Y GLU* 3.6 5.0 - - - +
131Y GLU* 2.9 36.3 + - - +
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Residues in contact with VAL 128 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603 TYR* 4.2 13.9 - - + -
633 ASP* 4.1 20.8 - - + +
643 ARG* 3.8 29.6 - - - +
1153 SER* 3.7 31.6 - - - +
124Y ILE 3.3 18.4 - - - +
125Y ASN* 3.7 11.7 - - - +
126Y GLU 3.2 0.2 - - - -
127Y GLN* 1.3 79.2 - - + +
129Y GLU* 1.3 61.5 + - + +
131Y GLU* 4.1 1.3 - - - +
132Y ALA* 3.2 24.1 + - - +
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Residues in contact with GLU 129 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633 ASP* 6.0 3.8 - - - +
170G MET* 4.1 21.5 - - + +
125Y ASN 3.8 9.1 + - - +
126Y GLU* 3.2 13.5 + - - +
128Y VAL* 1.3 79.3 - - + +
130Y GLU* 1.3 59.6 + - + +
132Y ALA* 3.5 4.2 + - - +
133Y SER* 2.9 32.8 + - - -
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Residues in contact with GLU 130 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G MET* 6.0 1.2 - - - +
24Y TYR* 4.7 0.2 + - - -
46Y GLN* 2.6 40.7 + - - +
49Y GLU* 4.7 1.0 - - - +
50Y GLU* 3.4 7.9 - - - +
53Y HIS* 3.9 5.2 - - - -
94Y GLU* 3.0 36.9 - - - +
126Y GLU* 3.0 39.1 + - + +
127Y GLN* 3.3 11.4 + - - +
129Y GLU* 1.3 75.9 - - + +
131Y GLU* 1.3 62.7 + - - +
133Y SER* 3.3 6.4 + - - -
134Y VAL* 3.1 32.6 + - - +
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Residues in contact with GLU 131 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 MET 5.4 5.7 + - - -
633 ASP 5.3 2.9 - - - +
643 ARG* 3.9 22.7 + - - +
91Y TYR* 3.8 22.6 + - + -
94Y GLU* 3.8 24.7 - - + +
95Y LYS* 4.0 24.0 - - - +
98Y SER* 2.8 30.7 + - - +
102Y TYR* 4.9 0.9 + - - -
127Y GLN 2.9 20.8 + - - +
128Y VAL* 4.1 3.6 - - - +
130Y GLU* 1.3 73.0 - - - +
132Y ALA* 1.3 58.3 + - - +
134Y VAL* 3.3 1.8 + - - -
135Y LYS* 2.8 33.8 + - - +
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Residues in contact with ALA 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 TYR 5.2 1.1 - - - +
633 ASP* 3.5 42.3 + - + +
128Y VAL 3.2 17.3 + - - +
129Y GLU* 3.9 4.7 - - - +
131Y GLU* 1.3 79.0 - - - +
133Y SER* 1.3 56.9 + - - +
135Y LYS* 4.1 5.5 - - - +
136Y LYS* 3.1 30.5 + - - +
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Residues in contact with SER 133 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Y TRP* 3.7 20.2 - - - -
46Y GLN* 5.2 3.3 + - - -
129Y GLU 2.9 19.8 + - - -
130Y GLU* 3.5 7.4 - - - -
131Y GLU 3.2 0.2 - - - -
132Y ALA* 1.3 78.3 - - - +
134Y VAL* 1.3 61.1 + - - +
136Y LYS* 3.8 7.3 - - - +
137Y ILE* 3.5 25.9 + - - +
161Y ARG* 5.3 0.7 + - - -
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Residues in contact with VAL 134 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Y TYR* 4.7 6.5 - - + +
42Y TRP* 4.3 19.7 - - + -
46Y GLN* 5.5 1.6 - - - +
87Y PHE* 3.9 26.9 - - + +
90Y ALA* 4.0 6.5 - - + -
91Y TYR* 3.8 33.9 - - + +
94Y GLU* 4.2 18.4 - - + -
130Y GLU* 3.1 20.8 + - - +
131Y GLU 3.9 2.9 - - - +
133Y SER* 1.3 76.6 - - - +
135Y LYS* 1.3 58.5 + - - +
136Y LYS 3.2 0.2 - - - -
137Y ILE* 3.3 5.5 + - - +
138Y LEU* 3.0 25.5 + - - +
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Residues in contact with LYS 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653 ASN* 3.4 41.7 + - + +
11743 AG 4.3 0.9 - - - -
91Y TYR* 3.6 43.2 - - + +
131Y GLU 2.8 19.7 + - - +
132Y ALA* 4.1 5.6 - - - +
134Y VAL* 1.3 73.7 - - - +
136Y LYS* 1.3 60.0 + - - +
138Y LEU* 3.5 12.5 - - + +
139Y ASP* 2.7 64.0 + - - +
142Y LYS* 5.6 4.2 - - - +
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Residues in contact with LYS 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLY* 5.9 3.4 - - - +
37L GLU* 3.0 41.2 + - + +
132Y ALA 3.1 19.1 + - - +
133Y SER* 3.8 9.0 - - - +
134Y VAL 3.2 0.2 - - - -
135Y LYS* 1.3 77.6 - - - +
137Y ILE* 1.3 64.3 + - + +
139Y ASP* 3.7 5.4 + - - +
140Y LYS* 3.4 54.0 + - + +
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Residues in contact with ILE 137 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Y PHE* 4.5 3.1 - - + -
42Y TRP* 3.6 33.0 - - + +
87Y PHE* 3.7 36.3 - - + -
133Y SER* 3.5 18.6 - - - +
134Y VAL 3.3 2.5 + - - +
136Y LYS* 1.3 80.0 - - + +
138Y LEU* 1.3 66.9 + - - +
140Y LYS* 3.2 11.0 + - + +
141Y LEU* 3.0 28.6 + - + +
154Y LEU* 4.8 9.2 - - + -
158Y LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 138 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y LEU* 4.1 3.2 - - + +
87Y PHE* 3.4 30.7 - - + +
88Y GLU* 3.7 23.3 - - + -
91Y TYR* 3.6 28.7 - - + -
134Y VAL 3.0 16.2 + - - +
135Y LYS* 3.5 13.5 - - + +
137Y ILE* 1.3 76.1 - - - +
139Y ASP* 1.3 65.8 + - - +
141Y LEU* 3.1 15.0 + - - +
142Y LYS* 3.0 53.6 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653 ASN* 4.4 3.8 - - - +
33L ASP 5.6 1.2 - - - +
34L LEU 6.0 2.0 - - - +
35L GLY* 6.1 5.3 - - - -
135Y LYS* 2.7 53.2 + - - +
136Y LYS* 3.9 6.4 - - - +
138Y LEU* 1.3 82.8 - - - +
140Y LYS* 1.3 56.9 + - + +
142Y LYS* 3.3 14.4 + - - +
143Y PHE* 3.0 27.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLY* 4.4 17.3 - - - +
37L GLU* 6.3 0.2 - - - -
152L PHE* 4.7 12.9 - - + -
155L ASP* 5.6 5.1 + - - -
136Y LYS* 3.4 47.1 + - - +
137Y ILE* 3.2 14.9 + - + +
139Y ASP* 1.3 77.9 - - + +
141Y LEU* 1.3 57.9 + - - +
143Y PHE* 3.4 14.0 + - + +
144Y ALA* 3.2 25.6 + - - +
150Y ILE* 5.1 0.7 - - - +
154Y LEU* 3.8 35.4 - - + +
157Y GLU* 3.5 22.6 + - - -
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Residues in contact with LEU 141 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Y PHE* 4.2 13.0 - - + -
83Y PRO* 3.5 31.9 - - + +
84Y LEU* 3.8 26.2 - - + +
87Y PHE* 3.6 29.8 - - + -
137Y ILE* 3.0 24.1 + - + +
138Y LEU* 3.1 7.6 + - - +
140Y LYS* 1.3 76.7 - - - +
142Y LYS* 1.3 61.3 + - - +
143Y PHE 3.2 0.4 - - - -
144Y ALA* 3.2 25.1 - - + +
145Y LYS* 3.7 3.3 + - - -
151Y LEU* 3.9 28.3 - - + -
154Y LEU* 4.6 8.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y LEU* 3.7 19.5 - - + -
88Y GLU* 4.3 12.6 - - - -
135Y LYS* 5.6 3.6 - - - +
138Y LEU* 3.0 31.1 + - + +
139Y ASP* 3.3 17.1 + - - +
141Y LEU* 1.3 73.9 - - - +
143Y PHE* 1.3 62.4 + - - +
144Y ALA 3.2 0.2 - - - -
145Y LYS* 3.3 36.0 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LEU 5.9 3.4 - - - -
36L LEU* 5.5 8.1 - - + -
148L PRO* 3.8 39.2 - - + +
151L LEU* 3.7 30.1 - - + -
152L PHE* 5.0 15.5 - + + -
139Y ASP 3.0 15.9 + - - +
140Y LYS* 3.5 15.5 - - + +
141Y LEU 3.2 0.2 - - - -
142Y LYS* 1.3 77.4 - - - +
144Y ALA* 1.3 58.1 + - - +
145Y LYS 3.8 1.8 + - - -
150Y ILE* 4.5 15.9 - - + +
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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