Contacts of the helix formed by residues 113 - 143 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020 TYR* 5.3 1.1 + - - -
2Z LEU* 3.8 12.2 - - - +
6Z MET* 3.6 16.6 - - + +
60Z TYR* 4.6 0.2 + - - -
64Z ARG* 4.6 6.1 + - - -
108Z ALA* 2.7 25.1 + - - +
111Z GLU* 3.2 17.4 - - + +
112Z LYS* 1.3 73.1 - - - +
114Z TYR* 1.3 61.1 + - - +
115Z SER* 3.6 10.6 + - - -
116Z THR* 2.7 33.5 + - - +
117Z ARG* 3.2 18.1 + - - +
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Residues in contact with TYR 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020 TYR* 3.5 57.7 - + + -
1050 ALA* 4.1 9.0 - - + -
1060 ALA* 3.5 19.6 - - + +
1090 GLU* 3.1 35.9 + - - -
1170 ARG* 3.5 22.2 + - - -
1240 ILE* 3.5 13.7 - - + +
112Z LYS* 3.1 46.3 + - + +
113Z ASP* 1.3 72.9 + - - +
115Z SER* 1.3 57.5 + - - +
117Z ARG* 3.7 8.3 - - + +
118Z ALA* 2.8 32.4 + - - +
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Residues in contact with SER 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020 TYR* 2.7 29.9 + - - -
1240 ILE* 3.8 11.1 + - - +
1250 ASN* 4.9 0.7 - - - +
1280 VAL* 3.8 16.5 - - - +
60Z TYR* 3.1 16.3 + - - -
64Z ARG* 3.2 27.2 + - - -
113Z ASP* 3.2 5.3 + - - -
114Z TYR* 1.3 78.3 - - - +
116Z THR* 1.3 57.4 + - - +
118Z ALA* 3.5 2.3 + - - +
119Z PHE* 3.0 25.3 + - - +
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Residues in contact with THR 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z LEU* 3.6 8.3 - - - +
6Z MET* 3.8 22.9 - - + -
10Z LEU* 3.9 23.6 - - + -
60Z TYR* 2.9 21.4 + - + -
108Z ALA* 4.2 4.5 - - + -
113Z ASP* 2.7 32.9 + - - -
114Z TYR 3.4 0.2 - - - -
115Z SER* 1.3 73.2 - - - +
117Z ARG* 1.3 60.8 + - - +
119Z PHE* 3.2 1.8 + - + +
120Z LEU* 2.9 43.8 + - + +
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Residues in contact with ARG 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170 ARG* 5.3 9.2 - - - +
1210 GLU* 4.7 2.9 + - - +
1147 TYR* 3.4 26.1 + - - +
1177 ARG* 5.3 9.7 - - - +
1187 ALA 6.1 0.4 - - - +
105Z ALA* 3.6 35.4 - - - +
108Z ALA* 3.7 10.2 - - + +
109Z GLU* 3.1 31.3 + - + +
113Z ASP 3.2 17.5 + - - +
114Z TYR* 3.7 11.0 - - + +
116Z THR* 1.3 77.2 - - - +
118Z ALA* 1.3 60.9 + - - +
120Z LEU* 3.5 3.6 + - - +
121Z GLU* 3.0 35.6 + - - +
124Z ILE* 3.7 14.5 - - - +
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Residues in contact with ALA 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170 ARG* 6.0 0.4 - - - +
1210 GLU* 3.6 26.9 - - - +
1240 ILE* 3.9 16.8 - - + -
1250 ASN* 3.4 31.7 + - - +
114Z TYR 2.8 17.9 + - - +
115Z SER 3.8 3.4 - - - +
117Z ARG* 1.3 73.8 - - - +
119Z PHE* 1.3 64.2 + - - +
121Z GLU* 3.4 15.9 - - - +
122Z TRP* 4.5 0.9 + - - +
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Residues in contact with PHE 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250 ASN* 4.0 5.8 + - - +
10Z LEU* 4.3 3.1 - - + -
56Z ARG* 3.5 29.2 - - + -
57Z PHE* 3.6 33.7 - + - -
60Z TYR* 3.5 49.8 - + + -
115Z SER 3.0 19.0 + - - +
116Z THR 3.2 6.9 + - - +
118Z ALA* 1.3 77.6 - - - +
120Z LEU* 1.3 67.1 + - + +
121Z GLU 3.2 1.3 + - - -
122Z TRP* 3.5 18.1 + - + +
123Z PHE* 3.5 31.4 - + - -
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Residues in contact with LEU 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z LEU* 5.2 0.2 - - + -
57Z PHE* 4.1 21.8 - - + -
101Z ILE* 4.3 15.3 - - + -
104Z LEU* 3.6 60.6 - - + +
105Z ALA* 3.7 8.5 - - + +
108Z ALA* 4.7 0.4 - - + -
116Z THR* 2.9 33.7 + - + +
117Z ARG* 3.5 11.6 + - - +
118Z ALA 3.3 0.2 - - - -
119Z PHE* 1.3 79.2 - - + +
121Z GLU* 1.3 64.6 + - - +
122Z TRP 3.2 2.9 - - - -
123Z PHE* 3.2 10.4 + - + +
124Z ILE* 3.1 29.3 + - + +
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Residues in contact with GLU 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210 GLU* 4.4 15.4 - - + +
1177 ARG* 4.7 1.9 + - - +
1187 ALA* 3.5 30.9 - - - +
1217 GLU* 4.3 18.9 - - + +
117Z ARG* 3.0 37.4 + - - +
118Z ALA 3.4 15.3 - - - +
119Z PHE 3.2 0.8 - - - -
120Z LEU* 1.3 78.6 - - - +
122Z TRP* 1.3 61.2 + - - +
124Z ILE* 3.6 9.7 + - - +
125Z ASN* 2.8 40.0 + - - +
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Residues in contact with TRP 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H MET* 3.9 23.1 - - + -
171H GLN 3.8 6.4 + - - -
172H GLY* 3.5 32.3 - - - -
53Z HIS* 4.2 5.6 - + - -
56Z ARG* 3.4 49.3 - - - +
118Z ALA 4.5 0.8 + - - -
119Z PHE* 3.5 13.2 + - + +
120Z LEU 3.2 0.6 - - - -
121Z GLU* 1.3 78.7 - - - +
123Z PHE* 1.3 91.5 + + + +
125Z ASN* 3.6 6.3 + - - +
126Z GLU* 3.0 41.4 + - + +
1173Z AG 3.9 18.4 - - - -
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Residues in contact with PHE 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Z GLU* 4.1 8.1 - - - -
53Z HIS* 3.6 31.2 - - + -
56Z ARG* 3.7 15.9 - - + -
57Z PHE* 3.4 36.3 - + - -
101Z ILE* 4.1 20.2 - - + -
119Z PHE* 3.5 42.2 - + - -
120Z LEU* 3.2 11.4 + - - +
122Z TRP* 1.3 94.9 - + + +
124Z ILE* 1.3 60.5 + - - +
126Z GLU* 3.2 22.0 - - - +
127Z GLN* 2.9 31.7 + - - +
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Residues in contact with ILE 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147 TYR* 3.5 37.5 - - + +
1157 SER* 3.8 16.7 + - - +
1187 ALA* 3.8 10.1 - - + -
101Z ILE* 3.8 18.2 - - + -
102Z TYR* 4.5 7.9 - - + -
105Z ALA* 4.5 9.6 - - + -
117Z ARG* 3.7 33.2 - - - +
120Z LEU 3.1 18.9 + - - +
121Z GLU* 3.8 10.8 - - - +
122Z TRP 3.4 0.2 - - - -
123Z PHE* 1.3 79.8 - - - +
125Z ASN* 1.3 61.4 + - - +
127Z GLN* 3.5 4.7 + - - +
128Z VAL* 3.3 21.8 + - - +
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Residues in contact with ASN 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157 SER 5.2 0.3 - - - +
1187 ALA* 3.6 30.5 + - - +
1197 PHE* 4.3 3.5 + - - -
121Z GLU* 2.8 37.0 + - - +
122Z TRP* 3.9 5.9 - - - +
124Z ILE* 1.3 76.3 - - - +
126Z GLU* 1.3 61.7 + - - +
128Z VAL* 3.6 19.2 + - - +
129Z GLU* 3.7 10.9 + - - +
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Residues in contact with GLU 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H MET* 3.7 29.1 - - + +
53Z HIS* 3.0 29.1 + - + -
122Z TRP* 3.0 27.2 + - + +
123Z PHE* 3.2 32.8 - - - +
125Z ASN* 1.3 75.9 - - - +
127Z GLN* 1.3 86.4 + - - +
129Z GLU* 3.2 8.7 + - - +
130Z GLU* 3.0 43.7 + - + +
1173Z AG 3.8 0.9 - - - -
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Residues in contact with GLN 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647 ARG* 5.3 0.4 - - - -
17Z GLU* 4.6 4.4 + - - -
50Z GLU* 5.0 3.8 + - - -
53Z HIS* 4.8 1.6 + - - -
94Z GLU* 3.0 30.9 + - - +
97Z ILE* 3.5 27.8 - - + +
98Z SER* 3.0 33.8 + - - +
101Z ILE* 4.7 7.4 - - + +
102Z TYR* 6.1 0.4 - - - +
123Z PHE* 2.9 22.2 + - + +
124Z ILE* 4.0 6.3 - - - +
125Z ASN 3.4 0.2 - - - -
126Z GLU* 1.3 100.0 + - - +
128Z VAL* 1.3 59.8 + - - +
130Z GLU* 3.6 5.4 + - - +
131Z GLU* 2.9 35.7 + - - +
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Residues in contact with VAL 128 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607 TYR* 4.2 14.8 - - + -
637 ASP* 4.1 21.0 - - + +
647 ARG* 3.9 28.5 - - - +
1157 SER* 3.8 31.0 - - - +
124Z ILE 3.3 17.5 - - - +
125Z ASN* 3.7 12.6 - - - +
126Z GLU 3.2 0.4 - - - -
127Z GLN* 1.3 76.9 - - + +
129Z GLU* 1.3 63.2 + - + +
131Z GLU* 4.2 1.4 - - - +
132Z ALA* 3.3 23.7 + - - +
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Residues in contact with GLU 129 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637 ASP* 6.0 3.6 - - - +
170H MET* 3.6 31.4 - - + +
125Z ASN 3.7 8.4 + - - +
126Z GLU 3.2 9.7 + - - +
128Z VAL* 1.3 80.1 - - + +
130Z GLU* 1.3 57.8 + - + +
132Z ALA* 3.4 4.8 + - - +
133Z SER* 2.9 32.7 + - - -
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Residues in contact with GLU 130 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H MET* 5.7 6.0 - - - +
46Z GLN* 2.6 34.6 + - - +
49Z GLU* 4.9 2.6 - - - +
50Z GLU* 3.0 14.7 - - - +
53Z HIS* 4.9 4.9 - - + -
94Z GLU* 2.9 39.8 - - - +
126Z GLU* 3.0 41.3 + - + +
127Z GLN* 3.6 6.6 + - - +
128Z VAL 3.4 0.2 - - - -
129Z GLU* 1.3 78.5 - - + +
131Z GLU* 1.3 62.0 + - - +
133Z SER* 3.4 6.3 + - - -
134Z VAL* 3.2 31.5 + - - +
161Z ARG* 5.4 0.3 + - - -
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Residues in contact with GLU 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17 MET 5.5 4.5 + - - -
637 ASP 5.4 2.5 - - - +
647 ARG* 4.1 24.9 + - - +
91Z TYR* 3.8 21.5 + - + -
94Z GLU* 3.9 22.8 - - + +
95Z LYS* 3.7 25.7 - - - +
98Z SER* 2.8 33.5 + - - +
102Z TYR* 4.9 0.2 + - - -
127Z GLN 2.9 16.9 + - - +
128Z VAL* 4.2 3.8 - - - +
130Z GLU* 1.3 76.0 - - - +
132Z ALA* 1.3 58.2 + - - +
134Z VAL 3.4 0.7 + - - -
135Z LYS* 2.9 31.8 + - - +
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Residues in contact with ALA 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 TYR 5.3 0.7 - - - +
637 ASP* 3.6 40.3 + - + +
128Z VAL 3.3 17.6 + - - +
129Z GLU* 3.9 4.5 - - - +
131Z GLU* 1.3 77.5 - - - +
133Z SER* 1.3 63.3 + - - +
135Z LYS* 4.3 4.8 - - - +
136Z LYS* 3.2 26.2 + - - +
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Residues in contact with SER 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Z TRP* 3.8 18.8 + - - -
46Z GLN* 5.2 3.1 + - - -
129Z GLU 2.9 19.3 + - - -
130Z GLU* 3.6 8.3 - - - -
131Z GLU 3.2 0.2 - - - -
132Z ALA* 1.3 79.7 - - - +
134Z VAL* 1.3 60.5 + - - +
136Z LYS* 3.8 6.9 - - - +
137Z ILE* 3.5 26.1 + - - +
161Z ARG* 5.3 0.9 + - - -
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Residues in contact with VAL 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Z TYR* 5.0 6.1 - - + +
42Z TRP* 4.3 18.4 - - + -
46Z GLN* 5.6 3.8 - - + +
87Z PHE* 3.7 26.7 - - + +
90Z ALA* 4.2 6.3 - - + -
91Z TYR* 3.7 34.1 - - + +
94Z GLU* 4.0 19.3 - - + +
130Z GLU* 3.2 19.3 + - - +
131Z GLU 4.1 2.5 - - - +
133Z SER* 1.3 77.7 - - - +
135Z LYS* 1.3 60.8 + - - +
136Z LYS 3.2 0.2 - - - -
137Z ILE* 3.3 4.3 + - - -
138Z LEU* 3.0 24.3 + - - +
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Residues in contact with LYS 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657 ASN* 3.6 37.8 + - + +
91Z TYR* 3.6 43.2 - - + +
131Z GLU 2.9 20.2 + - - +
132Z ALA* 4.3 4.9 - - - +
134Z VAL* 1.3 76.3 - - - +
136Z LYS* 1.3 56.7 + - - +
138Z LEU* 3.2 14.6 + - + +
139Z ASP* 2.7 69.1 + - - +
142Z LYS* 5.4 4.7 - - - +
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Residues in contact with LYS 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLY 6.0 1.6 - - - +
37P GLU* 3.1 43.2 + - + +
132Z ALA 3.2 20.8 + - - +
133Z SER* 3.8 9.2 - - - +
134Z VAL 3.2 0.2 - - - -
135Z LYS* 1.3 76.3 - - - +
137Z ILE* 1.3 64.5 + - + +
139Z ASP* 3.6 6.8 + - - +
140Z LYS* 3.4 50.1 + - - +
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Residues in contact with ILE 137 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z PHE* 4.4 6.1 - - + -
42Z TRP* 3.6 33.7 - - + +
87Z PHE* 3.7 35.2 - - + -
133Z SER* 3.5 18.4 - - - +
134Z VAL 3.3 2.3 + - - +
136Z LYS* 1.3 78.9 - - + +
138Z LEU* 1.3 66.2 + - - +
140Z LYS* 3.2 10.7 + - + +
141Z LEU* 3.1 24.8 + - + +
154Z LEU* 4.6 10.5 - - + -
158Z LEU* 3.9 32.1 - - + -
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Residues in contact with LEU 138 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Z LEU* 3.9 3.6 - - + +
87Z PHE* 3.4 37.2 - - + +
88Z GLU* 3.7 27.4 - - + +
91Z TYR* 3.6 28.3 - - + -
134Z VAL 3.0 13.1 + - - +
135Z LYS* 3.2 16.6 + - + +
137Z ILE* 1.3 77.4 - - - +
139Z ASP* 1.3 64.9 + - - +
141Z LEU* 3.1 7.5 + - - +
142Z LYS* 3.0 52.0 + - + +
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Residues in contact with ASP 139 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657 ASN* 4.5 3.8 - - - +
34P LEU 5.9 1.3 - - - +
35P GLY* 5.8 8.4 - - - -
135Z LYS* 2.7 55.1 + - - +
136Z LYS* 3.9 6.4 - - - +
137Z ILE 3.3 0.2 - - - -
138Z LEU* 1.3 82.5 - - - +
140Z LYS* 1.3 58.6 + - + +
142Z LYS* 3.6 15.5 + - - +
143Z PHE* 3.0 25.5 + - - +
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Residues in contact with LYS 140 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLY 4.8 14.6 - - - +
37P GLU* 6.5 0.7 - - - -
152P PHE* 4.5 19.2 - - + -
155P ASP* 5.6 5.5 + - - -
136Z LYS* 3.4 43.7 + - - +
137Z ILE* 3.2 14.8 + - + +
139Z ASP* 1.3 76.3 - - - +
141Z LEU* 1.3 57.7 + - - +
142Z LYS 3.4 0.2 - - - -
143Z PHE* 3.5 13.0 - - + +
144Z ALA* 3.3 24.3 + - - +
150Z ILE* 4.9 1.4 - - - +
154Z LEU* 3.8 37.0 - - + +
157Z GLU* 4.0 17.2 + - - -
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Residues in contact with LEU 141 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z PHE* 4.1 13.5 - - + -
83Z PRO* 3.4 31.9 - - + +
84Z LEU* 3.7 25.1 - - + +
87Z PHE* 3.6 31.2 - - + -
137Z ILE* 3.1 21.2 + - + +
138Z LEU* 3.1 6.7 + - - +
140Z LYS* 1.3 75.8 - - - +
142Z LYS* 1.3 62.5 + - - +
143Z PHE 3.2 0.9 - - - -
144Z ALA* 3.4 24.2 - - + +
145Z LYS* 3.8 3.3 + - - -
151Z LEU* 3.8 29.2 - - + -
154Z LEU* 4.1 9.2 - - + -
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Residues in contact with LYS 142 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Z LEU* 3.6 19.9 - - + +
88Z GLU* 4.0 14.4 - - - -
135Z LYS* 5.4 4.6 - - - +
138Z LEU* 3.0 33.3 + - + +
139Z ASP* 3.7 16.4 + - - +
141Z LEU* 1.3 76.0 - - - +
143Z PHE* 1.3 61.5 + - - +
144Z ALA 3.2 0.7 - - - -
145Z LYS* 3.4 35.0 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P LEU 5.4 9.0 - - - -
36P LEU* 5.0 11.0 - - + -
148P PRO* 3.6 44.9 - - + +
151P LEU* 3.6 31.2 - - + -
152P PHE* 4.4 22.4 - + + -
139Z ASP 3.0 19.3 + - - +
140Z LYS* 3.5 15.3 - - + +
141Z LEU 3.2 0.4 - - - -
142Z LYS* 1.3 77.8 - - - +
144Z ALA* 1.3 57.3 + - - +
145Z LYS 3.8 1.4 + - - -
150Z ILE* 4.5 8.4 - - + +
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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