Contacts of the helix formed by residues 128 - 155 (chain B) in PDB entry 1S13
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 LEU 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 4.3 4.9 - - - +
121B VAL* 3.6 9.9 - - + -
125B GLU* 2.9 31.1 + - + +
126B PRO 2.9 1.4 - - - -
127B GLU* 1.3 80.4 - - + +
129B LEU* 1.3 65.5 + - - +
130B VAL 3.0 3.1 - - - -
131B ALA* 2.8 22.7 + - - +
132B HIS* 3.7 2.6 + - - -
195B VAL* 4.7 0.7 - - + +
198B ARG* 3.6 45.1 - - + +
199B VAL* 3.7 37.2 - - + +
202B GLU* 3.5 33.1 - - + +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.1 16.4 - - + -
64B GLU* 3.3 48.0 - - + +
65B ILE* 3.9 13.2 - - + -
68B ASN* 4.5 11.9 - - + +
74B PHE* 3.8 24.2 - - + -
118B LEU* 4.5 7.2 - - + +
121B VAL* 3.3 20.5 - - + +
122B GLY* 4.3 7.0 - - - +
126B PRO* 3.0 15.4 + - + +
128B LEU* 1.3 75.9 - - - +
130B VAL* 1.3 62.6 + - - +
132B HIS* 3.0 9.7 + - + +
133B ALA* 2.9 21.1 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.1 4.7 - - + -
17B LEU* 6.4 1.3 - - + -
73B VAL 3.6 23.3 - - - +
74B PHE* 3.9 12.7 - - + -
77B VAL* 4.3 14.4 - - + -
126B PRO 4.7 0.2 - - - +
127B GLU 3.5 22.2 - - - +
129B LEU* 1.3 75.4 - - - +
131B ALA* 1.3 56.5 + - - +
133B ALA* 3.9 1.2 - - - +
134B TYR* 2.8 32.7 + - - +
182B TYR* 4.9 1.5 + - - +
186B MET* 4.4 18.2 - - + -
189B LEU* 3.6 28.0 - - + -
191B MET* 5.1 4.5 - - + -
199B VAL* 5.0 8.1 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 5.8 2.0 - - + -
128B LEU 2.8 12.5 + - - +
130B VAL* 1.3 78.7 - - - +
132B HIS* 1.3 59.9 + - - +
134B TYR* 3.5 6.4 - - - +
135B THR* 3.0 35.1 + - - +
199B VAL* 3.5 35.1 - - + +
202B GLU* 3.7 10.3 - - + -
203B ALA* 3.7 18.8 - - + +
206B ALA* 5.3 0.2 - - - -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.1 8.3 - - + -
114B TYR* 4.0 15.9 - + - -
117B ARG* 4.3 5.4 - - + +
118B LEU* 3.4 33.5 - - + +
121B VAL* 4.1 16.8 - - + +
128B LEU 3.7 4.6 + - - -
129B LEU* 3.0 9.2 + - + +
131B ALA* 1.3 76.9 - - - +
133B ALA* 1.3 65.4 + - - +
135B THR* 2.6 21.8 + - - -
136B ARG* 3.0 16.7 + - + +
202B GLU* 2.9 46.9 + - + +
206B ALA* 4.1 18.4 - - + +
209B LEU* 4.3 12.3 - - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.1 11.3 - - + +
65B ILE* 4.7 0.2 - - + -
74B PHE* 3.8 23.3 - - + -
129B LEU 2.9 14.6 + - - +
130B VAL* 3.9 2.9 - - - +
132B HIS* 1.3 75.7 - - - +
134B TYR* 1.3 58.6 + - - +
137B TYR* 2.9 53.3 + - + +
182B TYR* 3.3 20.0 - - - +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 4.6 2.0 + - - -
17B LEU* 3.8 36.9 + - + -
18B LYS* 3.8 15.9 + - - -
21B THR* 4.5 7.9 + - + -
130B VAL 2.8 19.8 + - - +
131B ALA* 3.5 8.5 - - - +
133B ALA* 1.3 77.7 - - - +
135B THR* 1.3 72.8 + - + +
138B LEU* 3.2 56.3 + - + +
139B GLY 3.7 0.5 + - - -
182B TYR* 4.1 9.1 + - - -
183B ARG* 5.9 0.2 - - + -
186B MET* 3.6 29.2 - - + -
203B ALA* 5.1 1.1 - - + -
300B 2FH 2.7 52.6 + - + +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.7 2.3 + - - -
131B ALA 3.0 20.0 + - - +
132B HIS* 2.6 26.5 + - - -
134B TYR* 1.3 85.9 - - + +
136B ARG* 1.3 61.7 + - - +
139B GLY* 3.3 15.6 + - - -
203B ALA* 3.9 14.1 - - + +
206B ALA* 3.5 28.1 - - + +
207B PHE* 3.9 15.9 - - + -
300B 2FH 3.3 35.8 - - - +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.9 17.0 - - - +
57B ILE* 3.7 23.5 - - + +
58B TYR* 3.5 27.2 - - + +
61B LEU* 4.0 19.3 - - + -
114B TYR* 3.4 24.8 + - + +
118B LEU* 6.5 0.4 - - + -
132B HIS* 3.0 14.1 + - + +
135B THR* 1.3 78.1 + - - +
137B TYR* 1.3 56.0 + - - +
140B ASP* 2.7 84.1 + - - +
210B ASN* 3.0 29.7 + - - +
300B 2FH 4.1 13.8 - - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.3 29.0 - + - -
61B LEU* 4.0 10.4 - - + +
62B GLU* 2.6 36.0 + - - +
65B ILE* 3.7 24.4 - - + +
74B PHE* 6.0 0.2 - + - -
83B LEU* 3.5 63.1 + - + -
84B HIS* 4.6 1.7 - - - -
85B ARG* 4.9 0.7 - - + -
133B ALA* 2.9 37.7 + - + +
136B ARG* 1.3 71.0 - - - +
138B LEU* 1.3 65.7 + - + +
140B ASP* 3.9 1.1 - - - +
141B LEU* 2.9 33.5 + - - +
169B PHE* 4.7 7.2 - + - -
182B TYR* 4.6 4.9 - - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 3.2 42.2 + - + +
137B TYR* 1.3 80.8 - - + +
139B GLY* 1.3 63.8 + - - +
141B LEU* 3.4 10.9 + - + +
142B SER* 2.9 28.4 + - - -
178B PHE* 4.8 0.9 - - + -
179B LYS* 3.6 24.8 - - + +
182B TYR* 3.8 37.0 - - + -
183B ARG* 4.3 13.7 - - + +
186B MET* 3.8 15.7 - - + -
300B 2FH 4.0 20.9 - - + +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR 3.7 0.8 + - - -
135B THR 3.3 21.0 + - - -
137B TYR 3.1 0.8 - - - -
138B LEU* 1.3 78.8 - - - +
140B ASP* 1.3 58.3 + - - +
142B SER* 2.9 19.6 + - - -
143B GLY* 3.0 11.4 + - - -
300B 2FH 3.5 34.6 + - - -
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.9 0.7 - - - +
58B TYR* 2.4 31.5 + - - +
136B ARG* 2.7 50.7 + - - +
137B TYR 4.3 1.3 - - - +
139B GLY* 1.3 71.3 - - - -
141B LEU* 1.3 56.3 + - - +
143B GLY 4.0 2.2 - - - +
144B GLY* 3.1 30.1 + - - +
147B LEU* 6.6 0.2 - - - -
166B PHE* 4.0 22.1 - - + -
169B PHE* 4.4 15.0 - - + -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.2 5.6 - - + -
137B TYR 2.9 18.8 + - - +
138B LEU* 3.6 9.6 - - + +
139B GLY 3.1 0.2 - - - -
140B ASP* 1.3 77.1 - - - +
142B SER* 1.3 59.3 + - - +
144B GLY* 4.5 0.6 - - - -
145B GLN* 3.6 12.6 - - - +
169B PHE* 4.0 37.2 - - + -
172B ILE* 4.3 8.7 - - + -
175B ALA* 3.7 33.0 - - + +
178B PHE* 3.4 37.0 - - + -
179B LYS* 4.1 20.8 + - + +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU 2.9 16.7 + - - -
139B GLY 2.9 5.2 + - - -
141B LEU* 1.3 80.8 - - - +
143B GLY* 1.3 58.2 + - - +
144B GLY 3.5 0.7 - - - -
145B GLN* 2.8 19.7 + - - +
146B VAL* 4.8 2.1 - - - +
179B LYS* 2.8 31.2 + - - +
300B 2FH 4.0 41.0 - - - +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLY 3.0 11.5 + - - -
140B ASP* 4.0 3.1 - - - -
142B SER* 1.3 76.3 - - - +
144B GLY* 1.3 64.3 + - - +
145B GLN* 3.4 4.7 - - - -
146B VAL* 3.6 12.8 - - - +
147B LEU* 3.2 33.5 + - - +
300B 2FH 4.8 18.0 - - - -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP* 3.1 20.4 + - - -
141B LEU 4.5 0.4 - - - -
142B SER 3.5 2.4 - - - -
143B GLY* 1.3 76.7 - - - +
145B GLN* 1.3 67.5 + - - +
147B LEU* 3.6 0.6 + - - -
148B LYS* 2.9 25.9 + - - +
167B PHE* 3.6 29.7 - - - -
169B PHE* 6.3 0.2 - - - -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU 3.6 14.4 - - - +
142B SER* 2.8 29.0 + - - +
143B GLY* 3.8 1.2 - - - -
144B GLY* 1.3 73.7 - - - +
146B VAL* 1.3 77.0 + - + +
148B LYS* 2.9 10.5 + - - +
149B LYS* 2.9 28.3 + - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 5.1 4.0 - - + +
142B SER 4.8 1.3 - - - +
143B GLY* 3.6 16.4 - - - +
145B GLN* 1.3 92.5 - - + +
147B LEU* 1.3 72.9 + - + +
149B LYS* 3.5 2.8 + - - +
150B ILE* 3.0 41.9 + - + +
300B 2FH 4.5 23.3 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 4.8 3.8 - - + -
37B PHE* 3.7 33.9 - - + -
38B GLN* 5.0 2.9 - - + -
47B PHE* 5.1 0.2 - - - -
140B ASP* 5.7 4.9 - - - +
143B GLY* 3.2 20.1 + - - +
144B GLY* 5.3 0.4 - - - -
145B GLN 3.3 0.2 - - - -
146B VAL* 1.3 89.4 - - + +
148B LYS* 1.3 63.2 + - - +
150B ILE* 3.7 1.3 - - - +
151B ALA* 3.0 27.4 + - - +
166B PHE* 6.4 0.2 - - + -
167B PHE* 4.0 25.8 - - + -
300B 2FH 3.8 35.0 - - + -
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY 2.9 19.3 + - - +
145B GLN* 2.9 10.5 + - - +
147B LEU* 1.3 78.0 - - - +
149B LYS* 1.3 62.0 + - - +
151B ALA* 3.9 1.9 - - - +
152B GLN* 2.9 54.1 + - - +
164B LEU* 4.3 23.0 - - + +
167B PHE* 4.1 32.9 - - + +
168B THR* 3.9 18.0 + - - -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 2.9 16.9 + - + +
146B VAL* 4.1 2.9 - - - +
148B LYS* 1.3 75.2 - - - +
150B ILE* 1.3 69.6 + - + +
152B GLN* 3.1 14.2 - - - +
153B LYS* 3.1 59.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.4 34.5 - - + +
38B GLN* 3.5 36.8 - - + +
40B GLY* 4.4 10.1 - - - -
42B VAL* 5.3 1.6 - - + -
146B VAL* 3.0 42.8 + - + +
147B LEU 3.7 3.8 - - - +
149B LYS* 1.3 83.3 - - + +
151B ALA* 1.3 60.3 + - - +
153B LYS* 3.8 2.0 - - - +
154B ALA* 2.8 31.8 + - + +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.1 6.3 - - + -
42B VAL* 5.1 2.7 - - + -
47B PHE* 3.6 33.9 - - + -
147B LEU 3.0 15.3 + - - +
148B LYS* 3.9 2.2 - - - +
150B ILE* 1.3 76.5 - - - +
152B GLN* 1.3 55.5 + - - +
153B LYS 2.7 17.0 + - - -
154B ALA* 2.8 15.0 + - - +
155B LEU* 2.8 33.0 + - + +
164B LEU* 5.4 1.8 - - + -
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS* 2.9 55.3 + - - +
149B LYS* 3.1 27.5 - - - +
151B ALA* 1.3 70.7 - - - +
153B LYS* 1.3 85.4 + - - +
155B LEU* 4.6 0.4 - - - +
156B ASP* 4.0 5.9 + - - -
157B LEU* 3.4 28.5 - - + +
164B LEU* 3.7 19.6 - - + +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LYS* 3.1 49.7 - - + +
150B ILE* 3.3 2.4 + - - +
151B ALA 2.7 4.8 + - - -
152B GLN* 1.3 108.1 + - - +
154B ALA* 1.3 56.2 + - - +
155B LEU 3.1 8.9 + - - -
156B ASP* 3.6 11.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY* 4.5 25.6 - - - +
42B VAL* 4.1 19.4 - - + +
150B ILE* 2.8 20.2 + - + +
151B ALA* 2.8 7.6 + - - +
153B LYS* 1.3 74.9 - - - +
155B LEU* 1.3 65.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.5 11.0 - - + +
43B THR* 4.1 28.3 - - - +
44B ARG* 4.1 8.1 - - + +
47B PHE* 4.0 14.4 - - + -
96B TRP* 4.0 27.1 - - + -
151B ALA* 2.8 38.3 + - + +
152B GLN 4.6 0.2 - - - +
154B ALA* 1.3 86.7 - - - +
156B ASP* 1.3 72.9 + - - +
157B LEU* 3.0 19.3 + - + +
164B LEU* 5.6 1.6 - - + -
----------------------------------------------------------
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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