Contacts of the helix formed by residues 128 - 156 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 3.9 4.0 - - - +
121A VAL* 3.7 7.9 - - + +
125A GLU* 3.0 39.8 + - + +
126A PRO 2.7 6.5 + - - -
127A GLU* 1.3 83.3 - - + +
129A LEU* 1.3 57.5 + - - +
130A VAL 3.1 3.1 - - - -
131A ALA* 2.8 28.6 + - - +
132A HIS* 3.8 1.7 + - - -
195A VAL* 4.2 2.0 - - + +
198A ARG* 3.6 26.9 - - + +
199A VAL* 3.5 40.2 - - + +
202A GLU* 3.7 33.5 - - + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.0 20.6 - - + -
64A GLU* 3.8 31.4 - - + +
65A ILE* 3.8 27.1 - - + +
68A ASN* 4.4 10.1 - - + +
74A PHE* 3.8 22.4 - - + -
118A LEU* 4.8 4.9 - - + +
121A VAL* 3.4 23.8 - - + +
122A GLY* 4.6 2.5 - - - +
126A PRO* 2.8 17.4 + - + +
128A LEU* 1.3 77.6 - - - +
130A VAL* 1.3 61.3 + - - +
132A HIS* 3.0 9.1 + - + +
133A ALA* 3.0 19.1 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.3 1.8 - - + -
17A LEU* 6.0 0.2 - - - -
73A VAL 4.3 3.8 - - - +
74A PHE* 3.8 12.9 - - + -
77A VAL* 3.3 37.7 - - + -
126A PRO 4.6 0.2 + - - -
127A GLU 3.7 19.3 - - - +
128A LEU 4.3 0.7 - - - -
129A LEU* 1.3 74.0 - - - +
131A ALA* 1.3 56.4 + - - +
133A ALA* 3.7 2.4 - - + +
134A TYR* 2.7 38.3 + - - +
182A TYR* 5.1 1.2 + - + +
186A MET* 4.9 10.7 - - + +
189A LEU* 3.6 32.8 - - + -
191A MET* 4.5 2.5 - - + -
199A VAL* 4.4 13.5 - - + -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.4 2.0 - - - -
128A LEU 2.8 16.1 + - - +
130A VAL* 1.3 81.7 - - - +
132A HIS* 1.3 51.8 + - - +
134A TYR* 3.6 6.0 - - - +
135A THR* 2.5 37.4 + - - -
199A VAL* 3.4 36.6 - - + +
202A GLU* 3.7 17.0 - - + -
203A ALA* 3.9 10.0 - - + +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.2 8.9 - - + +
114A TYR* 4.1 12.3 - + - -
117A ARG* 4.3 3.4 - - + +
118A LEU* 3.4 31.7 - - + +
121A VAL* 3.8 20.4 - - + +
128A LEU 3.8 3.8 + - - -
129A LEU* 3.0 10.0 + - + +
131A ALA* 1.3 75.2 - - - +
133A ALA* 1.3 66.2 + - - +
135A THR* 3.8 3.3 - - - -
136A ARG* 3.0 31.2 + - + +
202A GLU* 2.8 44.7 + - + +
206A ALA* 3.7 26.3 + - + +
209A LEU* 4.3 12.1 - - - +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.3 8.0 - - + +
65A ILE* 4.7 3.4 - - + -
74A PHE* 3.9 23.8 - - + -
129A LEU 3.0 13.8 + - - +
130A VAL* 3.7 4.5 - - - +
132A HIS* 1.3 76.6 - - - +
134A TYR* 1.3 58.2 + - - +
137A TYR* 2.9 51.7 + - + +
182A TYR* 3.4 18.8 - - - +
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 4.5 4.7 + - - -
17A LEU* 3.8 34.7 + - + -
18A LYS* 3.6 18.4 - - - -
21A THR* 4.5 4.6 + - + -
130A VAL 2.7 19.0 + - - +
131A ALA* 3.6 4.3 - - - +
133A ALA* 1.3 74.9 - - - +
135A THR* 1.3 83.5 + - - +
138A LEU* 3.1 43.5 + - + +
139A GLY 3.6 0.7 + - - -
182A TYR* 4.1 10.7 + - + -
183A ARG* 5.9 0.9 - - + -
186A MET* 3.5 31.6 - - + -
203A ALA* 4.8 4.5 - - + -
207A PHE* 5.5 0.4 - + - -
300A 2FH 2.6 63.9 + - + +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 5.1 1.8 - - - +
131A ALA 2.5 22.2 + - - -
132A HIS* 3.8 4.7 - - - -
134A TYR* 1.3 84.3 - - - +
136A ARG* 1.3 64.5 + - - +
139A GLY* 3.4 15.2 - - - -
203A ALA* 4.0 8.8 + - - +
206A ALA* 3.7 29.5 - - + +
207A PHE* 4.1 12.7 - - + -
210A ASN* 4.7 0.9 - - - +
300A 2FH 3.2 51.7 - - + +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.0 16.8 - - - +
57A ILE* 3.7 23.0 - - + +
58A TYR* 3.6 28.1 + - - +
61A LEU* 4.0 18.8 - - + -
114A TYR* 3.3 27.9 + - + +
132A HIS* 3.0 19.8 + - + +
135A THR* 1.3 76.2 + - - +
137A TYR* 1.3 56.3 + - - +
139A GLY 3.2 0.7 + - - -
140A ASP* 2.7 76.7 + - - +
210A ASN* 3.0 28.5 + - - +
214A PHE* 6.4 0.2 - - - -
300A 2FH 4.0 16.7 - - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.3 29.4 - + - -
61A LEU* 4.0 8.9 - - + +
62A GLU* 2.7 33.0 + - - +
65A ILE* 3.8 28.1 - - + +
83A LEU* 3.3 65.7 + - + -
84A HIS* 4.6 1.2 - - - -
85A ARG* 4.9 0.7 - - + -
133A ALA* 2.9 34.5 + - + +
136A ARG* 1.3 73.6 - - - +
138A LEU* 1.3 60.9 + - + +
140A ASP* 3.8 1.8 - - - +
141A LEU* 2.9 34.4 + - - +
169A PHE* 4.5 7.9 - + - -
182A TYR* 4.3 4.7 - - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.1 34.9 + - + +
137A TYR* 1.3 81.6 - - + +
139A GLY* 1.3 60.2 + - - +
141A LEU* 4.0 11.7 - - + +
142A SER* 3.0 27.4 + - - -
178A PHE* 4.7 3.6 - - + -
179A LYS* 3.9 32.6 + - + +
182A TYR* 3.6 46.4 - - + -
183A ARG* 4.3 20.0 - - + -
186A MET* 4.3 0.9 - - - -
300A 2FH 3.8 18.2 - - + +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR 3.6 0.8 + - - -
135A THR 3.4 19.4 + - - -
136A ARG 3.2 2.4 + - - -
137A TYR 3.1 0.6 - - - -
138A LEU* 1.3 79.6 - - - +
140A ASP* 1.3 60.3 + - - +
142A SER* 3.4 2.1 + - - -
143A GLY* 2.8 28.6 + - - -
300A 2FH 3.6 33.4 + - - -
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 5.2 0.7 - - - +
58A TYR* 2.5 32.7 + - - +
136A ARG* 2.7 50.4 + - - +
137A TYR 4.1 1.8 - - - +
139A GLY* 1.3 71.2 - - - +
141A LEU* 1.3 60.9 + - - +
142A SER 3.2 0.2 - - - -
143A GLY* 5.0 0.4 - - - -
144A GLY* 2.9 32.1 + - - +
166A PHE* 3.6 23.0 - - + -
167A PHE* 6.0 0.2 - - - -
169A PHE* 4.1 16.2 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.7 2.0 - - + -
137A TYR 2.9 18.8 + - - +
138A LEU* 4.0 11.0 - - + +
139A GLY 3.2 0.2 - - - -
140A ASP* 1.3 78.8 - - - +
142A SER* 1.3 62.7 + - - +
144A GLY 4.5 0.2 + - - -
145A GLN* 3.6 20.3 + - - +
169A PHE* 3.9 35.4 - - + -
172A ILE* 4.1 13.9 - - + -
175A ALA* 4.0 25.2 - - + +
178A PHE* 3.8 31.9 - - + -
179A LYS* 4.2 21.8 - - + -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 3.0 16.3 + - - -
139A GLY 3.4 3.0 + - - -
141A LEU* 1.3 77.1 - - - +
143A GLY* 1.3 65.2 + - - +
145A GLN* 3.4 22.3 - - - +
146A VAL* 4.1 6.5 - - - +
179A LYS* 3.5 22.1 + - - +
300A 2FH 3.9 34.3 - - - -
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY 2.8 19.7 + - - -
140A ASP* 5.0 0.2 - - - -
142A SER* 1.3 74.8 - - - +
144A GLY* 1.3 65.3 + - - +
146A VAL* 2.7 29.8 + - - +
147A LEU* 3.1 16.1 - - - +
300A 2FH 4.4 19.4 - - - -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 2.9 26.4 + - - +
142A SER 3.4 0.4 - - - -
143A GLY* 1.3 73.7 - - - +
145A GLN* 1.3 53.6 + - - +
146A VAL 2.6 12.6 + - - -
147A LEU* 3.0 2.7 + - - -
148A LYS* 2.9 21.1 + - - +
166A PHE* 6.0 0.9 - - - -
167A PHE* 3.5 32.8 - - - -
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP 4.8 0.2 + - - -
141A LEU 3.6 17.3 + - - +
142A SER* 3.4 18.7 + - - +
144A GLY* 1.3 68.4 - - - -
146A VAL* 1.3 63.3 + - + +
148A LYS* 4.2 12.9 - - + +
149A LYS* 3.7 18.2 + - - +
167A PHE 4.9 6.0 + - - +
175A ALA* 5.1 11.5 - - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 4.1 12.1 - - - +
143A GLY* 2.7 22.2 + - - +
144A GLY 2.6 5.3 + - - -
145A GLN* 1.3 72.7 - - + +
147A LEU* 1.3 66.1 + - + +
148A LYS 3.4 0.2 + - - -
149A LYS* 3.5 5.1 + - - +
150A ILE* 3.3 36.8 + - + +
300A 2FH 4.2 31.2 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET* 4.8 1.8 - - + -
37A PHE* 3.5 37.0 - - + -
38A GLN* 5.5 2.5 - - + -
47A PHE* 5.7 0.2 - - + -
143A GLY* 3.1 26.9 - - - +
144A GLY* 3.0 4.0 + - - +
146A VAL* 1.3 81.9 - - + +
148A LYS* 1.3 65.8 + - - +
150A ILE* 3.7 10.1 - - + +
151A ALA* 2.9 27.8 + - - +
167A PHE* 4.1 17.9 - - + -
300A 2FH 3.6 36.3 - - + -
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 2.9 15.7 + - - +
145A GLN* 4.3 10.1 - - + +
147A LEU* 1.3 77.2 - - - +
149A LYS* 1.3 55.1 + - - +
151A ALA* 3.7 3.3 - - - +
152A GLN* 2.8 55.4 + - - +
164A LEU* 4.4 24.6 - - + +
167A PHE* 3.8 38.2 - - + +
168A THR* 4.1 16.3 + - - -
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN 3.7 11.9 + - - +
146A VAL* 3.5 8.5 + - - +
148A LYS* 1.3 83.4 - - - +
150A ILE* 1.3 67.3 + - + +
152A GLN* 3.1 39.5 + - - +
153A LYS* 3.1 46.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.5 34.5 - - + +
38A GLN* 4.0 31.0 - - + +
40A GLY* 4.5 13.0 - - - +
42A VAL* 5.0 1.3 - - + -
146A VAL* 3.3 29.2 + - + +
147A LEU* 3.7 10.8 - - + +
149A LYS* 1.3 79.7 - - + +
151A ALA* 1.3 65.6 + - - +
153A LYS* 3.2 10.6 - - - +
154A ALA* 3.2 22.7 + - + +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.4 5.8 - - + -
42A VAL* 5.0 1.6 - - - -
47A PHE* 3.7 24.0 - - + -
147A LEU 2.9 21.5 + - - +
148A LYS* 3.7 2.9 - - - +
150A ILE* 1.3 70.9 - - - +
152A GLN* 1.3 69.7 + - - +
153A LYS 2.6 4.9 + - - -
154A ALA* 3.0 3.8 + - - +
155A LEU* 2.9 51.1 + - + +
164A LEU* 5.2 3.6 - - + -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 2.8 47.6 + - - +
149A LYS* 3.1 32.5 - - - +
151A ALA* 1.3 71.2 - - - +
153A LYS* 1.3 57.8 + - + +
155A LEU* 4.8 0.4 - - - +
156A ASP* 3.8 5.4 + - - -
157A LEU* 3.1 32.6 - - + +
164A LEU* 4.5 14.2 - - + +
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 3.1 49.9 - - - +
150A ILE* 3.2 15.5 - - - +
151A ALA 2.6 3.2 + - - -
152A GLN* 1.3 73.5 - - + +
154A ALA* 1.3 66.4 + - + +
155A LEU 2.8 11.2 + - - -
156A ASP* 3.1 23.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY* 3.3 30.1 - - - +
42A VAL* 3.8 22.1 - - + +
150A ILE* 3.2 15.2 + - + +
151A ALA 3.0 1.9 + - - +
153A LYS* 1.3 81.5 - - + +
155A LEU* 1.3 58.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.1 11.0 - - + +
43A THR 3.8 10.5 - - - +
44A ARG* 3.6 57.8 + - + +
47A PHE* 3.8 22.9 - - + -
96A TRP* 3.8 20.9 - - + -
151A ALA* 2.9 38.3 + - + +
154A ALA* 1.3 81.8 - - - +
156A ASP* 1.3 73.2 + - - +
157A LEU* 3.2 11.5 + - + +
164A LEU* 5.7 1.6 - - + -
----------------------------------------------------------
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 3.6 7.2 + - - +
152A GLN 3.8 8.0 + - - -
153A LYS* 3.1 19.5 + - - +
154A ALA 5.3 0.2 - - - -
155A LEU* 1.3 81.4 - - - +
157A LEU* 1.3 70.1 + - - +
158A PRO* 4.3 0.9 - - - +
----------------------------------------------------------
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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