Contacts of the helix formed by residues 126 - 150 (chain B) in PDB entry 3J41
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 SER 126 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY 4.0 1.6 + - - -
125B VAL* 1.3 77.8 - - - +
127B VAL* 1.3 60.0 + - - +
128B GLY* 3.2 6.0 + - - -
129B GLN* 3.0 39.6 + - - +
130B ALA* 2.9 25.2 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 5.1 3.4 - - + -
125B VAL 3.8 0.8 + - - -
126B SER* 1.3 75.1 - - - +
128B GLY* 1.3 54.5 + - - +
130B ALA* 3.7 8.2 - - - +
131B THR* 2.6 40.8 + - - +
200B ASN* 4.5 16.4 - - - +
202B TRP* 4.4 13.5 - - + +
203B VAL* 3.6 22.6 - - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 3.1 6.5 + - - -
127B VAL* 1.3 81.5 - - - +
129B GLN* 1.3 63.4 + - - +
131B THR* 3.3 7.0 + - - -
132B ILE* 3.2 29.8 + - - +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY 3.9 6.2 - - - +
125B VAL* 3.9 10.6 - - + +
126B SER* 3.0 37.1 + - - +
128B GLY* 1.3 75.9 - - - +
130B ALA* 1.3 58.4 + - - +
132B ILE* 3.1 8.0 + - + +
133B VAL* 2.9 17.3 + - - +
106C SER 2.6 30.1 + - - +
107C VAL* 2.8 48.5 - - + +
108C THR 4.1 6.3 + - - +
109C PRO* 5.2 2.5 - - - +
113C ARG* 5.0 4.2 - - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.0 39.3 - - + -
125B VAL* 3.6 8.0 - - + +
126B SER 2.9 17.2 + - - +
127B VAL* 3.7 5.4 - - - +
129B GLN* 1.3 79.3 - - - +
131B THR* 1.3 55.8 + - - +
133B VAL* 3.5 4.2 + - - +
134B GLU* 3.0 32.6 + - - +
179B THR* 3.5 9.6 - - + +
203B VAL* 3.9 4.9 - - + -
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 2.6 25.9 + - - +
128B GLY* 3.6 7.9 - - - -
129B GLN 3.2 0.4 - - - -
130B ALA* 1.3 74.1 - - - +
132B ILE* 1.3 62.2 + - + +
134B GLU* 3.5 2.1 + - - -
135B ILE* 2.9 41.4 + - + +
202B TRP* 4.4 5.8 + - - +
203B VAL* 3.6 23.1 - - - +
206B VAL* 3.6 31.4 - - + -
207B GLY* 3.7 8.9 - - - +
210B ILE* 5.3 0.7 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY 3.2 17.0 + - - +
129B GLN* 3.1 10.2 + - + +
131B THR* 1.3 75.1 - - - +
133B VAL* 1.3 67.0 + - - +
135B ILE* 3.2 13.9 + - + +
136B PHE* 3.0 45.6 + - + -
25C PHE* 6.0 0.4 - - + -
103C VAL* 4.6 4.5 - - + -
106C SER* 5.5 2.0 - - - +
107C VAL* 3.6 27.4 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLN 2.9 9.5 + - - +
130B ALA* 3.6 10.5 - - - +
132B ILE* 1.3 77.2 - - - +
134B GLU* 1.3 63.7 + - - +
136B PHE* 3.1 7.9 + - - +
137B LEU* 2.9 40.2 + - + +
174B PHE* 3.6 31.0 - - + -
175B GLY* 4.6 0.9 - - - -
178B TYR* 4.1 32.5 - - + -
179B THR* 4.5 6.7 - - + +
25C PHE* 5.1 3.6 - - + -
107C VAL* 3.1 31.9 - - + -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 3.0 20.5 + - - +
131B THR 3.8 1.1 - - - +
132B ILE 3.3 0.2 - - - -
133B VAL* 1.3 75.7 - - - +
135B ILE* 1.3 57.6 + - - +
137B LEU* 3.6 8.5 - - - +
138B THR* 2.8 34.8 + - - -
179B THR* 2.6 27.4 + - - +
181B ALA* 3.4 2.8 - - - -
182B GLY* 2.7 22.8 + - - -
183B MET* 2.7 29.5 + - - -
203B VAL* 3.9 19.1 - - + +
204B TYR* 3.8 8.2 - - + -
207B GLY* 3.8 19.4 - - - -
208B PRO* 3.6 8.2 - - + +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 2.9 37.0 + - + +
132B ILE* 3.3 16.4 - - + +
133B VAL 3.1 0.2 - - - -
134B GLU* 1.3 74.3 - - - +
136B PHE* 1.3 71.2 + - + +
138B THR 3.4 0.2 + - - -
139B LEU* 2.8 34.6 + - + +
207B GLY* 3.4 24.0 - - - +
210B ILE* 3.7 25.4 - - + -
211B GLY* 3.3 15.6 - - - -
214B LEU* 3.9 19.5 - - + -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.0 43.4 + - + +
133B VAL 3.7 5.8 - - - +
135B ILE* 1.3 85.3 - - + +
137B LEU* 1.3 63.2 + - - +
139B LEU* 3.6 12.1 - - + +
140B GLN* 3.1 26.3 + - - +
21C LEU* 3.6 28.7 - - + -
22C PHE* 4.0 20.3 - + - -
25C PHE* 3.8 36.8 - + + -
26C PHE* 3.4 5.4 - - + -
103C VAL* 3.5 27.1 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 2.9 32.4 + - + +
134B GLU* 3.6 29.6 - - - +
136B PHE* 1.3 77.0 - - - +
138B THR* 1.3 61.6 + - - +
140B GLN* 3.0 26.0 - - - +
141B PHE* 3.2 7.1 + - - +
171B GLY* 3.5 20.2 - - - +
174B PHE* 3.3 37.0 - - + -
175B GLY* 4.1 2.9 - - - -
179B THR* 4.3 0.2 - - - +
181B ALA* 4.1 10.1 - - - -
183B MET* 3.5 24.5 - - + +
26C PHE* 3.7 14.1 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 5.6 0.2 - - - +
70B ALA* 4.3 6.3 - - + -
71B VAL* 5.9 0.2 - - + -
134B GLU 2.8 17.5 + - - -
135B ILE 4.0 2.0 - - - -
137B LEU* 1.3 74.3 - - - +
139B LEU* 1.3 56.5 + - - +
141B PHE* 3.9 9.2 - - + -
142B VAL* 2.7 45.4 + - + +
183B MET* 3.6 20.7 - - - +
208B PRO* 3.0 47.5 - - + +
211B GLY 4.2 0.9 - - - -
212B ALA* 3.7 9.4 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 2.8 21.6 + - + +
136B PHE* 3.6 14.1 - - + +
137B LEU 3.3 0.4 - - - -
138B THR* 1.3 74.0 - - - +
140B GLN* 1.3 60.9 + - - +
142B VAL* 4.0 0.7 - - - +
143B LEU* 2.9 32.6 + - + +
211B GLY* 3.5 11.4 + - - +
214B LEU* 3.8 24.2 - - + +
215B GLY* 3.2 30.7 - - - +
218B LEU* 4.2 17.7 - - + -
22C PHE* 3.7 29.8 - - + -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE 3.1 13.3 + - - +
137B LEU 3.0 17.9 - - - +
139B LEU* 1.3 79.0 - - - +
141B PHE* 1.3 70.3 + - - +
143B LEU* 3.6 11.3 - - - +
144B CYS* 3.0 21.5 + - - +
167B SER* 2.6 44.2 + - - +
170B LEU* 4.0 12.0 - - + +
171B GLY* 3.8 8.3 + - - -
183B MET* 3.7 7.3 - - - +
22C PHE* 4.9 12.3 - - + -
26C PHE* 3.3 27.4 - - + -
54C THR* 3.5 20.0 - - + +
55C LEU* 5.5 3.6 - - + -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 5.7 0.4 - - - -
52B LEU* 3.3 28.5 - - + -
68B ASN* 3.9 11.9 - - + -
71B VAL* 3.8 26.0 - - + -
137B LEU 3.2 15.5 - - - +
138B THR* 3.4 11.4 - - + +
140B GLN* 1.3 83.0 - - - +
142B VAL* 1.3 62.5 + - + +
144B CYS* 3.1 6.8 + - - +
145B ILE* 3.0 35.3 + - + +
164B VAL* 3.5 27.8 - - + -
167B SER* 3.3 22.0 - - - +
168B LEU* 3.9 21.3 - - + -
183B MET* 3.7 22.4 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.6 16.4 - - + -
74B ALA* 3.8 12.3 - - + -
138B THR* 2.7 28.8 + - + +
139B LEU 4.1 2.2 - - - +
141B PHE* 1.3 69.8 - - + +
143B LEU* 1.3 60.9 + - - +
145B ILE* 3.0 9.8 + - + +
146B PHE* 2.8 49.1 + - + -
212B ALA* 3.5 46.0 - - + +
215B GLY* 4.1 1.8 - - - -
216B SER 3.9 10.3 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 2.9 21.7 + - + +
140B GLN* 3.6 7.2 - - - +
142B VAL* 1.3 78.4 - - - +
144B CYS* 1.3 56.9 + - - +
146B PHE* 4.0 3.3 - - - +
147B ALA* 3.0 24.3 + - - +
215B GLY* 4.6 7.6 - - - +
218B LEU* 4.2 16.2 - - + -
219B TYR* 3.7 32.8 - - + +
18C PHE* 5.9 1.3 - - + -
22C PHE* 3.9 30.1 - - + -
55C LEU* 5.4 2.7 - - + -
58C ALA* 3.7 29.8 - - + +
59C VAL* 5.0 9.4 - - + -
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN 3.0 13.9 + - - +
141B PHE 3.1 9.4 + - - +
143B LEU* 1.3 74.0 - - - +
145B ILE* 1.3 56.0 + - + +
147B ALA* 4.6 1.3 - - - -
148B THR* 2.6 56.2 + - - +
163B ALA* 3.9 28.5 - - - -
164B VAL* 4.3 3.1 - - - -
167B SER* 3.8 15.3 - - - +
54C THR* 3.9 25.4 - - + +
57C GLN* 4.4 2.0 - - - -
58C ALA* 4.6 7.9 - - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.7 35.4 - - + -
75B PHE* 3.5 32.3 - - + -
141B PHE* 3.0 34.0 + - + +
142B VAL* 3.0 12.2 + - + +
144B CYS* 1.3 74.3 - - - +
146B PHE* 1.3 63.5 + - + +
148B THR* 3.2 6.3 + - - -
149B TYR* 2.8 50.8 + - + +
164B VAL* 3.9 23.8 - - + -
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 6.1 0.4 - - + -
74B ALA* 3.3 34.1 - - + -
75B PHE* 3.7 34.5 - + - -
78B GLY* 4.6 3.4 - - - -
80B GLN* 4.2 14.4 - - - -
142B VAL* 2.8 38.5 + - + +
143B LEU* 4.0 2.5 - - - +
145B ILE* 1.3 75.9 - - + +
147B ALA* 1.3 63.2 + - - +
149B TYR* 3.9 3.7 - - - +
150B ASP* 2.9 26.7 + - - +
215B GLY 5.2 0.2 - - - -
216B SER* 3.3 25.8 - - - -
219B TYR* 3.8 25.1 - + + -
220B ASP* 3.5 24.7 - - - -
222B LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 3.0 19.8 + - - +
144B CYS 4.1 1.6 - - - +
146B PHE* 1.3 76.0 - - - +
148B THR* 1.3 56.9 + - - +
150B ASP* 3.3 17.5 - - - +
153B ARG* 3.0 21.6 + - - +
219B TYR* 3.5 19.0 - - + -
57C GLN 3.6 7.6 - - - +
58C ALA* 3.4 36.6 - - - +
61C HIS* 4.1 0.2 - - - +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.8 11.6 + - - -
144B CYS* 2.6 30.5 + - - +
145B ILE 3.2 6.2 + - - -
147B ALA* 1.3 73.9 - - + +
149B TYR* 1.3 70.9 + - - +
150B ASP 3.3 0.9 - - - -
157B LEU* 3.9 11.6 - - + +
160B VAL* 3.6 30.9 - - - +
163B ALA* 4.1 11.7 - - + -
164B VAL* 3.6 10.9 - - - +
57C GLN* 3.8 35.9 - - + +
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 4.7 6.2 + - - +
56B VAL* 4.0 18.8 - - + +
60B GLY* 6.1 0.7 - - - -
64B GLY* 2.7 37.4 + - - -
65B ALA 3.5 9.9 + - - -
66B HIS* 5.0 0.7 - + - -
71B VAL* 6.2 0.2 - - + -
75B PHE* 3.5 33.0 - + + -
80B GLN* 6.0 2.5 - - - +
145B ILE* 2.8 35.8 + - + +
146B PHE* 4.0 3.4 - - - +
148B THR* 1.3 83.0 - - - +
150B ASP* 1.3 66.3 + - - +
151B GLU* 3.0 9.4 + - - +
160B VAL* 4.2 15.7 - - + -
164B VAL* 4.1 18.9 - - + +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.3 13.4 + - - -
146B PHE 2.9 18.5 + - - +
147B ALA 3.3 11.4 - - - +
148B THR 3.3 0.2 - - - -
149B TYR* 1.3 73.8 - - - +
151B GLU* 1.3 70.1 + - - +
152B ARG* 3.0 55.9 + - - +
153B ARG* 3.4 17.8 + - + +
219B TYR* 2.4 25.0 + - + +
222B LEU* 4.1 7.3 - - + +
61C HIS* 4.6 1.7 - - - -
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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