Contacts of the helix formed by residues 9 - 36 (chain B) in PDB entry 2GFP
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 9 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 1.3 86.5 + - + +
11B LEU* 3.3 2.3 - - - +
12B MET* 2.8 63.7 + - + +
13B LEU* 3.2 11.8 + - - +
120B LEU* 6.5 1.3 - - + -
182B TRP* 4.9 17.7 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 1.3 97.3 - - + +
11B LEU* 1.3 85.0 + - + +
13B LEU* 3.0 33.4 + - - +
14B VAL* 3.1 19.4 + - + +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.3 1.4 - - - +
10B LEU* 1.3 95.5 - - + +
12B MET* 1.3 66.6 + - + +
14B VAL* 2.9 37.0 - - + +
15B LEU* 3.1 18.2 + - + +
175B VAL* 6.0 5.8 - - + -
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Residues in contact with MET 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 2.8 44.2 + - + +
11B LEU* 1.3 73.2 - - + +
13B LEU* 1.3 60.4 - - + +
15B LEU* 3.4 4.8 + - - +
16B LEU* 3.1 8.6 + - - +
172B CYS* 3.0 24.6 - - - +
175B VAL* 3.2 32.8 - - + +
176B THR* 3.4 42.6 - - + +
177B PHE* 3.9 17.0 - - + -
178B SER* 5.3 6.3 - - - -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.9 7.6 - - - +
10B LEU* 3.0 21.2 + - - +
12B MET* 1.3 81.3 - - + +
14B VAL* 1.3 65.2 + - + +
15B LEU 3.0 0.9 + - - -
16B LEU* 3.2 2.9 + - - -
17B VAL* 2.8 36.7 + - + +
72B ARG* 6.1 3.1 - - - +
113B GLY 5.7 0.4 - - - +
116B MET 5.3 1.1 - - - +
117B ALA* 3.7 30.7 - - + +
120B LEU* 5.7 6.7 - - + -
121B PRO* 3.5 35.0 - - + -
135B SER* 5.1 1.3 - - - +
138B ASN* 4.7 7.2 - - - +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.1 18.3 + - + +
11B LEU* 2.9 35.7 - - + +
13B LEU* 1.3 75.0 - - + +
15B LEU* 1.3 69.9 + - + +
17B VAL* 3.3 2.0 - - - +
18B ALA* 3.0 30.1 + - - +
138B ASN* 3.4 28.5 + - + +
142B LEU* 3.4 10.4 - - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.1 19.6 + - + +
12B MET* 5.0 0.4 - - - -
13B LEU 3.0 0.2 + - - -
14B VAL* 1.3 94.6 - - + +
16B LEU* 1.3 66.0 + - - +
18B ALA* 3.0 15.0 + - + +
19B VAL* 3.1 15.4 + - - +
168B LEU* 3.6 21.9 - - + +
171B LEU* 3.7 32.8 - - + +
172B CYS* 3.5 30.5 - - + +
175B VAL* 4.4 13.7 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET 3.1 7.2 + - - +
13B LEU* 4.0 3.1 - - - +
15B LEU* 1.3 78.5 - - - +
17B VAL* 1.3 58.8 + - + +
19B VAL* 2.9 24.1 - - + +
20B GLY* 3.0 8.8 + - - -
72B ARG* 4.7 15.9 - - + +
76B ILE* 4.9 10.1 - - + -
77B LEU* 3.9 28.0 - - + -
110B THR* 3.9 29.1 - - + +
113B GLY* 4.4 15.5 - - - +
169B LEU* 4.8 5.4 - - + -
172B CYS* 3.1 30.8 - - + +
176B THR* 5.2 0.2 - - + -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 2.8 33.2 + - + +
14B VAL 3.3 7.9 - - - +
16B LEU* 1.3 72.6 - - + +
18B ALA* 1.3 64.2 + - - +
20B GLY* 2.9 4.0 + - - +
21B GLN* 2.8 41.3 + - - +
110B THR 5.3 1.6 - - - -
113B GLY 5.0 1.6 - - - +
114B GLY* 4.1 12.6 - - - +
117B ALA* 3.9 28.5 - - + -
138B ASN* 3.3 27.4 - - - +
139B MET* 3.5 22.9 - - + -
142B LEU* 4.3 0.2 - - + -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL 3.0 23.0 + - - +
15B LEU* 3.0 6.7 + - + +
17B VAL* 1.3 76.8 - - - +
19B VAL* 1.3 64.1 + - - +
21B GLN* 3.0 13.1 - - - +
22B MET* 2.8 36.3 + - + +
142B LEU* 3.7 14.6 - - + -
168B LEU* 3.5 24.0 - - + -
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 3.1 11.4 - - - +
16B LEU* 2.9 22.0 - - - +
18B ALA* 1.3 74.2 - - - +
20B GLY* 1.3 64.0 + - - +
22B MET* 3.5 7.7 - - - +
23B ALA* 2.9 24.4 + - - +
110B THR* 3.5 15.5 - - + -
164B CYS 3.8 2.2 - - - +
165B TYR* 3.2 50.0 - - + +
168B LEU* 3.7 10.8 - - + +
169B LEU* 3.4 26.0 - - + +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 3.0 10.2 + - - -
17B VAL* 2.9 10.8 + - - -
19B VAL* 1.3 75.8 - - - +
21B GLN* 1.3 55.2 + - - -
24B GLN* 3.0 30.4 + - - +
107B GLY 3.5 8.1 - - - +
110B THR* 3.2 31.9 - - - -
111B GLY* 4.3 5.1 + - - -
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.8 27.6 + - - +
18B ALA* 3.0 22.8 + - - +
20B GLY* 1.3 70.7 - - - -
22B MET* 1.3 74.5 + - + +
24B GLN* 3.7 15.0 - - + +
25B THR* 2.7 33.2 + - - -
139B MET* 3.2 43.2 + - - +
142B LEU* 2.9 28.8 - - - +
143B VAL* 3.3 28.5 - - + +
147B LEU* 4.2 0.2 - - - -
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 2.8 41.4 + - + +
19B VAL* 3.5 7.6 - - - +
21B GLN* 1.3 94.3 - - + +
23B ALA* 1.3 58.0 + - - +
26B ILE* 2.8 30.7 + - - +
142B LEU* 3.4 29.2 - - + +
146B LEU* 3.5 20.0 - - + -
147B LEU* 3.0 19.5 - - + +
150B LEU* 4.0 7.4 - - + -
164B CYS* 3.2 35.2 - - + -
168B LEU* 3.6 22.4 - - - -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL 2.9 10.3 + - - +
20B GLY 4.2 0.9 - - - +
22B MET* 1.3 76.5 - - - +
24B GLN* 1.3 66.6 + - - +
26B ILE* 3.5 8.9 - - - +
27B TYR* 2.9 27.9 + - - +
107B GLY* 3.6 16.1 - - - -
161B TRP* 6.2 2.2 - - + -
165B TYR* 3.4 38.3 - - + +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 3.0 22.5 + - - +
21B GLN* 3.1 14.2 + - - +
23B ALA* 1.3 74.2 - - - +
25B THR* 1.3 79.6 + - + +
27B TYR* 2.8 50.0 + - + +
28B ILE* 5.8 2.1 - - + +
52B TYR* 4.6 10.4 - - + -
107B GLY* 4.1 4.6 - - - +
108B MET* 3.3 38.8 - - - +
111B GLY* 4.3 7.1 - - - -
143B VAL* 5.4 0.3 - - - +
249B PHE* 4.4 12.1 - - - -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN 2.7 21.9 + - - -
24B GLN* 1.3 89.8 - - - +
26B ILE* 1.3 46.9 + - - -
28B ILE* 2.7 22.2 + - + +
29B PRO* 2.7 31.5 - - - +
143B VAL* 2.9 19.4 - - + +
147B LEU* 3.0 9.2 - - - +
242B SER* 2.9 17.1 - - - -
245B VAL* 3.8 18.4 - - + -
246B SER* 3.3 21.8 - - - +
249B PHE* 4.4 5.2 - - + -
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET 2.8 25.8 + - - +
23B ALA* 3.5 11.9 - - - +
25B THR* 1.3 76.1 - - - +
27B TYR* 1.3 60.2 + - - +
29B PRO* 3.0 10.2 - - + +
30B ALA* 2.9 31.0 + - + +
147B LEU* 3.2 37.3 - - + +
150B LEU* 3.9 17.7 - - + -
151B ILE* 3.5 36.1 - - + +
157B THR* 4.4 1.3 - - - +
161B TRP* 4.7 18.4 - - + -
239B GLY 4.8 0.9 - - - +
242B SER* 4.2 3.8 - - - +
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 2.9 17.4 + - - +
24B GLN* 2.8 38.8 + - + +
26B ILE* 1.3 76.3 - - + +
28B ILE* 1.3 72.8 + - + +
30B ALA* 3.6 10.1 - - + -
31B ILE* 2.6 47.6 + - + +
48B VAL* 4.8 12.6 - - + -
52B TYR* 3.9 19.4 - + + +
103B SER* 5.1 2.2 - - - +
104B ALA* 3.1 42.0 - - + +
107B GLY* 3.6 7.0 - - - -
108B MET* 3.1 38.6 - - + +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.9 5.8 - - + +
25B THR* 2.7 44.3 + - + +
27B TYR* 1.3 97.0 - - + +
29B PRO* 1.4 68.8 - - + +
31B ILE* 3.4 5.9 - - - +
32B ALA* 3.1 15.9 + - - +
45B VAL* 5.4 1.4 - - + +
48B VAL* 6.1 0.4 - - - -
52B TYR* 6.6 0.2 - - + -
228B ALA* 5.1 16.4 - - + +
238B LEU* 4.9 3.4 - - + -
241B SER* 4.0 20.4 - - - +
242B SER* 4.8 1.8 - - - +
245B VAL* 4.2 18.2 - - + -
249B PHE* 5.9 1.8 - - + -
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR 2.7 24.5 - - - +
26B ILE* 3.0 20.2 - - + +
28B ILE* 1.4 79.3 - - + +
30B ALA* 1.3 48.6 + - - +
32B ALA* 2.7 28.8 + - + +
33B ASP* 2.5 27.0 + - - +
151B ILE* 3.7 17.5 - - + -
234B MET 5.2 0.2 - - - +
238B LEU* 3.0 36.8 - - + +
239B GLY* 3.6 10.1 - - - +
242B SER* 3.6 11.4 - - - -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 2.9 23.5 + - + +
27B TYR* 3.6 11.2 - - + -
29B PRO* 1.3 75.4 - - - +
31B ILE* 1.3 62.7 + - + +
33B ASP* 3.3 12.7 + - - +
34B MET* 3.0 30.1 + - + +
151B ILE* 4.3 6.2 - - + +
161B TRP* 5.9 9.6 - - + -
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 2.6 31.8 + - + +
28B ILE* 3.4 5.2 - - - +
30B ALA* 1.3 69.4 - - + +
32B ALA* 1.3 65.9 + - - +
33B ASP 2.9 0.5 + - - -
34B MET* 5.5 0.2 - - - -
35B ALA* 2.6 38.5 + - + +
45B VAL* 3.6 27.1 - - + -
48B VAL* 3.4 45.1 - - + -
100B ILE* 4.0 22.2 - - + +
103B SER* 6.1 0.4 - - - -
104B ALA* 3.5 28.3 - - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE 3.1 5.0 + - - +
29B PRO 2.7 15.7 + - - +
31B ILE* 1.3 78.9 - - - +
33B ASP* 1.3 54.5 + - - +
36B ARG* 2.9 22.7 + - - +
45B VAL* 4.3 2.9 - - + -
233B LEU* 2.8 67.5 - - + +
238B LEU* 3.5 11.4 - - + -
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 2.5 28.0 + - - +
30B ALA* 3.3 12.4 - - - +
31B ILE 2.9 0.4 + - - -
32B ALA* 1.3 76.5 - - - +
34B MET* 1.3 69.0 + - + +
36B ARG* 3.2 2.8 + - - +
37B ASP* 3.2 19.4 + - - +
151B ILE* 4.2 16.6 - - - +
156B ASP* 4.1 9.7 - - - +
233B LEU 2.4 30.5 - - - +
234B MET* 3.1 43.7 - - + +
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.0 15.7 + - + +
33B ASP* 1.3 83.1 - - + +
35B ALA* 1.3 57.3 + - - +
37B ASP* 2.9 33.4 + - - +
38B LEU* 3.0 17.4 + - - +
88B LEU* 5.7 4.7 - - + -
91B VAL 5.0 3.6 - - - +
92B THR* 5.3 12.8 - - + +
95B SER* 3.4 32.7 + - - +
100B ILE* 4.2 7.2 - - + -
156B ASP* 5.5 2.9 - - - +
158B MET* 5.2 15.0 - - + -
234B MET* 4.5 15.7 - - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 2.6 37.3 + - + +
34B MET* 1.3 69.2 - - - +
36B ARG* 1.3 55.7 + - - +
37B ASP 3.0 6.4 + - - -
38B LEU* 3.0 41.5 + - + +
40B VAL 4.1 0.5 - - - +
41B ARG* 4.0 9.1 - - - -
44B ALA* 4.9 4.9 - - + -
45B VAL* 3.6 27.4 - - + +
48B VAL* 5.4 0.9 - - + -
100B ILE* 4.5 5.5 - - + +
----------------------------------------------------------
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 2.9 20.5 + - - +
33B ASP 3.6 2.0 - - - +
35B ALA* 1.3 75.7 - - - +
37B ASP* 1.3 57.7 + - - +
38B LEU 3.5 2.4 - - - +
41B ARG* 3.0 47.7 - - + +
42B GLU* 4.3 15.8 + - - +
45B VAL* 4.8 0.8 - - + +
229B CYS* 5.1 5.4 + - - -
230B SER* 6.2 0.2 - - - +
231B GLY 2.8 29.6 + - - +
232B VAL* 3.5 5.1 - - - +
233B LEU* 3.3 43.9 - - + +
----------------------------------------------------------
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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