Contacts of the helix formed by residues 8 - 34 (chain P) in PDB entry 5VAI
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 ALA 8 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 1.3 88.6 - - + +
9P GLU* 1.3 58.4 + - - +
11P THR* 4.8 1.4 - - - -
12P PHE* 4.4 5.5 + - - +
237R VAL* 4.1 2.0 - - - +
241R TYR* 3.3 35.4 - - + +
313R ILE* 5.8 0.9 - - + -
364R GLU* 4.7 5.6 - - - +
367R PHE* 6.1 5.6 - - + -
384R LEU* 5.2 5.2 - - - +
387R GLU* 5.7 4.1 - - - +
388R LEU* 3.3 16.7 - - - +
391R THR* 5.8 1.8 - - + -
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Residues in contact with GLU 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS 3.8 1.0 - - - +
8P ALA* 1.3 77.3 - - - +
10P GLY* 1.3 70.8 + - - +
12P PHE* 3.4 10.0 + - + +
13P THR* 3.1 16.4 + - - -
145R TYR* 4.8 8.6 + - + -
190R ARG* 3.7 23.0 + - - +
194R VAL* 3.2 37.0 - - - +
233R MET* 3.4 22.0 - - + +
237R VAL* 4.3 9.1 - - + +
241R TYR* 4.7 1.9 + - - +
388R LEU* 3.3 32.5 - - + +
391R THR* 5.8 0.7 - - + -
392R SER* 4.4 5.8 + - - -
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Residues in contact with GLY 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 3.1 20.5 - - - +
9P GLU* 1.3 76.4 - - - +
11P THR* 1.3 52.5 + - - +
13P THR* 2.2 46.1 + - - +
14P SER* 2.7 11.2 + - - -
233R MET* 4.7 10.1 - - - +
234R GLN* 5.1 5.8 - - - -
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Residues in contact with THR 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 2.8 18.3 + - - +
8P ALA* 4.8 2.5 - - - -
10P GLY* 1.3 66.4 - - - -
12P PHE* 1.3 63.1 + - - +
14P SER* 3.0 21.4 + - - -
15P ASP* 3.1 12.5 + - - +
234R GLN* 5.9 0.2 - - - +
299R ARG* 2.3 44.1 + - + +
300R ASN* 4.4 22.0 + - - +
306R TRP* 4.0 20.5 + - + -
376R ARG* 6.4 2.7 - - + -
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Residues in contact with PHE 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ALA 4.4 2.3 + - - +
9P GLU* 3.4 8.8 + - + +
10P GLY 2.8 2.6 + - - -
11P THR* 1.3 79.2 - - - +
13P THR* 1.3 65.9 + - - +
15P ASP* 3.7 7.4 + - + +
16P VAL* 3.1 34.6 + - + +
142R LEU* 4.6 19.1 - - + -
145R TYR* 4.2 16.4 - + + -
381R PHE* 4.1 29.8 - + - -
384R LEU* 4.7 12.5 - - + +
385R PHE* 3.3 42.6 - + + -
388R LEU* 3.6 32.8 - - + -
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Residues in contact with THR 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P GLU* 3.1 10.6 + - + +
10P GLY* 2.2 48.1 + - - +
12P PHE* 1.3 73.4 - - - +
14P SER* 1.3 59.5 + - - +
15P ASP 3.1 2.0 - - - -
16P VAL* 2.7 31.0 + - - +
17P SER* 2.8 14.4 + - - -
197R LYS* 2.2 50.5 + - + -
230R PHE* 5.2 7.4 - - + -
233R MET* 5.6 5.8 - - + -
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Residues in contact with SER 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P GLY 2.7 9.1 + - - -
11P THR* 3.2 17.3 - - - -
13P THR* 1.3 79.8 - - - +
15P ASP* 1.3 61.5 + - - +
17P SER* 2.7 23.7 + - - -
18P SER* 3.0 13.0 + - - -
297R TRP* 3.5 4.5 + - - +
298R THR* 2.9 35.1 + - - -
299R ARG* 2.9 15.3 + - - +
300R ASN* 4.8 4.8 + - - -
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Residues in contact with ASP 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P THR 3.1 10.0 + - - +
12P PHE* 3.7 13.7 - - + +
13P THR 3.1 0.6 - - - -
14P SER* 1.3 77.0 - - - +
16P VAL* 1.3 63.2 + - + +
18P SER* 2.9 24.3 + - - -
19P TYR* 3.0 42.2 + - - -
138R GLU* 4.8 2.4 - - - +
298R THR* 4.9 0.4 - - - -
300R ASN* 5.2 13.6 + - - +
381R PHE* 4.7 15.3 - - + -
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Residues in contact with VAL 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.1 35.4 - - + +
13P THR* 2.7 28.3 + - - +
15P ASP* 1.3 72.4 - - + +
17P SER* 1.3 54.2 + - - +
19P TYR* 3.1 7.6 + - - +
20P LEU* 2.9 26.1 + - + +
142R LEU* 3.3 36.8 - - + -
146R ILE* 5.2 14.6 - - + -
197R LYS* 5.2 0.7 - - - +
201R LEU* 4.6 11.0 - - + -
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Residues in contact with SER 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P THR 2.8 8.7 + - - -
14P SER* 2.7 23.6 + - - -
16P VAL* 1.3 73.9 - - - +
18P SER* 1.3 60.5 + - - +
20P LEU* 3.5 9.6 - - - +
21P GLU* 2.8 35.6 + - - +
201R LEU* 4.3 24.1 - - - +
204R MET* 5.9 0.2 - - - +
230R PHE* 5.7 4.9 - - - -
296R CYS* 5.7 4.7 - - - -
297R TRP 3.0 21.5 + - - -
298R THR* 4.8 0.3 - - - -
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Residues in contact with SER 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P SER 3.0 7.5 + - - -
15P ASP* 2.9 20.4 + - - -
17P SER* 1.3 76.5 + - - +
19P TYR* 1.3 62.2 + - - +
21P GLU* 3.3 9.3 + - - +
22P GLY* 3.0 23.4 + - - -
29R THR* 5.3 18.8 - - - +
298R THR* 2.5 36.7 + - - +
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Residues in contact with TYR 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P ASP* 3.0 40.3 + - - -
16P VAL 3.1 6.3 + - - +
18P SER* 1.3 76.2 - - - +
20P LEU* 1.3 60.9 + - - +
22P GLY* 4.4 1.3 - - - +
23P GLN* 2.9 47.3 + - + +
136R SER* 6.0 0.2 - - - -
138R GLU* 2.7 46.8 + - + -
139R GLU* 4.0 4.0 - - - -
142R LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 20 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P VAL* 2.9 15.3 + - + +
17P SER* 3.2 9.8 + - - +
19P TYR* 1.3 76.2 - - - +
21P GLU* 1.3 56.7 - - - +
23P GLN* 4.9 7.9 - - + +
24P ALA* 2.8 37.8 + - + +
201R LEU* 3.7 42.8 - - + +
204R MET* 3.3 33.0 - - + -
205R TYR* 4.2 35.0 - - + +
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Residues in contact with GLU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P SER* 2.8 22.1 + - - +
18P SER* 3.6 7.0 - - - +
20P LEU* 1.3 74.6 - - - +
22P GLY* 1.3 58.2 + - - +
24P ALA* 3.9 3.2 - - - +
25P ALA* 2.9 30.5 + - - +
30R VAL 4.0 14.1 - - - +
31R SER* 3.3 13.1 - - - -
32R LEU* 2.5 45.7 + - - +
33R SER 4.5 0.2 + - - -
204R MET* 3.4 31.5 - - - +
296R CYS* 6.1 0.3 - - - +
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Residues in contact with GLY 22 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P SER 3.0 14.8 + - - -
19P TYR* 3.3 3.8 + - - -
21P GLU* 1.3 76.7 - - - +
23P GLN* 1.3 56.5 + - - +
25P ALA* 3.1 6.4 + - - +
26P LYS* 2.9 34.5 + - - +
29R THR* 5.4 8.3 - - - -
30R VAL 4.3 7.3 + - - -
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Residues in contact with GLN 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P TYR* 2.9 34.0 + - + +
20P LEU* 4.1 8.6 - - + +
22P GLY* 1.3 72.7 - - - -
24P ALA* 1.3 56.6 + - - +
26P LYS* 3.2 11.1 + - - +
27P GLU* 2.9 34.3 + - + +
139R GLU* 3.9 21.0 + - - -
142R LEU* 5.7 0.4 - - - +
205R TYR* 5.3 10.1 - - + -
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Residues in contact with ALA 24 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P LEU* 2.8 28.8 + - + +
21P GLU* 3.9 5.6 - - - +
23P GLN* 1.3 73.8 - - - +
25P ALA* 1.3 60.2 + - - +
27P GLU* 3.2 10.0 + - - +
28P PHE* 2.9 27.0 + - - +
32R LEU* 5.3 13.7 - - + +
204R MET* 5.3 8.7 - - + -
208R ALA* 4.7 18.7 - - + +
212R HIS* 5.4 3.8 - - + -
215R ASP* 5.7 1.8 - - - +
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Residues in contact with ALA 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P GLU 2.9 19.5 + - - +
22P GLY* 3.4 6.5 - - - +
24P ALA* 1.3 75.0 - - - +
26P LYS* 1.3 58.6 + - + +
28P PHE* 3.1 10.9 + - - +
29P ILE* 2.9 33.9 + - + +
30R VAL* 4.8 8.3 - - + +
32R LEU* 5.1 8.2 - - - +
35R THR* 3.9 28.2 - - + +
90R PRO* 5.2 10.1 - - + -
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Residues in contact with LYS 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P GLY 2.9 23.6 + - - +
23P GLN* 3.4 10.5 - - - +
25P ALA* 1.3 77.7 - - + +
27P GLU* 1.3 57.6 + - + +
29P ILE* 2.9 28.9 + - + +
30P ALA* 2.9 16.0 + - - +
90R PRO* 5.4 4.7 - - + -
91R TRP* 3.4 34.8 - - + -
128R GLU* 2.7 27.0 + - - +
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Residues in contact with GLU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P GLN* 2.9 20.5 + - + +
24P ALA* 3.2 11.9 + - - +
26P LYS* 1.3 76.0 - - + +
28P PHE* 1.3 57.8 + - - +
30P ALA* 3.5 8.9 + - - +
31P TRP* 2.9 32.7 + - - +
205R TYR* 6.0 6.6 - - + -
208R ALA* 5.2 16.4 - - + +
212R HIS* 4.9 3.4 - - + -
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Residues in contact with PHE 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ALA 2.9 13.2 + - - +
25P ALA* 3.1 11.4 + - - +
27P GLU* 1.3 76.8 - - - +
29P ILE* 1.3 64.4 + - + +
31P TRP* 3.6 21.0 - + - +
32P LEU* 2.8 52.0 + - + +
37P GLY 5.4 0.2 - - - -
32R LEU* 5.1 6.5 - - + -
35R THR* 4.0 23.1 - - + -
36R VAL* 5.3 11.9 - - + -
39R TRP* 3.9 41.5 - + + -
88R TYR* 5.1 6.1 - + - -
212R HIS* 3.0 36.9 + + + +
213R GLN* 6.0 2.5 - - - -
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Residues in contact with ILE 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P ALA* 3.1 17.3 - - + +
26P LYS* 2.9 21.6 + - + +
28P PHE* 1.3 87.6 - - + +
30P ALA* 1.3 58.2 + - - +
32P LEU* 4.7 1.6 - - - -
33P VAL* 2.8 51.0 + - + +
35R THR* 5.4 4.0 - - + -
88R TYR* 5.7 9.0 - - + -
89R LEU* 5.3 4.5 - - + -
90R PRO* 4.4 17.9 - - + -
91R TRP* 4.0 30.7 - - + -
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Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LYS 2.9 14.4 + - - +
27P GLU* 4.1 11.2 - - - +
29P ILE* 1.3 76.7 - - - +
31P TRP* 1.3 54.7 + - - +
33P VAL* 4.9 2.0 - - - -
34P LYS* 2.7 40.9 + - + +
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Residues in contact with TRP 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P GLU* 2.9 20.8 + - - +
28P PHE* 3.6 20.0 - + - +
30P ALA* 1.3 78.2 - - - +
32P LEU* 1.3 60.0 + - - +
34P LYS 3.2 12.9 - - - +
36P ARG* 2.7 51.8 + - + +
37P GLY* 3.3 33.4 - - - -
210R GLN 5.6 2.2 + - - -
211R GLN* 3.2 40.6 + - - -
212R HIS* 3.2 35.2 - + + +
213R GLN* 4.8 12.3 - - - -
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Residues in contact with LEU 32 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P PHE* 2.8 41.1 + - + +
29P ILE* 4.0 2.2 - - - +
31P TRP* 1.3 75.2 - - - +
33P VAL* 1.3 67.8 + - + +
34P LYS* 4.5 0.7 - - - -
35P GLY 4.7 3.6 - - - +
37P GLY* 3.2 39.0 + - - +
39R TRP* 3.8 20.4 - - + +
67R ASP 4.7 5.9 - - - +
68R ASP* 3.1 39.8 - - + +
69R TYR* 3.4 23.1 - - + -
88R TYR* 4.9 2.2 - - - +
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Residues in contact with VAL 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P ILE* 2.8 39.7 + - + +
30P ALA* 4.4 2.2 - - - +
32P LEU* 1.3 79.4 - - + +
34P LYS* 1.3 61.7 + - + +
35P GLY 4.3 1.0 + - - +
67R ASP 5.4 3.0 - - - +
69R TYR* 3.9 24.7 - - + +
86R PRO* 6.4 1.1 - - + -
88R TYR* 6.0 0.4 - - - +
118R LEU* 5.7 3.1 - - - +
121R ARG* 4.4 18.3 + - - +
123R LEU* 3.6 30.5 - - + -
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Residues in contact with LYS 34 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ALA* 2.7 26.9 + - + +
31P TRP* 3.2 6.7 - - - +
33P VAL* 1.3 83.3 - - + +
35P GLY* 1.3 72.2 + - - +
113R LYS* 5.5 3.1 - - - +
118R LEU* 3.9 29.2 - - + -
121R ARG* 5.0 5.2 - - - +
----------------------------------------------------------
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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