Contacts of the helix formed by residues 22 - 49 (chain E) in PDB entry 6M04
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 PRO 22 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 3.9 4.3 - - + +
20E LEU 4.3 1.1 - - - +
21E LYS* 1.3 91.0 - - - +
23E TRP* 1.3 66.3 + - - +
24E TRP* 3.4 52.9 - - + +
25E ASP* 3.5 17.2 + - + +
26E VAL* 3.7 12.3 + - - +
308E TYR* 4.4 7.4 - - + +
422E MET* 4.0 21.5 - - + -
425E GLN* 4.6 20.2 - - + +
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Residues in contact with TRP 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D TYR* 4.8 13.7 - - + +
187D PRO* 3.6 25.0 - - + +
188D LYS* 5.1 20.6 - - + -
22E PRO* 1.3 76.0 - - + +
24E TRP* 1.3 101.6 + + + +
26E VAL* 3.0 8.3 + - - +
27E PHE* 3.0 54.1 + + + -
379E ILE* 5.5 5.8 - - + +
383E THR* 3.6 28.7 + - + +
425E GLN* 4.2 21.2 + - + -
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Residues in contact with TRP 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PRO* 3.4 25.7 - - + +
23E TRP* 1.3 135.7 - + + +
25E ASP* 1.3 65.6 + - - +
26E VAL 3.2 0.2 - - - -
27E PHE* 4.1 6.5 - - - +
28E MET* 2.9 44.2 + - + +
308E TYR* 3.1 25.5 + + - -
379E ILE* 5.0 7.6 - - + -
380E CYS* 4.8 4.9 - - - -
383E THR* 3.6 15.0 - - + -
384E LEU* 3.4 32.7 - - + +
387E LEU* 3.6 39.3 - - + -
422E MET* 6.0 1.1 - - + -
425E GLN* 4.8 8.3 - - + -
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Residues in contact with ASP 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLN* 5.1 6.6 + - - -
20E LEU 4.0 5.2 - - - +
21E LYS* 3.4 23.9 - - + +
22E PRO* 3.5 27.5 + - + +
23E TRP 3.2 0.4 - - - -
24E TRP* 1.3 83.8 - - + +
26E VAL* 1.3 57.3 + - - +
28E MET* 4.0 4.1 - - - +
29E ASP* 2.9 33.2 + - - +
180E SER* 5.0 12.8 - - - +
181E ASN* 5.3 7.2 + - - +
183E TRP* 5.9 2.9 - - - -
308E TYR* 5.8 0.7 - - - +
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Residues in contact with VAL 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS* 4.2 18.8 - - + +
187D PRO* 4.1 15.0 - - + -
21E LYS* 3.7 36.1 - - + -
22E PRO 3.8 11.0 - - - +
23E TRP 3.0 7.7 + - - +
25E ASP* 1.3 75.1 - - - +
27E PHE* 1.3 62.0 + - + +
29E ASP* 3.7 5.0 - - + +
30E TYR* 2.9 35.1 + - + +
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Residues in contact with PHE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D PHE* 5.7 12.1 - + - -
186D TYR* 4.3 22.9 - + - -
187D PRO* 5.9 1.1 - - + -
23E TRP* 3.0 54.4 + + + +
24E TRP* 4.0 6.5 - - - +
26E VAL* 1.3 78.8 - - + +
28E MET* 1.3 68.8 + - + +
30E TYR* 4.5 1.5 - - - +
31E LEU* 2.9 42.1 + - + +
379E ILE* 5.1 7.6 - - + -
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Residues in contact with MET 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 2.9 38.9 + - + +
25E ASP* 4.1 4.0 - - - +
27E PHE* 1.3 83.5 - - + +
29E ASP* 1.3 56.3 + - - +
31E LEU* 4.6 5.2 - - + -
32E ALA* 2.9 32.2 + - - +
180E SER* 5.7 7.9 - - - -
376E TYR* 3.4 73.6 + - + +
379E ILE* 3.9 16.8 - - + -
380E CYS* 3.6 30.7 - - + -
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP* 2.9 31.6 - - - +
14E GLN* 4.7 14.4 + - - +
25E ASP* 2.9 25.2 + - - +
26E VAL* 3.7 5.6 - - - +
27E PHE 3.2 0.2 - - - -
28E MET* 1.3 79.1 - - - +
30E TYR* 1.3 63.5 + - - +
32E ALA* 3.3 3.8 + - - +
33E VAL* 3.0 29.8 + - - +
177E MET* 4.5 1.4 - - - +
180E SER* 5.8 4.9 - - - +
181E ASN* 5.2 2.3 + - - -
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Residues in contact with TYR 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.8 34.8 - - - -
12D ASP* 5.7 0.9 - - + -
174D ILE* 3.4 22.9 - - - +
175D ILE* 5.4 5.6 - - + +
178D VAL* 3.2 48.0 - - + +
26E VAL* 2.9 20.9 + - + +
27E PHE* 4.5 2.0 - - - +
29E ASP* 1.3 77.6 - - - +
31E LEU* 1.3 60.3 + - + +
33E VAL* 3.1 8.8 + - + +
34E VAL* 3.0 46.2 + - + +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PHE* 2.9 28.8 + - + +
28E MET* 4.0 8.5 - - + +
30E TYR* 1.3 81.4 - - + +
32E ALA* 1.3 57.6 + - - +
34E VAL* 3.3 9.2 + - + +
35E MET* 3.0 24.5 + - + +
372E ILE* 3.6 34.3 - - + +
373E ILE* 5.4 1.3 - - + -
375E VAL* 3.9 26.7 - - + -
376E TYR* 3.5 29.8 - - + -
379E ILE* 6.1 0.7 - - + -
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Residues in contact with ALA 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E MET 2.9 20.3 + - - +
29E ASP* 3.7 4.7 - - - +
31E LEU* 1.3 76.5 - - - +
33E VAL* 1.3 59.5 + - - +
35E MET* 3.7 11.3 - - + +
36E LEU* 2.9 28.2 + - - +
173E THR* 4.0 5.6 - - + +
176E LEU* 4.7 12.8 - - + -
177E MET* 4.7 26.4 - - + +
376E TYR* 4.6 10.7 - - + +
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.3 37.2 - - - +
9E SER* 5.1 16.6 - - - +
29E ASP* 3.0 25.5 + - - +
30E TYR* 3.1 12.9 + - + +
32E ALA* 1.3 76.6 - - - +
34E VAL* 1.3 57.1 + - - +
36E LEU* 3.2 10.3 + - + +
37E MET* 2.9 26.7 + - + +
177E MET* 3.8 24.2 - - + -
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 5.3 2.2 - - - +
171D ILE* 6.1 2.5 - - + -
174D ILE* 4.9 8.1 - - + -
175D ILE* 6.3 4.3 - - + -
30E TYR* 3.0 50.0 + - + +
31E LEU* 3.6 9.2 - - + +
33E VAL* 1.3 74.6 - - + +
35E MET* 1.3 58.5 + - - +
37E MET* 3.1 22.1 + - + +
38E VAL* 3.0 28.6 + - + +
372E ILE* 4.2 20.4 - - + -
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Residues in contact with MET 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.0 16.8 + - + +
32E ALA* 3.8 6.5 - - + +
33E VAL 3.3 0.2 - - - -
34E VAL* 1.3 75.8 - - - +
36E LEU* 1.3 57.6 + - - +
38E VAL* 3.3 9.5 + - - +
39E ALA* 3.0 23.7 + - - +
172E HIS* 4.9 3.1 - - + +
173E THR* 2.6 48.7 - - + +
176E LEU* 4.0 19.1 - - + -
369E TYR* 3.5 37.4 - - + +
372E ILE* 3.9 16.8 - - + +
373E ILE* 3.8 26.0 - - + -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA* 4.5 5.2 - - + -
8E ALA* 3.8 37.5 - - + +
9E SER* 4.0 20.4 - - - +
32E ALA 2.9 13.1 + - - +
33E VAL* 3.2 12.3 + - + +
35E MET* 1.3 75.9 - - - +
37E MET* 1.3 62.7 + - - +
39E ALA* 3.2 4.2 + - + +
40E ILE* 2.9 52.3 + - + +
170E LEU* 6.4 1.8 - - + -
173E THR* 3.6 23.9 - - + +
174E ILE* 4.3 9.9 - - + -
177E MET* 4.0 16.8 - - + -
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Residues in contact with MET 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D THR* 4.5 23.4 + - + +
8D ALA* 6.2 0.4 - - - -
11D ASN* 5.5 7.2 - - - +
170D LEU* 4.1 21.1 - - + -
171D ILE* 4.6 12.1 - - + -
174D ILE* 3.9 44.0 - - + -
5E ALA* 6.3 0.9 - - - -
33E VAL* 2.9 14.6 + - + +
34E VAL* 3.1 24.7 + - + +
36E LEU* 1.3 75.2 - - - +
38E VAL* 1.3 66.8 + - + +
40E ILE* 3.4 5.1 + - - +
41E PHE* 3.0 27.0 + - + +
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Residues in contact with VAL 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ILE* 5.4 11.9 - - + -
34E VAL* 3.0 16.4 + - + +
35E MET* 3.5 10.3 - - - +
37E MET* 1.3 78.4 - - + +
39E ALA* 1.3 58.8 + - - +
41E PHE* 3.8 4.9 - - - +
42E ALA* 2.9 27.7 + - + +
365E LEU* 3.8 30.6 - - + +
368E SER* 4.9 7.0 - - - +
369E TYR* 4.4 26.0 - - + +
372E ILE* 4.1 21.8 - - + -
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E MET* 3.0 16.7 + - - +
36E LEU* 3.2 6.9 + - + +
38E VAL* 1.3 79.0 - - - +
40E ILE* 1.3 59.5 - - + +
42E ALA* 3.3 7.9 + - - +
43E GLY* 2.9 24.9 + - - -
166E PRO 4.6 4.6 - - - +
169E ALA* 4.2 11.2 - - + -
170E LEU* 4.0 38.3 - - + +
173E THR* 4.1 9.0 - - - +
369E TYR* 5.8 0.7 - - + -
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Residues in contact with ILE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D PHE* 5.9 4.0 - - + -
3D THR* 5.0 10.8 - - - +
2E PHE* 5.0 11.2 - - + +
3E THR 3.3 26.5 - - - +
4E LEU* 4.5 0.7 - - - -
5E ALA* 3.8 29.6 - - + +
8E ALA* 5.7 1.3 - - + -
36E LEU* 2.9 38.9 + - + +
37E MET* 4.0 5.4 - - - +
39E ALA* 1.3 72.1 - - + +
41E PHE* 1.3 63.2 + - - +
43E GLY* 3.2 2.6 + - - +
44E THR* 3.0 38.2 + - - +
170E LEU* 3.7 22.7 - - + -
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Residues in contact with PHE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D PHE* 4.4 25.6 - + - -
3D THR* 5.4 7.5 + - - +
47D LEU* 6.3 1.3 - - + -
167D TYR* 3.4 61.5 - + + -
170D LEU* 5.5 11.2 - - + -
37E MET* 3.0 20.4 + - + +
38E VAL* 3.9 2.9 - - - +
40E ILE* 1.3 77.1 - - - +
42E ALA* 1.3 59.5 + - - +
44E THR* 3.5 5.6 + - + -
45E MET* 2.9 43.7 + - + +
361E MET* 5.0 7.0 - - - -
365E LEU* 4.3 23.8 - - + -
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E VAL* 2.9 20.7 + - + +
39E ALA* 3.3 10.1 - - - +
40E ILE 3.2 0.2 - - - -
41E PHE* 1.3 76.3 - - - +
43E GLY* 1.3 56.9 + - - +
45E MET* 3.8 4.7 - - - +
46E GLN* 2.8 31.2 + - - +
165E PHE* 5.7 4.7 - - + -
166E PRO* 3.7 22.6 - - + +
169E ALA* 6.1 0.9 - - + -
365E LEU* 3.6 26.7 - - + -
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Residues in contact with GLY 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 6.3 2.9 - - - -
39E ALA 2.9 14.6 + - - -
40E ILE* 3.2 3.8 + - - -
42E ALA* 1.3 77.1 - - - +
44E THR* 1.3 55.0 + - - +
46E GLN* 3.3 6.2 + - - +
47E LEU* 2.9 30.9 + - - +
166E PRO* 3.9 12.0 - - - +
167E TYR* 5.7 7.7 - - - -
170E LEU* 6.0 4.0 - - - -
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D PHE* 4.2 37.1 - - + +
47D LEU* 4.3 11.9 - - + -
2E PHE* 4.8 13.3 - - - -
40E ILE* 3.0 20.8 + - - +
41E PHE* 3.9 8.0 - - + -
43E GLY* 1.3 76.2 - - - +
45E MET* 1.3 51.9 + - - +
47E LEU* 3.2 7.3 + - - +
48E THR* 2.6 41.7 + - - +
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Residues in contact with MET 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 5.4 3.4 - - + -
167D TYR* 4.9 9.2 - - + +
41E PHE* 2.9 35.4 + - + +
42E ALA 4.3 4.0 - - - +
44E THR* 1.3 77.3 - - - +
46E GLN* 1.3 65.0 + - + +
48E THR* 3.3 19.4 + - - -
49E LYS* 3.7 19.2 + - + +
166E PRO* 6.2 0.9 - - + -
358E MET* 3.3 39.9 - - - +
361E MET* 3.6 34.3 - - + -
362E LEU* 4.9 8.7 - - + +
365E LEU* 4.1 21.8 - - + -
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Residues in contact with GLN 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ALA 2.8 20.1 + - - +
43E GLY* 3.7 5.9 - - - +
45E MET* 1.3 82.4 - - + +
47E LEU* 1.3 64.4 + - - +
48E THR 3.4 0.2 + - - -
50E ASP* 3.2 46.5 + - - +
154E TYR* 4.7 2.6 + - - -
163E LYS* 4.4 13.8 + - - +
166E PRO* 3.9 22.6 - - + +
167E TYR* 2.9 37.4 + - - -
358E MET* 3.6 14.8 - - + +
362E LEU* 5.6 4.7 - - + -
49F LYS* 4.6 11.7 - - - +
361F MET* 6.2 0.2 - - - +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 5.5 15.3 - - + -
43E GLY 2.9 16.8 + - - +
44E THR* 3.2 6.0 + - - +
46E GLN* 1.3 82.1 + - - +
48E THR* 1.3 66.9 + - - +
50E ASP* 5.1 2.8 + - - +
167E TYR* 5.2 7.4 - - + +
45F MET* 6.2 4.0 - - + -
48F THR* 4.5 30.3 - - + +
----------------------------------------------------------
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Residues in contact with THR 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 3.5 49.8 - - + +
44E THR* 2.6 22.7 + - - +
45E MET* 3.6 9.2 - - - -
46E GLN 3.2 1.2 - - - -
47E LEU* 1.3 84.3 - - - +
49E LYS* 1.3 76.9 + - + +
50E ASP 3.9 1.3 + - - -
51E GLN* 4.9 0.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLN* 4.0 21.4 + - - +
50D ASP* 4.4 8.2 + - + +
154D TYR* 4.1 20.0 + - + -
167D TYR* 5.4 4.1 + - - -
45E MET* 3.7 25.8 + - - +
48E THR* 1.3 92.7 - - + +
50E ASP* 1.3 61.3 + - - +
51E GLN* 3.3 16.6 + - - +
357E ASN* 3.8 34.2 - - - +
358E MET* 3.2 14.0 - - + +
361E MET* 5.7 8.5 - - - +
----------------------------------------------------------
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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