Contacts of the helix formed by residues 22 - 49 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 3.9 4.7 - - + +
20B LEU 4.3 1.3 - - - +
21B LYS* 1.3 90.7 - - - +
23B TRP* 1.3 67.6 + - + +
24B TRP* 3.4 52.3 - - + +
25B ASP* 3.5 17.3 + - + +
26B VAL* 3.7 13.0 + - - +
308B TYR* 4.4 7.2 - - + +
422B MET* 4.0 21.1 - - + -
425B GLN* 4.6 21.3 - - + +
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 4.8 14.1 - - + +
187A PRO* 3.6 25.7 - - + +
188A LYS* 5.1 19.7 - - + -
22B PRO* 1.3 75.2 - - + +
24B TRP* 1.3 102.3 + + + +
26B VAL* 3.0 7.8 + - - +
27B PHE* 3.0 54.5 + + + -
379B ILE* 5.5 5.1 - - + +
383B THR* 3.6 30.0 + - + +
425B GLN* 4.2 21.9 + - + -
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Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.4 25.7 - - + +
23B TRP* 1.3 137.2 - + + +
25B ASP* 1.3 66.0 + - + +
27B PHE* 3.7 6.7 - - - +
28B MET* 2.9 45.4 + - + +
308B TYR* 3.1 24.9 + + - -
379B ILE* 5.0 6.3 - - + -
380B CYS* 4.8 4.9 - - - -
383B THR* 3.6 16.2 - - + -
384B LEU* 3.4 33.4 - - + +
387B LEU* 3.6 38.6 - - + -
422B MET* 6.0 1.3 - - + -
425B GLN* 4.8 8.1 - - + -
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 5.1 6.9 + - - -
20B LEU 3.9 4.9 - - - +
21B LYS* 3.4 24.5 - - + +
22B PRO* 3.5 26.6 + - + +
23B TRP 3.2 0.8 - - - -
24B TRP* 1.3 85.3 - - + +
26B VAL* 1.3 56.9 + - - +
28B MET* 3.9 3.1 - - - +
29B ASP* 2.9 33.4 + - - +
180B SER* 5.0 12.6 - - - +
181B ASN* 5.3 6.1 + - - +
183B TRP* 5.9 2.8 - - - -
308B TYR* 5.8 0.4 - - - +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LYS* 4.2 20.0 - - + +
187A PRO* 4.1 15.3 - - + -
21B LYS* 3.7 36.3 - - + -
22B PRO 3.8 9.9 - - - +
23B TRP 3.0 7.7 + - - +
25B ASP* 1.3 72.9 - - - +
27B PHE* 1.3 62.1 + - + +
29B ASP* 3.7 4.6 - - - +
30B TYR* 2.9 34.5 + - + +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 5.7 11.7 - + - -
186A TYR* 4.3 23.1 - + - -
187A PRO* 5.9 0.7 - - + -
23B TRP* 3.0 56.1 + + + +
24B TRP* 4.0 6.5 - - + +
26B VAL* 1.3 78.7 - - + +
28B MET* 1.3 67.8 + - + +
30B TYR* 4.5 2.3 - - - +
31B LEU* 2.9 43.1 + - + +
379B ILE* 5.1 7.6 - - + -
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 2.9 39.3 + - + +
25B ASP* 4.1 4.7 - - - +
27B PHE* 1.3 83.2 - - + +
29B ASP* 1.3 56.4 + - - +
31B LEU* 4.6 5.4 - - + -
32B ALA* 2.9 32.4 + - - +
180B SER* 5.7 7.4 - - - -
376B TYR* 3.4 70.7 + - + +
379B ILE* 3.9 16.8 - - + -
380B CYS* 3.6 30.7 - - + -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 2.9 31.9 - - - +
14B GLN* 4.7 14.2 + - - +
25B ASP* 2.9 25.8 + - - +
26B VAL* 3.7 6.1 - - - +
27B PHE 3.2 0.2 - - - -
28B MET* 1.3 77.0 - - - +
30B TYR* 1.3 63.4 + - - +
32B ALA* 3.3 4.6 + - - +
33B VAL* 3.0 29.1 + - - +
177B MET* 4.5 1.4 - - - +
180B SER* 5.8 4.9 - - - -
181B ASN* 5.2 3.2 + - - -
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Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.8 33.0 - - - -
12A ASP* 5.7 0.9 - - + -
174A ILE* 3.4 23.2 + - - +
175A ILE* 5.4 5.5 - - + +
178A VAL* 3.2 51.1 - - + +
26B VAL* 2.9 20.3 + - + +
27B PHE* 4.5 1.8 - - - +
29B ASP* 1.3 77.1 - - - +
31B LEU* 1.3 61.1 + - + +
33B VAL* 3.1 8.2 + - + +
34B VAL* 3.0 46.3 + - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 2.9 28.2 + - + +
28B MET* 4.0 7.9 - - + +
30B TYR* 1.3 80.9 - - + +
32B ALA* 1.3 58.5 + - - +
34B VAL* 3.3 7.7 + - + +
35B MET* 3.0 25.4 + - + +
372B ILE* 3.6 36.3 - - + +
373B ILE* 5.4 0.9 - - + -
375B VAL* 3.9 25.8 - - + -
376B TYR* 3.5 30.3 - - + -
379B ILE* 6.1 1.1 - - + -
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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 MET 2.9 19.8 + - - +
29B ASP* 3.7 4.9 - - - +
31B LEU* 1.3 77.3 - - - +
33B VAL* 1.3 60.1 + - - +
35B MET* 3.7 11.7 - - + +
36B LEU* 2.9 28.4 + - - +
173B THR* 4.0 5.5 - - + +
176B LEU* 4.7 12.3 - - + -
177B MET* 4.7 25.1 - - + -
376B TYR* 4.6 11.6 - - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.3 37.0 - - - +
9B SER* 4.9 17.7 - - - +
29B ASP* 3.0 26.4 + - - +
30B TYR* 3.1 12.3 + - + +
32B ALA* 1.3 75.8 - - - +
34B VAL* 1.3 57.6 + - - +
36B LEU* 3.2 9.9 + - + +
37B MET* 2.9 26.5 + - + +
177B MET* 3.8 23.8 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 5.3 2.2 - - - +
171A ILE* 6.1 2.2 - - + -
174A ILE* 4.9 7.2 - - + -
175A ILE* 6.3 4.5 - - + -
30B TYR* 3.0 49.1 + - + +
31B LEU* 3.3 9.8 + - + +
33B VAL* 1.3 76.5 - - + +
35B MET* 1.3 57.1 + - - +
37B MET* 3.1 23.2 + - + +
38B VAL* 3.0 28.5 + - + +
372B ILE* 4.2 19.3 - - + -
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Residues in contact with MET 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.0 17.2 + - + +
32B ALA* 3.8 7.6 - - - +
34B VAL* 1.3 76.3 - - - +
36B LEU* 1.3 56.3 + - - +
38B VAL* 3.3 10.0 + - + +
39B ALA* 3.0 23.0 + - - +
172B HIS* 4.9 2.9 - - + +
173B THR* 2.6 48.9 - - + +
176B LEU* 4.0 19.3 - - + -
369B TYR* 3.5 38.3 - - + +
372B ILE* 3.9 16.1 - - + +
373B ILE* 3.8 26.0 - - + -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 4.5 6.1 - - + +
8B ALA* 3.9 37.0 - - + +
9B SER* 4.1 19.7 - - - +
32B ALA 2.9 13.7 + - - +
33B VAL* 3.2 11.6 + - + +
35B MET* 1.3 74.8 - - - +
37B MET* 1.3 61.7 + - - +
39B ALA* 3.2 4.0 + - + +
40B ILE* 2.9 52.6 + - + +
170B LEU* 6.4 2.0 - - + -
173B THR* 3.6 25.5 - - + +
174B ILE* 4.3 9.9 - - + -
177B MET* 4.0 15.9 - - + -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 4.4 24.5 + - + +
11A ASN* 5.5 7.0 - - - +
170A LEU* 4.1 20.9 - - + -
171A ILE* 4.6 12.3 - - + -
174A ILE* 3.9 44.9 - - + -
5B ALA* 6.4 0.4 - - - -
33B VAL* 2.9 13.1 + - + +
34B VAL* 3.1 24.9 + - + +
36B LEU* 1.3 76.3 - - - +
38B VAL* 1.3 67.7 + - + +
40B ILE* 3.9 5.0 - - - +
41B PHE* 3.0 27.4 + - + +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 5.4 12.3 - - + -
34B VAL* 3.0 16.6 + - + +
35B MET* 3.5 10.1 - - - +
36B LEU 3.3 0.2 - - - -
37B MET* 1.3 78.9 - - + +
39B ALA* 1.3 58.3 + - - +
41B PHE* 3.5 4.7 + - - +
42B ALA* 2.9 27.7 + - + +
365B LEU* 3.8 29.8 - - + +
368B SER* 4.9 6.5 - - - +
369B TYR* 4.4 26.5 - - + +
372B ILE* 4.1 20.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET* 3.0 16.5 + - - +
36B LEU* 3.2 6.9 + - + +
38B VAL* 1.3 79.3 - - - +
40B ILE* 1.3 58.1 + - + +
42B ALA* 3.3 8.8 + - - +
43B GLY* 2.9 23.7 + - - -
166B PRO 4.6 3.7 - - - +
169B ALA* 4.2 10.5 - - + -
170B LEU* 4.0 39.8 - - + +
173B THR* 4.1 8.7 - - - +
369B TYR* 5.8 0.7 - - + -
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 5.8 4.0 - - + -
3A THR* 4.9 11.4 - - - +
2B PHE* 5.0 11.2 - - + +
3B THR 3.4 25.8 - - - +
4B LEU* 4.8 0.7 - - - +
5B ALA* 3.8 29.8 - - + +
8B ALA* 5.6 1.6 - - + -
36B LEU* 2.9 40.0 + - + +
37B MET* 4.0 5.2 - - - +
39B ALA* 1.3 72.6 - - + +
41B PHE* 1.3 60.8 + - - +
43B GLY* 3.2 2.1 + - - -
44B THR* 3.0 38.3 + - - +
170B LEU* 3.7 21.3 - - + -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 4.4 26.2 - + - -
3A THR* 5.2 7.4 + - - +
47A LEU* 6.3 2.0 - - + -
167A TYR* 3.4 61.9 - + + -
170A LEU* 5.5 11.7 - - + -
37B MET* 3.0 20.9 + - + +
38B VAL* 3.9 2.9 - - - +
40B ILE* 1.3 78.1 - - - +
42B ALA* 1.3 60.0 + - - +
44B THR* 3.9 5.8 - - + -
45B MET* 2.9 44.0 + - + +
361B MET* 5.0 7.2 - - - -
365B LEU* 4.3 22.7 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 2.9 20.1 + - + +
39B ALA* 3.3 10.8 - - - +
41B PHE* 1.3 77.5 - - - +
43B GLY* 1.3 57.4 + - - +
45B MET* 3.8 4.3 - - - +
46B GLN* 2.9 31.9 + - - +
165B PHE* 5.7 4.3 - - + -
166B PRO* 3.7 23.4 - - + +
169B ALA* 6.1 0.9 - - + -
365B LEU* 3.6 28.3 - - + -
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 6.3 2.7 - - - -
39B ALA 2.9 14.2 + - - -
40B ILE* 3.2 3.8 + - - -
42B ALA* 1.3 77.1 - - - +
44B THR* 1.3 55.8 + - - +
46B GLN* 3.3 5.6 + - - +
47B LEU* 2.9 31.5 + - - +
166B PRO* 3.9 11.8 - - - +
167B TYR* 5.6 7.9 + - - -
170B LEU* 6.0 3.8 - - - -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 4.1 40.8 - - + +
47A LEU* 4.3 9.0 - - + -
2B PHE* 4.8 13.2 - - - -
40B ILE* 3.0 21.1 + - - +
41B PHE* 3.9 8.7 - - + -
43B GLY* 1.3 75.8 - - - +
45B MET* 1.3 52.8 + - - +
47B LEU* 3.2 6.9 + - - +
48B THR* 2.6 40.9 + - - +
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Residues in contact with MET 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 5.4 3.6 - - + -
167A TYR* 5.0 9.9 - - + +
41B PHE* 2.9 35.6 + - + +
42B ALA 4.3 4.5 - - - +
44B THR* 1.3 78.2 - - - +
46B GLN* 1.3 64.8 + - + +
48B THR* 3.3 19.1 + - - -
49B LYS* 3.7 19.2 + - - +
166B PRO* 6.2 1.1 - - + -
358B MET* 3.3 40.5 - - - +
361B MET* 3.6 33.7 - - + -
362B LEU* 4.9 9.2 - - + +
365B LEU* 4.1 21.8 - - + -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 2.9 19.9 + - - +
43B GLY* 3.7 5.6 - - - +
44B THR 3.2 0.4 - - - -
45B MET* 1.3 82.1 - - + +
47B LEU* 1.3 63.5 + - - +
48B THR 3.4 0.3 + - - -
50B ASP* 3.2 47.9 + - - +
154B TYR* 4.7 2.8 + - - -
163B LYS 4.4 13.4 + - - +
166B PRO* 3.9 23.5 - - + +
167B TYR* 2.9 39.0 + - - -
358B MET* 3.6 14.7 - - + +
362B LEU* 5.6 4.5 - - + -
49C LYS* 4.6 11.3 - - - +
361C MET* 6.2 0.4 - - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 5.5 15.5 - - + -
43B GLY 2.9 18.0 + - - +
44B THR* 3.2 6.0 + - - +
46B GLN* 1.3 82.1 + - - +
48B THR* 1.3 66.3 + - - +
50B ASP* 5.1 2.7 + - - +
167B TYR* 5.2 8.3 - - + +
45C MET* 6.2 4.0 - - + -
48C THR* 4.5 30.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.5 49.4 - - + +
44B THR* 2.6 22.9 + - - +
45B MET* 3.6 9.6 - - - -
46B GLN 3.2 1.6 - - - -
47B LEU* 1.3 82.3 - - - +
49B LYS* 1.3 76.2 + - + +
50B ASP 3.9 1.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 4.0 21.0 - - - +
50A ASP* 4.4 7.7 + - + +
154A TYR* 4.1 19.5 + - + -
167A TYR* 5.4 3.7 + - - -
45B MET* 3.7 25.9 + - - +
48B THR* 1.3 91.6 - - + +
50B ASP* 1.3 61.1 + - - +
51B GLN* 3.3 16.3 + - - +
357B ASN* 3.8 33.5 - - - +
358B MET* 3.2 14.4 - - + +
361B MET* 5.7 8.3 - - - +
----------------------------------------------------------
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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