Contacts of the helix formed by residues 30 - 53 (chain B) in PDB entry 3W7F
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 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 4.5 1.3 - - - +
29B LEU* 1.3 97.9 - - + +
31B GLU* 1.3 65.6 + - - +
32B ASP* 3.4 3.6 - - + +
33B GLN* 3.1 32.2 + - - +
34B ARG* 3.0 17.3 + - - +
236B GLU* 3.8 30.1 - - + +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU 3.6 0.8 + - - -
30B PRO* 1.3 72.6 - - - +
32B ASP* 1.3 66.5 + - - +
34B ARG* 3.1 40.2 + - - +
35B LYS* 3.2 52.2 + - + +
38B TRP* 4.8 3.6 - - - -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 3.4 2.3 - - + +
31B GLU* 1.3 82.2 - - - +
33B GLN* 1.3 63.6 + - + +
35B LYS* 3.8 12.1 + - - +
36B ALA* 3.5 20.4 + - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.1 18.6 - - + +
30B PRO* 3.1 36.8 + - - +
32B ASP* 1.3 79.4 - - + +
34B ARG* 1.3 64.5 + - - +
36B ALA* 3.3 4.5 + - - +
37B VAL* 3.1 24.8 + - - +
144B ILE* 3.6 34.0 + - + +
145B LEU* 4.6 1.1 - - + +
234B SER* 3.4 26.5 + - - -
236B GLU* 4.6 7.0 + - - +
237B ALA* 4.2 12.3 - - - +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B HIS* 5.2 4.2 - - - -
26B PHE 3.5 18.6 - - - +
27B ASP* 3.7 24.6 + - - +
29B LEU* 3.4 27.8 + - + +
30B PRO 3.0 10.4 + - - +
31B GLU* 3.1 35.7 + - - +
33B GLN* 1.3 74.4 - - - +
35B LYS* 1.3 68.7 + - - +
37B VAL* 3.2 3.4 + - - +
38B TRP* 3.0 63.7 + - + +
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASP* 4.8 13.9 - - - +
8B PHE* 3.3 56.3 - - + -
31B GLU* 3.2 44.7 + - + +
32B ASP* 3.9 11.9 + - - +
34B ARG* 1.3 77.8 - - - +
36B ALA* 1.3 62.5 + - - +
38B TRP* 3.3 32.5 + - + +
39B ALA 3.1 17.3 + - - -
92B HIS* 4.8 6.7 + - - -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.4 0.4 - - - -
32B ASP 3.5 10.9 + - - +
33B GLN 3.3 7.9 + - - +
34B ARG 3.3 0.4 - - - -
35B LYS* 1.3 78.3 - - - +
37B VAL* 1.3 58.3 + - - +
39B ALA* 3.4 2.6 + - - +
40B ILE* 3.0 34.0 + - - +
93B VAL* 3.8 36.3 - - + +
97B LYS* 5.6 1.1 - - + -
144B ILE* 3.8 21.8 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 4.2 14.8 - - + -
26B PHE* 4.0 31.0 - - + -
29B LEU* 3.8 19.5 - - + -
33B GLN 3.1 19.3 + - - +
34B ARG* 3.2 10.0 + - - +
36B ALA* 1.3 75.0 - - - +
38B TRP* 1.3 61.0 + - + +
40B ILE* 3.2 7.1 + - - +
41B TYR* 2.8 28.8 + - - +
141B LEU* 4.2 22.2 - - + -
144B ILE* 4.4 9.4 - - + -
145B LEU* 4.4 5.6 - - + -
301B FPS 4.8 5.2 - - + -
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Residues in contact with TRP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.3 30.5 - - + -
9B LYS* 4.9 4.9 - - - -
11B CYS* 3.6 8.0 - - + +
12B HIS* 3.3 60.2 - + + +
15B MET* 4.0 17.5 - - - -
26B PHE* 5.4 1.3 + - + -
27B ASP* 3.0 22.8 + - - -
31B GLU* 4.8 3.8 - - - -
34B ARG* 3.0 62.6 + - + +
35B LYS* 3.3 33.4 + - + +
37B VAL* 1.3 77.0 - - + +
39B ALA* 1.3 58.5 + - - +
41B TYR* 3.3 6.3 + - - +
42B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.9 18.4 - - + -
11B CYS* 3.9 12.5 - - - +
35B LYS 3.1 9.8 + - - +
36B ALA 3.6 8.5 - - - +
38B TRP* 1.3 79.5 - - - +
40B ILE* 1.3 63.3 + - - +
42B ALA* 3.3 1.6 + - - +
43B VAL* 3.0 29.3 + - - +
86B ILE* 4.3 0.4 - - - +
89B ALA* 3.9 17.3 - - + -
90B LEU* 4.2 7.9 - - + +
93B VAL* 4.1 10.8 - - + -
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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
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36B ALA* 3.0 27.4 + - + +
37B VAL* 3.2 4.0 + - - +
39B ALA* 1.3 77.1 - - + +
41B TYR* 1.3 63.4 + - - +
43B VAL* 3.4 6.6 + - - +
44B CYS* 3.0 29.8 + - - -
90B LEU* 4.6 10.3 - - + -
93B VAL* 5.0 4.9 - - + -
99B ILE* 5.7 4.3 - - + -
104B PHE* 4.4 14.4 - - + -
140B VAL* 3.6 36.1 - - + +
141B LEU* 4.0 14.8 - - + -
144B ILE* 3.7 29.8 - - + -
301B FPS 4.0 15.3 - - + -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE 4.1 2.7 - - - -
15B MET* 3.6 50.7 - - + -
18B HIS* 3.5 0.9 - - - +
19B SER* 3.2 26.0 + - - -
22B PHE* 5.9 0.2 - + - -
37B VAL 2.8 17.1 + - - +
38B TRP 3.5 3.6 - - - +
40B ILE* 1.3 78.1 - - - +
42B ALA* 1.3 61.0 + - - +
44B CYS* 3.0 3.6 + - - +
45B ARG* 2.8 66.5 + - + +
301B FPS 3.5 53.5 - - + +
302B FPS 2.4 30.8 + - - -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B CYS* 3.7 32.3 - - + +
14B ILE* 4.2 13.2 - - + -
38B TRP 2.9 17.7 + - - +
39B ALA 3.6 4.5 - - - +
41B TYR* 1.3 75.2 - - - +
43B VAL* 1.3 58.2 + - - +
45B ARG* 3.5 5.6 - - - +
46B LYS* 3.0 35.3 + - - +
86B ILE* 3.9 17.0 - - + +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA 3.0 17.7 + - - +
40B ILE 3.7 5.8 - - - +
42B ALA* 1.3 77.0 - - - +
44B CYS* 1.3 60.9 + - - +
46B LYS* 3.7 4.7 + - - +
47B ILE* 3.2 37.9 + - + +
63B ILE* 4.5 0.8 - - + +
67B ILE* 4.1 15.5 - - + -
86B ILE* 3.2 26.0 - - + -
87B MET* 4.4 12.6 - - + -
90B LEU* 4.1 28.9 - - + -
104B PHE* 4.0 16.8 - - + -
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Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.0 27.6 + - - -
41B TYR 3.6 5.4 - - - +
43B VAL* 1.3 75.0 - - - +
45B ARG* 1.3 57.8 + - - +
47B ILE* 3.3 10.4 + - - +
48B ASP* 2.9 32.6 + - - +
104B PHE* 4.0 16.8 - - - -
107B LEU* 3.8 19.1 - - + +
137B VAL* 4.0 16.8 - - - -
140B VAL* 5.0 1.8 - - - -
301B FPS 3.5 30.9 - - + +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.8 18.4 - - + -
18B HIS* 3.4 36.8 + - + +
41B TYR* 2.8 46.6 + - + +
42B ALA* 3.5 7.4 - - - +
44B CYS* 1.3 74.8 - - - +
46B LYS* 1.3 69.3 + - + +
48B ASP* 3.0 18.2 + - - +
49B ASP* 2.9 50.0 + - - +
301B FPS 2.8 65.0 + - + +
302B FPS 3.6 7.7 + - - -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL 4.2 5.3 + - - -
54A TYR* 4.1 19.8 + - - +
10B TYR* 3.9 9.1 + - - -
14B ILE* 3.7 26.0 - - + +
42B ALA 3.0 20.4 + - - +
43B VAL* 3.9 5.6 - - - +
45B ARG* 1.3 79.5 - - + +
47B ILE* 1.3 53.2 + - - +
49B ASP* 3.4 3.5 + - + +
50B SER* 2.8 35.3 + - - -
54B TYR* 3.4 30.5 + - + +
59B PHE* 4.3 11.1 - - + -
63B ILE* 3.9 15.8 - - + +
83B ASP* 3.8 15.4 + - + +
86B ILE* 3.3 20.4 - - + -
87B MET* 6.3 2.0 - - + -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.2 33.5 + - + +
44B CYS* 3.5 11.7 - - - +
45B ARG 3.2 0.6 - - - -
46B LYS* 1.3 76.9 - - - +
48B ASP* 1.3 66.5 + - - +
50B SER* 3.1 16.9 + - - -
60B LEU* 3.7 15.3 - - + -
63B ILE* 3.7 27.8 - - + -
67B ILE* 4.4 2.9 - - + -
104B PHE* 4.4 6.3 - - + -
107B LEU* 4.3 14.1 - - + -
108B ILE* 3.8 31.0 - - + -
111B VAL* 3.4 27.9 - - + +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B CYS 2.9 14.6 + - - +
45B ARG* 3.0 19.6 + - - +
47B ILE* 1.3 78.3 - - - +
49B ASP* 1.3 62.2 + - - +
50B SER 3.4 0.2 + - - -
51B ILE* 3.5 2.1 + - - +
52B ASP* 2.9 43.5 + - - +
111B VAL* 4.3 15.7 - - - +
301B FPS 2.8 36.1 + - + +
305B MG 2.2 31.5 - - - -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 3.7 25.3 + - - -
45B ARG* 2.9 45.2 + - - +
46B LYS* 3.9 2.1 - - - +
48B ASP* 1.3 78.0 - - - +
50B SER* 1.3 59.3 + - - +
51B ILE 3.0 3.1 - - - -
52B ASP* 4.0 1.5 - - - +
53B VAL* 3.0 27.5 + - + +
54B TYR* 2.8 58.7 + - + +
301B FPS 4.6 0.5 + - - -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS 2.8 20.0 + - - -
47B ILE 3.1 15.5 + - - -
48B ASP 3.3 0.4 - - - -
49B ASP* 1.3 73.6 - - - +
51B ILE* 1.3 58.8 + - - +
54B TYR* 3.6 4.0 - - - +
55B GLY 3.3 4.3 + - - -
56B ASP* 2.9 29.6 + - - +
59B PHE* 3.5 29.2 - - - -
60B LEU* 3.1 39.4 - - - +
63B ILE* 4.5 1.6 - - - -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP 3.5 1.0 + - - -
49B ASP 3.0 0.2 - - - -
50B SER* 1.3 79.6 + - - +
52B ASP* 1.3 61.2 + - - +
53B VAL* 2.8 15.3 + - - -
55B GLY* 3.3 18.6 + - - +
56B ASP 4.2 0.7 - - - +
57B ILE* 3.7 42.2 - - + +
60B LEU* 3.7 19.1 - - + -
111B VAL* 3.7 39.9 - - + +
112B TYR* 4.6 3.4 - - + -
114B ASP* 5.2 2.2 - - + +
115B GLN* 3.6 38.5 + - + +
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.5 14.9 + - - -
48B ASP* 2.9 31.2 + - - +
49B ASP* 4.0 2.9 - - - +
51B ILE* 1.3 85.6 - - - +
53B VAL* 1.3 68.6 + - + +
111B VAL* 5.0 4.0 - - - +
114B ASP* 5.4 8.3 - - - +
301B FPS 3.9 1.1 + - - +
305B MG 2.2 32.4 - - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 4.3 15.1 + - - -
46A LYS* 4.0 21.5 + - - +
54A TYR* 4.5 9.2 - - + +
83A ASP* 4.9 2.1 - - - +
85A ARG* 5.8 1.2 + - - -
49B ASP* 3.0 31.4 + - + +
51B ILE 2.8 5.4 + - - -
52B ASP* 1.3 85.5 - - + +
54B TYR* 1.3 80.7 + - + +
55B GLY 3.3 4.5 + - - -
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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