Contacts of the helix formed by residues 31 - 59 (chain B) in PDB entry 5SY1
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 CYS 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PRO* 3.8 14.1 + - - -
30B PRO* 1.3 81.9 - - - +
32B ASP* 1.3 59.3 + - - +
33B PRO* 3.9 9.4 - - + -
34B THR* 3.3 30.9 - - - +
35B ALA* 3.0 27.1 + - - +
170B ASP* 5.7 0.4 - - - -
171B CYS* 3.6 33.2 - - - -
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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
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30B PRO 4.2 0.4 - - - -
31B CYS* 1.3 70.9 - - - +
33B PRO* 1.3 68.4 - - + +
35B ALA* 4.1 8.9 - - - +
36B ASP* 3.2 22.0 + - - +
166B TRP* 4.7 8.3 - - + -
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Residues in contact with PRO 33 (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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31B CYS* 3.6 11.2 - - + -
32B ASP* 1.3 91.2 - - + +
34B THR* 1.3 52.9 + - - +
36B ASP* 3.0 4.6 + - + +
37B GLU* 2.4 36.6 + - - +
40B PHE* 4.1 3.5 - - + -
166B TRP* 3.6 36.6 - - + -
167B GLN* 3.8 28.5 - - + +
170B ASP* 3.6 31.4 - - - +
171B CYS* 5.3 1.6 - - - -
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS* 3.2 29.9 + - - +
33B PRO* 1.3 74.8 - - - +
35B ALA* 1.3 62.5 + - - +
37B GLU* 3.0 28.5 + - + +
38B GLY 3.5 5.5 + - - -
167B GLN* 5.7 1.1 - - - +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS 3.0 16.3 + - - +
32B ASP* 4.2 11.2 - - - +
34B THR* 1.3 75.8 - - - +
36B ASP* 1.3 58.8 + - - +
38B GLY* 4.4 4.5 + - - -
39B LEU* 4.6 4.3 + - - +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP 3.2 18.4 + - - +
33B PRO* 3.0 3.1 + - + +
35B ALA* 1.3 73.8 - - - +
37B GLU* 1.3 53.0 + - - +
38B GLY 3.2 2.7 - - - -
39B LEU* 2.9 31.8 + - - +
40B PHE* 2.4 71.9 + - + -
166B TRP* 5.4 2.9 - - + -
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Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO 2.4 25.3 + - - +
34B THR* 3.0 18.8 + - + +
36B ASP* 1.3 71.3 - - - +
38B GLY* 1.3 49.4 + - - +
40B PHE* 3.7 17.0 - - - +
41B HIS* 2.5 73.8 + - + -
163B ILE* 4.4 3.3 - - - +
167B GLN* 2.4 34.1 + - - +
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Residues in contact with GLY 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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34B THR 3.5 8.0 + - - -
35B ALA 4.4 3.1 + - - -
36B ASP 3.2 0.8 - - - -
37B GLU* 1.3 78.4 - - - +
39B LEU* 1.3 56.5 + - - +
41B HIS* 3.7 12.0 + - - +
42B ILE* 3.3 27.5 + - - +
113B PHE* 4.8 12.3 - - - -
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Residues in contact with LEU 39 (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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35B ALA 4.6 3.0 + - - +
36B ASP* 2.9 29.0 + - - +
38B GLY* 1.3 75.7 - - - +
40B PHE* 1.3 52.9 + - - +
41B HIS 3.2 1.3 - - - -
42B ILE* 3.0 26.8 + - + +
43B CYS* 2.6 41.9 + - + +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO* 4.1 4.0 - - + -
36B ASP* 2.4 70.4 + - + +
37B GLU* 3.2 26.7 + - - +
39B LEU* 1.3 65.7 - - - +
41B HIS* 1.3 64.6 + - - +
43B CYS* 3.8 16.8 - - + -
44B ILE* 3.3 28.2 + - + +
163B ILE* 4.0 40.6 - - + -
166B TRP* 4.2 25.6 - + - -
167B GLN* 4.9 1.1 - - - -
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Residues in contact with HIS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 2.5 64.9 + - + +
38B GLY* 3.7 13.2 - - - +
40B PHE* 1.3 74.8 - - - +
42B ILE* 1.3 60.6 + - - +
44B ILE* 5.5 0.2 - - - -
45B ALA* 3.4 25.1 + - - +
110B PRO 5.2 3.1 - - - -
111B LEU* 3.4 32.4 - - + +
113B PHE* 3.8 34.5 - + + +
130B TYR* 4.0 19.4 + + - -
131B TYR* 5.5 2.4 + - - -
134B LEU* 6.2 1.1 - - + -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.3 17.9 - - - +
39B LEU* 3.0 28.7 + - + +
41B HIS* 1.3 77.5 - - + +
43B CYS* 1.3 65.1 + - - +
45B ALA* 4.1 2.2 - - - +
46B ALA* 3.2 23.3 + - + +
113B PHE* 5.2 9.0 - - + -
114B THR* 5.4 13.0 - - + +
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Residues in contact with CYS 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 LEU* 2.6 25.5 + - + +
40B PHE* 4.1 18.6 - - + -
41B HIS 3.4 0.2 - - - -
42B ILE* 1.3 73.6 - - - +
44B ILE* 1.3 70.8 + - + +
46B ALA* 3.1 16.2 + - - +
47B ILE* 3.1 28.6 + - - +
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.3 20.6 + - + +
41B HIS* 5.0 0.4 - - - +
43B CYS* 1.3 85.0 - - + +
45B ALA* 1.3 58.4 + - - +
47B ILE* 2.8 14.8 + - + +
48B SER* 2.8 29.8 + - - -
134B LEU* 4.3 19.7 - - + -
156B LEU* 6.6 0.2 - - + -
159B THR* 3.8 19.5 - - + -
160B HIS* 3.5 33.7 - - + +
163B ILE* 3.8 31.4 - - + -
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Residues in contact with ALA 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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41B HIS 3.4 19.8 + - - +
42B ILE* 4.3 2.5 - - - +
43B CYS 3.3 0.4 - - - -
44B ILE* 1.3 78.3 - - - +
46B ALA* 1.3 60.6 + - - +
48B SER* 3.4 18.3 + - - +
49B LEU* 3.4 17.2 + - - +
130B TYR* 4.0 19.7 + - + +
134B LEU* 5.4 4.4 - - + +
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Residues in contact with ALA 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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42B ILE* 3.2 15.3 + - + +
43B CYS* 3.1 13.0 + - - +
45B ALA* 1.3 76.4 - - - +
47B ILE* 1.3 67.6 + - + +
49B LEU* 3.8 4.8 + - - +
50B VAL* 3.3 25.8 + - - +
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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 CYS* 3.2 26.9 - - - +
44B ILE* 2.8 19.1 + - + +
46B ALA* 1.3 81.9 - - + +
48B SER* 1.3 62.6 + - - +
50B VAL* 3.2 15.1 + - + +
51B VAL* 3.3 19.5 + - + +
156B LEU* 3.7 29.8 - - + -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 2.8 17.6 + - - -
45B ALA* 3.4 17.7 + - - +
47B ILE* 1.3 74.0 - - - +
49B LEU* 1.3 62.9 + - - +
51B VAL* 5.0 0.9 - - - -
52B MET* 3.2 31.1 + - - +
133B THR* 4.7 3.8 + - - +
134B LEU* 3.8 32.0 - - - -
137B PRO* 3.7 15.1 - - - +
156B LEU* 6.1 1.8 - - - -
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Residues in contact with LEU 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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45B ALA 3.4 15.6 + - - +
46B ALA* 4.3 4.7 - - - +
47B ILE 3.2 0.8 - - - -
48B SER* 1.3 80.5 + - - +
50B VAL* 1.3 66.6 + - + +
52B MET* 3.9 13.7 + - + +
53B LEU* 3.5 37.4 + - + +
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Residues in contact with VAL 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 ALA 3.3 17.9 - - - +
47B ILE* 3.2 9.3 + - + +
49B LEU* 1.3 78.1 - - + +
51B VAL* 1.3 64.3 + - + +
53B LEU* 3.0 8.7 + - - +
54B VAL* 2.9 39.5 + - + +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.3 24.5 + - + +
48B SER 3.9 0.2 + - - -
50B VAL* 1.3 79.4 - - + +
52B MET* 1.3 61.6 + - - +
54B VAL* 3.4 8.8 + - + +
55B LEU* 3.3 32.7 + - + +
137B PRO* 3.9 27.4 - - + +
141B CYS* 5.3 3.1 - - - -
152B LEU* 4.6 33.4 - - + -
156B LEU* 4.3 22.4 - - + -
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Residues in contact with MET 52 (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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48B SER* 3.2 23.0 + - - +
49B LEU* 4.1 15.9 - - + +
50B VAL 3.2 0.6 - - - -
51B VAL* 1.3 79.7 - - - +
53B LEU* 1.3 64.4 + - + +
55B LEU* 3.5 9.6 + - - +
56B ALA* 3.3 15.1 + - - +
74B LEU* 3.7 34.8 - - + +
133B THR* 4.2 27.4 - - + +
136B TYR* 3.5 41.3 - - + -
137B PRO* 3.7 9.0 - - + -
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Residues in contact with LEU 53 (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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49B LEU* 3.5 28.7 + - + +
50B VAL* 3.0 9.2 + - - +
52B MET* 1.3 79.9 - - + +
54B VAL* 1.3 65.0 + - + +
55B LEU 3.3 0.4 - - - -
56B ALA* 3.4 14.8 + - + +
57B ILE* 3.3 27.4 + - + +
74B LEU* 5.7 3.6 - - + -
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Residues in contact with VAL 54 (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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50B VAL* 2.9 32.3 + - + +
51B VAL* 3.7 11.2 - - - +
52B MET 3.4 0.2 - - - -
53B LEU* 1.3 77.2 - - - +
55B LEU* 1.3 59.1 + - + +
57B ILE* 3.0 28.5 + - + +
58B LEU* 3.1 29.1 + - + +
148B VAL* 5.1 2.7 - - + -
152B LEU* 4.5 20.6 - - + -
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Residues in contact with LEU 55 (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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51B VAL* 3.3 27.9 + - + +
52B MET* 3.7 9.9 - - - +
53B LEU 3.3 0.2 - - - -
54B VAL* 1.3 77.1 - - + +
56B ALA* 1.3 62.0 + - - +
58B LEU* 3.9 15.1 - - + +
59B ALA* 3.3 23.4 + - - +
74B LEU* 5.6 2.5 - - + -
75B LEU* 3.7 26.3 + - + +
136B TYR* 5.9 1.3 - - + -
137B PRO* 5.3 2.9 - - + +
140B ALA* 3.7 34.3 - - + +
141B CYS* 5.0 5.8 - - - +
144B LEU* 3.7 30.1 - - + -
148B VAL* 5.7 3.1 - - + -
149B GLY* 6.1 3.1 - - - -
152B LEU* 5.7 3.8 - - + -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B MET 3.3 11.9 + - - +
53B LEU* 3.5 21.8 - - + +
54B VAL 3.2 0.6 - - - -
55B LEU* 1.3 76.9 - - - +
57B ILE* 1.3 63.9 + - + +
59B ALA* 3.9 5.6 + - - +
60B ARG* 3.7 27.6 + - - +
73B GLY 5.1 10.2 - - - +
74B LEU* 4.9 11.8 - - + +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.3 17.0 - - + +
54B VAL* 3.0 18.0 + - + +
56B ALA* 1.3 77.9 - - + +
58B LEU* 1.3 61.6 + - + +
60B ARG* 3.1 22.1 + - - +
61B ARG* 3.3 46.8 + - - +
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.1 22.3 + - + +
55B LEU* 3.7 22.2 + - + +
57B ILE* 1.3 77.9 - - + +
59B ALA* 1.3 57.4 + - - +
61B ARG* 3.0 41.0 + - + +
62B GLN* 3.1 35.2 + - + +
64B LEU* 5.6 0.4 - - - -
144B LEU* 4.5 12.8 - - + -
146B ASN* 5.1 3.6 - - - +
148B VAL* 3.8 35.9 - - + -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU 3.3 18.8 + - - +
56B ALA 4.2 5.2 - - - +
57B ILE 3.2 0.6 - - - -
58B LEU* 1.3 77.1 - - - +
60B ARG* 1.3 59.7 + - + +
61B ARG 3.2 1.4 + - - -
62B GLN 3.9 5.1 + - - +
63B LYS* 4.0 8.0 + - - +
64B LEU* 4.2 19.6 + - + -
68B GLN* 3.0 40.7 + - + +
73B GLY 4.5 10.5 - - - +
75B LEU* 4.6 6.7 - - + -
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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