Contacts of the helix formed by residues 31 - 59 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 3.8 14.4 - - - -
30A PRO* 1.3 82.0 - - - +
32A ASP* 1.3 60.1 + - - +
33A PRO* 3.9 9.4 - - + -
34A THR* 3.3 30.9 - - - +
35A ALA* 3.0 27.6 + - - +
170A ASP* 5.7 0.7 - - - -
171A CYS* 3.6 31.9 - - - -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO 4.2 1.0 + - - -
31A CYS* 1.3 70.5 - - - +
33A PRO* 1.3 68.1 - - + +
35A ALA* 4.1 8.9 - - - +
36A ASP* 3.2 22.5 + - - +
166A TRP* 4.7 9.2 - - + -
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Residues in contact with PRO 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A CYS* 3.6 11.4 - - + -
32A ASP* 1.3 91.7 - - + +
34A THR* 1.3 52.7 + - - +
36A ASP* 3.0 4.8 + - + +
37A GLU* 2.4 37.0 + - - +
40A PHE* 4.1 3.4 - - + -
166A TRP* 3.6 37.0 - - + -
167A GLN* 3.8 27.1 - - + +
170A ASP* 3.6 31.9 - - - +
171A CYS* 5.3 1.6 - - - -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 3.2 28.8 + - - +
33A PRO* 1.3 73.9 - - - +
35A ALA* 1.3 61.4 + - - +
37A GLU* 3.0 28.2 + - + +
38A GLY 3.5 5.9 + - - -
167A GLN* 5.4 1.5 + - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS 3.0 16.8 + - - +
32A ASP* 4.2 11.0 - - - +
34A THR* 1.3 76.2 - - - +
36A ASP* 1.3 58.1 + - - +
38A GLY* 4.4 4.2 + - - -
39A LEU* 4.6 4.3 + - - +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP 3.2 17.5 + - - +
33A PRO* 3.0 2.7 + - + +
35A ALA* 1.3 73.5 - - - +
37A GLU* 1.3 53.1 + - - +
38A GLY 3.2 2.2 - - - -
39A LEU* 2.9 31.2 + - - +
40A PHE* 2.4 70.1 + - + -
166A TRP* 5.4 2.9 - - + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 2.4 25.1 + - - +
34A THR* 3.0 19.0 + - + +
36A ASP* 1.3 70.8 - - - +
38A GLY* 1.3 50.4 + - - +
40A PHE* 3.7 17.1 - - - +
41A HIS* 2.5 72.9 + - + -
163A ILE* 4.4 2.6 - - - +
167A GLN* 2.4 33.6 + - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR 3.5 7.5 + - - -
35A ALA 4.4 3.1 + - - -
36A ASP* 3.2 1.0 - - - +
37A GLU* 1.3 79.5 - - - +
39A LEU* 1.3 56.2 + - - +
41A HIS* 3.7 11.2 - - - +
42A ILE* 3.3 27.5 + - - +
113A PHE* 4.8 13.1 - - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 4.6 2.7 + - - +
36A ASP* 2.9 29.8 + - - +
38A GLY* 1.3 75.3 - - - +
40A PHE* 1.3 52.8 + - - +
41A HIS 3.2 1.1 - - - -
42A ILE* 3.0 27.0 + - + +
43A CYS* 2.6 41.9 + - + +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 4.1 3.8 - - + -
36A ASP* 2.4 70.1 + - + +
37A GLU* 3.2 26.4 + - - +
39A LEU* 1.3 65.9 - - - +
41A HIS* 1.3 63.4 + - - +
43A CYS* 3.8 17.3 - - + -
44A ILE* 3.3 28.4 + - + +
163A ILE* 4.0 39.9 - - + -
166A TRP* 4.2 24.9 - + - -
167A GLN* 4.9 1.6 - - - -
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 2.5 66.6 + - + +
38A GLY* 3.7 11.6 - - - +
39A LEU 3.2 0.2 - - - -
40A PHE* 1.3 73.9 - - - +
42A ILE* 1.3 60.5 - - - +
44A ILE* 5.0 0.6 - - - +
45A ALA* 3.4 24.4 + - - +
110A PRO 5.2 3.4 - - - -
111A LEU* 3.4 32.4 - - + +
113A PHE* 3.8 35.1 - + + -
130A TYR* 4.0 19.4 + + - +
131A TYR* 5.5 2.8 + - - -
134A LEU* 6.2 0.9 - - + -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 3.3 18.2 - - - +
39A LEU* 3.0 29.0 + - + +
41A HIS* 1.3 79.0 - - + +
43A CYS* 1.3 64.6 + - - +
45A ALA* 4.1 1.9 - - - +
46A ALA* 3.2 22.0 + - + +
113A PHE* 5.2 9.0 - - + -
114A THR* 5.4 13.9 - - + +
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 2.6 24.1 + - + +
40A PHE* 3.7 18.8 + - + -
42A ILE* 1.3 73.4 - - - +
44A ILE* 1.3 71.5 + - + +
46A ALA* 3.1 16.2 + - - +
47A ILE* 3.1 29.3 + - - +
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.3 20.5 + - + +
41A HIS* 5.0 0.7 - - - +
43A CYS* 1.3 85.0 - - + +
45A ALA* 1.3 57.9 + - - +
47A ILE* 2.8 14.6 + - + +
48A SER* 2.8 30.2 + - - +
134A LEU* 4.3 19.3 - - + +
159A THR* 3.8 19.1 - - + -
160A HIS* 3.5 33.9 - - + +
163A ILE* 3.8 31.0 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A HIS 3.4 20.7 + - - +
42A ILE* 4.3 2.7 - - - +
43A CYS 3.3 0.2 - - - -
44A ILE* 1.3 78.6 - - - +
46A ALA* 1.3 59.3 + - - +
48A SER* 3.4 19.1 + - - +
49A LEU* 3.4 17.2 + - - +
130A TYR* 4.0 19.9 + - + +
134A LEU* 5.4 3.5 - - + +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.2 15.1 + - + +
43A CYS* 3.1 12.4 + - - +
45A ALA* 1.3 76.8 - - - +
47A ILE* 1.3 66.8 + - + +
49A LEU* 3.8 4.4 + - - +
50A VAL* 3.3 26.2 + - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS* 3.2 28.5 - - - +
44A ILE* 2.8 18.8 + - + +
46A ALA* 1.3 80.9 - - + +
48A SER* 1.3 63.0 + - - +
50A VAL* 3.2 14.5 + - + +
51A VAL* 3.3 19.9 + - + +
156A LEU* 3.7 29.8 - - + -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 2.8 16.8 + - - -
45A ALA* 3.4 17.7 + - - +
47A ILE* 1.3 73.5 - - - +
49A LEU* 1.3 64.0 + - - +
51A VAL* 4.2 1.3 - - - -
52A MET* 3.2 30.9 + - - +
133A THR* 4.7 4.4 + - - +
134A LEU* 3.8 32.3 - - - -
137A PRO* 3.7 14.3 - - - +
156A LEU* 6.1 1.8 - - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 3.4 16.0 + - - +
46A ALA* 4.3 6.1 - - - +
47A ILE 3.2 1.0 - - - -
48A SER* 1.3 79.0 + - - +
50A VAL* 1.3 65.9 + - + +
52A MET* 3.9 13.6 + - + +
53A LEU* 3.5 36.2 + - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA 3.3 17.0 - - - +
47A ILE* 3.2 9.3 + - + +
49A LEU* 1.3 77.6 - - + +
51A VAL* 1.3 64.8 + - + +
53A LEU* 3.0 9.0 + - - +
54A VAL* 2.9 38.4 + - + +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.3 24.6 + - + +
48A SER* 3.9 0.6 + - - -
50A VAL* 1.3 80.2 - - + +
52A MET* 1.3 61.4 + - - +
54A VAL* 3.4 8.7 + - + +
55A LEU* 3.3 33.5 + - + +
137A PRO* 3.9 26.7 - - + +
141A CYS* 5.3 3.4 - - - -
152A LEU* 4.6 33.0 - - + -
156A LEU* 4.3 21.1 - - + -
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Residues in contact with MET 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 3.2 21.8 + - - +
49A LEU* 4.1 15.5 - - + +
50A VAL 3.2 0.6 - - - -
51A VAL* 1.3 78.2 - - - +
53A LEU* 1.3 64.2 + - + +
55A LEU* 3.5 8.8 + - - +
56A ALA* 3.3 15.2 + - - +
74A LEU* 3.7 34.4 - - + +
133A THR* 4.2 27.1 - - + +
136A TYR* 3.5 42.2 - - + -
137A PRO* 3.7 8.7 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 28.9 - - + +
50A VAL* 3.0 9.8 + - - +
52A MET* 1.3 81.0 - - + +
54A VAL* 1.3 64.3 + - - +
55A LEU 3.3 0.7 - - - -
56A ALA* 3.3 15.0 + - + +
57A ILE* 3.3 28.0 + - + +
74A LEU* 5.7 3.8 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 2.9 33.2 + - + +
51A VAL* 3.7 12.1 - - + +
52A MET 3.3 0.2 - - - -
53A LEU* 1.3 77.5 - - - +
55A LEU* 1.3 57.6 + - + +
57A ILE* 3.0 28.6 + - + +
58A LEU* 3.1 30.1 + - + +
148A VAL* 5.1 2.2 - - + -
152A LEU* 4.5 20.6 - - + -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.3 27.5 + - + +
52A MET* 3.7 10.5 - - - +
53A LEU 3.3 0.2 - - - -
54A VAL* 1.3 76.8 - - + +
56A ALA* 1.3 63.3 + - - +
58A LEU* 3.9 14.8 - - + +
59A ALA* 3.3 22.7 + - - +
74A LEU* 5.6 3.1 - - + -
75A LEU* 3.7 26.2 - - + +
136A TYR* 5.9 1.3 - - + -
137A PRO* 5.3 2.9 - - + +
140A ALA* 3.7 34.5 - - + +
141A CYS* 5.0 6.1 - - - +
144A LEU* 3.7 30.7 - - + -
148A VAL* 5.7 3.4 - - + -
149A GLY* 6.1 2.9 - - - -
152A LEU* 5.7 3.4 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A MET 3.3 12.7 + - - +
53A LEU* 3.5 21.3 - - + +
54A VAL 3.2 0.6 - - - -
55A LEU* 1.3 76.8 - - - +
57A ILE* 1.3 64.2 + - + +
59A ALA* 3.9 5.9 + - - +
60A ARG* 3.7 27.5 + - - +
73A GLY 5.1 9.0 - - - +
74A LEU* 4.9 12.5 - - + +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.3 16.6 - - + +
54A VAL* 3.0 17.8 + - + +
56A ALA* 1.3 78.3 - - + +
58A LEU* 1.3 62.3 + - + +
60A ARG* 3.1 22.1 + - + +
61A ARG* 3.3 46.6 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.1 23.1 + - + +
55A LEU* 4.1 21.3 - - + +
56A ALA 3.5 0.2 - - - -
57A ILE* 1.3 78.6 - - + +
59A ALA* 1.3 57.9 + - - +
61A ARG* 3.0 40.1 + - + +
62A GLN* 3.1 35.0 + - + +
64A LEU* 5.6 0.2 - - - -
144A LEU* 4.5 12.3 - - + -
146A ASN* 5.1 3.6 - - - +
148A VAL* 3.8 36.3 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU 3.3 17.8 + - - +
56A ALA* 4.2 5.4 - - - +
57A ILE 3.2 1.0 - - - -
58A LEU* 1.3 77.4 - - - +
60A ARG* 1.3 59.0 + - + +
61A ARG 3.2 1.1 + - - -
62A GLN 3.9 5.8 + - - -
63A LYS* 4.0 8.0 + - - +
64A LEU* 4.2 18.8 - - + -
68A GLN* 3.0 41.7 + - + +
73A GLY 4.5 10.5 - - - +
75A LEU* 4.6 7.0 - - + -
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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