Contacts of the helix formed by residues 30 - 54 (chain A) in PDB entry 2QV8
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 ASP 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 1.3 65.6 + - - +
32A ALA* 3.1 10.1 - - - +
33A LYS* 3.3 33.5 - - + +
34A ILE* 2.9 39.5 + - - +
167A TRP* 4.3 6.9 - - - +
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Residues in contact with GLU 31 (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 ASP* 1.3 79.9 - - - +
32A ALA* 1.3 61.8 + - - +
34A ILE* 3.5 9.4 + - + +
35A SER* 3.1 26.9 + - - -
94A LYS* 3.5 38.3 + - + +
95A GLU 4.8 5.4 - - - +
96A GLY* 6.1 0.7 - - - -
97A LEU* 3.6 19.9 - - + +
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Residues in contact with ALA 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 ASP 3.1 6.2 - - - +
31A GLU* 1.3 78.6 - - - +
33A LYS* 1.3 58.1 + - - +
35A SER* 3.2 3.1 + - - -
36A ALA* 2.9 31.2 + - - +
97A LEU* 3.9 25.9 - - + +
156A ILE* 3.9 26.1 - - - +
157A PHE* 4.5 3.6 - - - -
158A PRO* 4.9 7.0 - - + -
167A TRP* 3.9 15.4 - - + +
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Residues in contact with LYS 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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30A ASP* 3.3 24.6 - - - +
32A ALA* 1.3 77.0 - - - +
34A ILE* 1.3 65.1 + - + +
36A ALA* 3.2 3.1 + - - +
37A GLN* 2.9 52.7 + - - +
167A TRP* 3.6 51.2 - - + +
179A LEU* 6.0 0.4 - - - -
52B LEU 5.7 2.2 + - - -
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Residues in contact with ILE 34 (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 ASP* 2.9 34.5 + - - +
31A GLU* 3.8 10.3 - - + +
33A LYS* 1.3 76.1 - - + +
35A SER* 1.3 59.8 + - - +
37A GLN* 3.4 15.8 + - - +
38A SER* 2.9 29.6 + - - -
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Residues in contact with SER 35 (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 GLU 3.1 17.9 + - - -
32A ALA 3.2 4.0 + - - -
34A ILE* 1.3 79.0 - - - +
36A ALA* 1.3 58.6 + - - +
38A SER* 3.3 9.0 + - - -
39A PHE* 3.0 27.4 + - - +
68A LEU* 5.9 0.3 - - - +
93A LEU* 3.9 26.4 - - - +
94A LYS* 5.4 2.4 + - - +
97A LEU* 3.5 12.8 - - - +
156A ILE* 3.8 13.5 - - - +
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Residues in contact with ALA 36 (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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32A ALA 2.9 16.1 + - - +
33A LYS 3.7 3.8 - - - +
35A SER* 1.3 73.7 - - - +
37A GLN* 1.3 65.7 + - - +
39A PHE* 3.2 1.6 + - - -
40A TYR* 2.9 24.8 + - - +
156A ILE* 3.7 15.4 - - + +
167A TRP* 4.0 23.6 - - + -
168A ARG* 5.4 0.2 - - - -
169A VAL* 3.4 12.0 - - + +
179A LEU* 3.6 22.9 - - + -
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Residues in contact with GLN 37 (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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33A LYS* 2.9 45.1 + - + +
34A ILE* 3.6 21.4 - - - +
36A ALA* 1.3 74.6 - - - +
38A SER* 1.3 56.9 + - - +
40A TYR* 3.3 6.8 + - - +
41A GLN* 2.9 46.8 + - - +
179A LEU* 4.0 20.7 - - + +
52B LEU* 4.3 29.4 + - + +
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Residues in contact with SER 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 ILE* 2.9 16.3 + - - -
35A SER* 3.4 12.6 - - - -
36A ALA 3.3 0.2 - - - -
37A GLN* 1.3 75.4 - - - +
39A PHE* 1.3 58.1 + - - +
41A GLN* 3.3 13.4 + - - +
42A ARG* 3.0 59.4 + - - +
91A THR* 4.7 5.0 - - - +
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Residues in contact with PHE 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 SER 3.0 15.1 + - - +
36A ALA* 3.2 4.9 + - - +
38A SER* 1.3 72.9 + - - +
40A TYR* 1.3 60.1 + - - +
42A ARG* 3.2 4.6 + - - +
43A LEU* 2.8 42.2 + - + +
59A VAL* 4.0 24.5 - - + -
61A ILE* 6.0 0.4 - - + -
68A LEU* 3.9 27.1 - - + -
70A PHE* 4.0 17.9 - + - -
141A LEU* 4.5 10.8 - - + -
152A PHE* 3.8 26.5 - + - -
154A LEU* 3.6 22.2 - - + -
156A ILE* 4.8 0.7 - - + -
169A VAL* 3.6 37.0 - - + -
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Residues in contact with TYR 40 (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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36A ALA 2.9 17.1 + - - +
37A GLN* 3.6 6.3 - - - +
39A PHE* 1.3 77.3 - - - +
41A GLN* 1.3 64.0 + - + +
43A LEU* 3.8 1.5 - - - +
44A LEU* 3.1 68.1 + - + +
169A VAL* 3.9 20.6 - - + -
177A LEU* 4.1 7.8 + - + -
178A ARG* 3.9 16.7 - - - -
179A LEU* 3.7 32.5 - - + -
48B GLU* 4.4 3.5 - - + -
51B ILE* 3.8 31.4 - - + +
52B LEU* 3.9 39.5 - - + -
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Residues in contact with GLN 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 GLN* 2.9 29.6 + - - +
38A SER* 3.7 11.5 - - - +
40A TYR* 1.3 76.8 - - - +
42A ARG* 1.3 60.2 + - + +
44A LEU* 3.6 2.3 + - - +
45A LEU* 3.0 29.2 + - - +
48B GLU* 3.4 26.1 + - - +
52B LEU* 3.7 24.9 - - + +
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Residues in contact with ARG 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 SER* 3.0 40.7 + - - +
39A PHE* 3.2 4.7 + - - +
41A GLN* 1.3 76.8 - - + +
43A LEU* 1.3 60.0 + - - +
45A LEU* 3.3 2.6 + - - +
46A LEU* 2.8 31.2 + - - +
70A PHE* 3.8 34.4 - - + -
87A MSE 3.9 26.8 - - + +
88A THR* 2.8 54.0 + - - +
91A THR* 3.5 20.7 - - - +
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Residues in contact with LEU 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 PHE* 2.8 30.6 + - + +
40A TYR 3.8 3.8 - - - +
42A ARG* 1.3 70.5 - - - +
44A LEU* 1.3 66.1 + - + +
46A LEU* 3.3 4.5 + - + +
47A ASN* 2.9 24.1 + - - +
59A VAL* 4.5 13.0 - - + -
70A PHE* 4.7 3.2 - - - -
141A LEU* 5.6 1.3 - - + -
143A VAL* 3.9 27.6 - - + -
149A VAL* 4.5 12.1 - - + -
152A PHE* 3.7 33.2 - - + -
169A VAL* 4.1 15.0 - - + -
171A ALA* 5.1 0.2 - - + -
177A LEU* 4.2 27.4 - - + -
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Residues in contact with LEU 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 TYR* 3.1 77.6 + - + +
41A GLN 4.0 3.1 - - - +
43A LEU* 1.3 80.2 - - + +
45A LEU* 1.3 61.9 + - - +
47A ASN* 3.4 8.4 + - - +
48A GLU* 3.0 24.8 + - - +
177A LEU* 3.8 27.4 - - + -
44B LEU* 4.8 15.6 - - + +
47B ASN* 6.0 1.8 - - - +
48B GLU* 3.9 31.2 - - + +
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Residues in contact with LEU 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 GLN 3.0 18.4 + - - +
42A ARG* 3.7 4.7 - - - +
43A LEU 3.2 0.2 - - - -
44A LEU* 1.3 75.8 - - - +
46A LEU* 1.3 58.1 + - - +
48A GLU* 3.1 27.3 + - + +
49A GLU* 2.8 30.5 + - - +
82A TRP* 5.4 3.4 - - + -
86A LYS* 3.9 46.4 - - + +
87A MSE 4.1 21.1 - - + -
41B GLN* 6.2 0.4 - - - +
44B LEU* 5.9 0.2 - - - -
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Residues in contact with LEU 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 ARG 2.8 15.8 + - - +
43A LEU* 3.3 6.7 + - + +
45A LEU* 1.3 77.4 - - - +
47A ASN* 1.3 56.7 + - - +
49A GLU* 3.2 5.0 + - - +
50A ALA* 2.9 28.9 + - - +
57A PHE* 3.7 29.6 - - + -
58A GLY 3.7 22.7 - - - +
59A VAL* 3.8 20.4 - - + -
70A PHE* 4.2 11.9 - - + -
71A LEU 4.8 1.1 - - - +
82A TRP* 3.6 34.1 - - + -
87A MSE 4.4 9.6 - - + -
143A VAL* 3.8 18.0 - - + +
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Residues in contact with ASN 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 LEU* 2.9 16.4 + - + +
44A LEU* 3.6 6.3 - - - +
46A LEU* 1.3 75.1 - - - +
48A GLU* 1.3 64.9 + - - +
50A ALA* 3.4 3.3 + - - +
51A ILE* 3.1 37.8 + - - +
143A VAL* 3.5 15.1 - - + +
144A LEU 4.9 0.8 + - - -
147A GLY* 3.4 35.6 + - - -
149A VAL* 3.9 10.7 - - + +
177A LEU* 4.3 22.1 - - + +
40B TYR* 5.0 1.4 + - - -
44B LEU* 5.2 5.4 - - - +
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Residues in contact with GLU 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 LEU 3.0 13.6 + - - +
45A LEU* 3.1 30.9 - - - +
47A ASN* 1.3 76.1 - - - +
49A GLU* 1.3 59.6 + - - +
51A ILE* 3.2 2.6 + - - +
52A LEU* 2.8 47.6 + - + +
86A LYS* 6.2 0.4 - - - -
40B TYR* 4.0 18.8 - - + -
41B GLN* 3.1 42.4 + - - +
44B LEU* 3.8 32.3 - - + +
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Residues in contact with GLU 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 LEU* 2.8 22.4 + - - +
46A LEU* 3.5 7.4 - - - +
48A GLU* 1.3 72.7 - - - +
50A ALA* 1.3 53.0 + - - +
52A LEU* 3.8 8.8 - - - +
53A SER* 2.6 50.2 + - - +
55A GLN* 5.1 1.7 - - - +
57A PHE* 3.6 17.5 - - + -
82A TRP* 3.6 36.0 + - + -
86A LYS* 3.0 34.1 + - - +
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Residues in contact with ALA 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 LEU 2.9 13.2 + - - +
47A ASN 3.6 8.5 - - - +
48A GLU 3.3 0.2 - - - -
49A GLU* 1.3 74.2 - - - +
51A ILE* 1.3 57.5 + - - +
54A GLY* 2.8 32.4 + - - -
55A GLN 3.2 21.8 - - - +
57A PHE* 3.9 5.8 - - + -
143A VAL* 3.6 15.3 - - + +
144A LEU 3.5 23.3 - - - +
145A SER* 3.4 8.2 - - - -
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Residues in contact with ILE 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 ASN* 3.1 29.6 + - - +
48A GLU 3.7 5.2 - - - +
50A ALA* 1.3 77.9 - - - +
52A LEU* 1.3 63.1 + - - +
54A GLY* 3.9 5.0 + - - -
144A LEU 5.0 0.2 - - - +
145A SER 3.7 18.3 - - - +
146A SER 4.7 1.3 - - - -
147A GLY* 3.9 22.2 - - - +
40B TYR* 3.2 36.1 - - + +
177B LEU 5.5 3.6 - - - +
178B ARG* 6.5 0.7 - - - -
179B LEU* 4.4 25.4 - - + +
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Residues in contact with LEU 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 GLU* 2.8 37.4 + - + +
49A GLU* 3.9 15.5 - - - +
51A ILE* 1.3 76.2 - - - +
53A SER* 1.3 59.5 + - - +
86A LYS* 4.7 2.0 - - - +
33B LYS* 5.1 5.4 + - - -
37B GLN* 3.2 61.4 + - + +
40B TYR* 4.0 12.3 - - + -
41B GLN* 3.5 32.3 - - + +
179B LEU* 4.0 12.6 - - + -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 2.6 39.5 + - - -
52A LEU* 1.3 75.4 - - - +
54A GLY* 1.3 61.8 + - - +
55A GLN* 3.1 43.5 + - - +
57A PHE* 3.9 2.1 - - - -
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Residues in contact with GLY 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 ALA 2.8 13.3 + - - -
51A ILE 3.9 3.6 + - - -
52A LEU 3.5 2.4 - - - -
53A SER* 1.3 76.7 - - - +
55A GLN* 1.3 58.8 + - - +
56A ASP* 4.7 0.9 - - - +
145A SER* 3.5 21.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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