Contacts of the helix formed by residues 34 - 56 (chain A) in PDB entry 2OB1
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 SER 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG 4.0 1.8 + - - -
33A LEU* 1.3 73.1 - - - +
35A VAL* 1.3 64.0 + - - +
36A ASP* 4.2 0.5 - - - +
37A LEU* 2.9 36.2 + - - +
38A SER* 2.7 26.8 + - - -
37B LEU* 5.3 3.4 - - - -
117B GLN* 3.2 29.9 + - - -
118B MET* 3.7 18.2 - - - -
120B PRO* 3.9 1.6 - - - -
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Residues in contact with VAL 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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34A SER* 1.3 70.9 - - - +
36A ASP* 1.3 71.2 + - - +
38A SER* 3.6 4.4 - - - -
39A LYS* 3.2 21.8 + - - +
116B LEU 3.7 3.8 - - - +
117B GLN* 2.7 31.8 + - - +
120B PRO* 3.7 23.3 - - + +
168B ARG* 3.6 28.0 - - - +
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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
----------------------------------------------------------
34A SER* 4.2 0.9 - - - +
35A VAL* 1.3 86.2 - - - +
37A LEU* 1.3 59.3 + - + +
39A LYS* 3.3 8.0 + - - +
40A LYS* 2.9 42.3 + - - +
117B GLN* 2.8 35.6 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.9 18.4 - - + +
34A SER* 2.9 26.8 + - - +
36A ASP* 1.3 76.2 - - + +
38A SER* 1.3 55.2 + - - +
40A LYS* 3.6 8.5 - - + +
41A TYR* 2.7 35.4 + - - +
44A TRP* 3.6 32.8 - - + -
114A PRO* 4.4 6.1 - - + +
117A GLN* 4.1 25.4 - - + -
118A MET* 3.5 35.9 - - + -
34B SER* 5.3 4.0 - - - -
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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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26A PRO* 3.6 25.2 - - - +
28A SER* 3.4 26.2 - - - -
33A LEU* 3.4 10.8 - - - +
34A SER 2.7 25.1 + - - -
35A VAL* 3.6 6.1 - - - -
37A LEU* 1.3 76.1 - - - +
39A LYS* 1.3 64.4 + - - +
41A TYR* 3.4 3.3 + - - +
42A THR* 3.4 17.3 + - - -
120B PRO* 4.5 2.2 - - - +
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Residues in contact with LYS 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 VAL 3.2 11.3 + - - +
36A ASP* 3.6 9.9 - - - +
38A SER* 1.3 79.9 - - - +
40A LYS* 1.3 62.8 - - + +
42A THR* 3.3 8.0 + - - -
43A GLU* 3.0 50.6 + - + +
35C VAL* 4.0 24.9 + - - +
36C ASP* 4.8 4.0 + - - -
39C LYS* 3.9 34.1 - - + +
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Residues in contact with LYS 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 ASP* 2.9 31.8 + - + +
37A LEU* 3.7 10.0 - - + +
39A LYS* 1.3 75.3 - - + +
41A TYR* 1.3 57.0 + - - +
43A GLU* 3.7 19.3 - - - +
44A TRP* 2.7 80.3 + - + +
145A ILE* 4.3 9.4 - - + -
149A SER* 5.2 0.7 - - - +
36B ASP* 5.8 2.0 + - - -
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Residues in contact with TYR 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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16A LYS* 3.6 10.2 - - - +
20A ILE* 3.6 26.2 - - + -
25A LEU* 3.9 5.5 - - + +
26A PRO* 3.6 28.0 - - + -
31A GLN* 3.4 24.7 + - - -
33A LEU* 4.0 18.8 - - + -
37A LEU 2.7 21.0 + - - +
38A SER 3.5 6.7 - - - +
39A LYS 3.2 0.2 - - - -
40A LYS* 1.3 73.7 - - - +
42A THR* 1.3 62.8 + - - +
44A TRP* 3.9 9.7 - - + +
45A HIS* 2.6 40.9 + + - -
82A THR* 3.8 4.5 - - - +
114A PRO* 4.8 15.3 - - + -
2001A PO4 2.6 41.5 + - - -
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Residues in contact with THR 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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20A ILE* 3.9 23.1 - - + +
26A PRO* 3.3 25.6 - - - +
38A SER 3.4 4.4 + - - -
39A LYS* 3.3 9.5 + - - -
40A LYS 3.2 0.4 - - - -
41A TYR* 1.3 79.1 - - - +
43A GLU* 1.3 58.9 + - + +
45A HIS* 3.3 3.3 + - - +
46A ARG* 2.9 55.1 + - - +
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Residues in contact with GLU 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 LYS* 3.0 53.9 + - + +
40A LYS* 3.1 22.0 + - - +
42A THR* 1.3 75.1 - - + +
44A TRP* 1.3 61.5 + - - +
46A ARG* 3.7 8.2 - - - +
47A SER* 2.8 31.4 + - - -
145A ILE* 3.7 28.2 - - + +
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Residues in contact with TRP 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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37A LEU* 3.6 26.0 - - + -
40A LYS* 2.7 52.9 + - + +
41A TYR* 3.9 11.2 - + - +
43A GLU* 1.3 73.2 - - - +
45A HIS* 1.3 58.2 + + - +
47A SER* 3.4 2.7 + - - -
48A TYR* 2.8 28.6 + - - +
110A LEU* 3.7 8.4 - - + +
113A LEU* 3.5 31.0 - - + -
114A PRO* 3.5 29.4 - - + -
117A GLN* 5.5 1.3 - - + -
145A ILE* 3.5 27.0 - - + +
146A LEU* 3.7 27.1 - - + +
149A SER* 2.6 37.3 + - - -
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Residues in contact with HIS 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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13A LEU* 5.3 7.2 - - + -
16A LYS* 3.7 12.9 - - + +
17A LEU* 3.5 20.2 - - + +
20A ILE* 3.3 30.3 - - + +
41A TYR* 2.6 50.9 + + - +
42A THR 3.3 4.1 + - - +
44A TRP* 1.3 76.4 - + + +
46A ARG* 1.3 65.8 + - - +
48A TYR* 3.2 5.1 + - + +
49A LEU 3.0 18.2 + - - -
108A SER 5.5 1.3 - - - -
110A LEU* 3.9 27.0 - - + +
114A PRO* 6.3 0.2 - - + -
2001A PO4 2.7 33.0 + - - -
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Residues in contact with ARG 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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17A LEU* 5.0 3.8 - - + -
20A ILE* 5.2 5.8 - - + -
21A SER* 5.6 7.5 + - - +
42A THR* 2.9 42.2 + - + +
43A GLU* 3.7 8.1 - - - +
45A HIS* 1.3 77.0 - - - +
47A SER* 1.3 61.7 + - - +
49A LEU* 3.2 9.9 + - - +
50A ILE* 3.1 29.5 + - + +
20C ILE 4.0 3.9 + - - -
21C SER* 2.8 33.5 + - - +
22C VAL 3.4 20.0 + - - -
23C GLY* 3.6 10.1 - - - -
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Residues in contact with SER 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 GLU 2.8 19.3 + - - -
44A TRP 3.7 2.9 - - - -
46A ARG* 1.3 73.7 - - - +
48A TYR* 1.3 58.0 + - - +
50A ILE* 3.8 7.3 - - - +
51A THR* 2.7 39.6 + - - -
143A SER* 2.5 28.0 + - - -
145A ILE* 3.4 20.1 - - - +
146A LEU* 4.6 1.6 - - - -
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Residues in contact with TYR 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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10A TYR* 6.5 0.2 - + - -
13A LEU* 4.0 29.2 - - + -
44A TRP 2.8 14.7 + - - +
45A HIS* 3.2 10.5 + - - +
47A SER* 1.3 77.3 - - - +
49A LEU* 1.3 57.3 + - - +
51A THR* 3.7 1.2 - - - -
52A LEU* 2.8 26.9 + - + +
107A GLY 5.0 0.3 - - - -
108A SER* 3.6 33.1 - - - -
110A LEU* 3.6 36.6 - - + -
135A LEU* 5.4 1.2 - - - +
136A LYS* 3.7 31.6 - - + +
139A ILE* 3.5 43.6 - - + +
140A LEU* 4.5 3.8 - - + -
146A LEU* 3.9 8.9 - - + +
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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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17A LEU* 3.7 19.7 - - + +
45A HIS 3.0 9.9 + - - +
46A ARG* 3.2 9.2 + - - +
48A TYR* 1.3 76.6 - - - +
50A ILE* 1.3 70.1 + - + +
52A LEU* 3.2 13.4 + - + +
53A LYS* 3.0 21.1 + - - +
60A PHE* 3.7 30.1 - - + +
63A VAL* 3.5 30.7 - - + -
64A ASP* 5.2 2.2 - - - +
67A MET* 3.9 26.7 - - + -
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Residues in contact with ILE 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 ARG* 3.1 23.3 + - + +
47A SER* 3.8 7.4 - - - +
49A LEU* 1.3 86.9 - - + +
51A THR* 1.3 64.3 + - - +
53A LYS* 3.2 18.7 + - - +
54A LYS* 3.3 6.9 + - - +
60A PHE* 5.2 1.8 - - + -
22C VAL* 5.2 4.3 - - + +
304C SER* 3.4 42.2 - - - +
305C LEU* 4.1 31.4 - - + +
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Residues in contact with THR 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 SER* 2.7 23.0 + - - -
50A ILE* 1.3 78.3 - - - +
52A LEU* 1.3 64.5 + - - +
53A LYS 3.1 1.1 - - - -
54A LYS* 3.1 15.8 + - + +
55A PHE* 3.2 14.7 + - + -
139A ILE* 3.7 38.6 - - - +
142A GLU* 3.7 29.8 - - + -
143A SER* 3.5 16.5 - - - +
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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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10A TYR* 4.6 4.9 - - + -
13A LEU* 3.7 28.9 - - + -
48A TYR* 2.8 19.9 + - + +
49A LEU* 3.3 15.7 - - + +
51A THR* 1.3 71.8 - - - +
53A LYS* 1.3 58.3 + - - +
55A PHE* 3.0 2.6 + - - +
56A SER* 2.9 29.5 + - - +
59A ALA* 3.8 34.5 - - + -
60A PHE* 4.3 6.5 - - - +
63A VAL* 4.1 13.5 - - + -
135A LEU* 3.9 21.1 - - + -
139A ILE* 3.8 25.7 - - + +
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Residues in contact with LYS 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 3.0 7.3 + - - +
50A ILE* 3.2 9.6 - - - +
52A LEU* 1.3 79.6 - - - +
54A LYS* 1.3 62.7 + - - +
55A PHE 3.3 0.3 + - - -
56A SER 3.5 12.0 + - - -
57A ARG 4.0 2.3 + - - -
60A PHE* 3.4 29.6 - - + -
303C ARG 3.2 18.6 + - - -
304C SER* 3.1 21.7 - - - +
305C LEU 3.9 7.9 - - - +
306C GLN* 3.3 35.5 + - - +
307C PHE* 3.3 48.9 - - + +
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Residues in contact with LYS 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 ILE 3.3 6.2 + - - +
51A THR* 3.1 14.9 + - + +
53A LYS* 1.3 81.7 - - - +
55A PHE* 1.3 71.0 + - + +
142A GLU* 3.4 43.2 + - + +
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Residues in contact with PHE 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 THR* 3.2 23.7 + - + -
52A LEU* 3.0 6.9 + - - +
54A LYS* 1.3 93.2 - - + +
56A SER* 1.3 60.3 + - - +
135A LEU* 3.9 20.6 - - + +
138A SER* 3.6 37.7 - - - -
139A ILE* 4.1 9.2 - - + -
142A GLU* 3.5 40.2 - - + -
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 5.1 2.4 + - - -
52A LEU* 2.9 15.0 + - - +
53A LYS 3.5 5.4 + - - -
54A LYS 3.9 0.2 + - - -
55A PHE* 1.3 80.5 - - - +
57A ARG* 1.3 63.0 + - - +
58A ARG* 3.5 11.4 + - - +
59A ALA* 3.0 33.4 + - - +
60A PHE* 3.0 22.2 + - - +
135A LEU* 5.4 4.0 - - - -
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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
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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) + - + + + + + -
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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