Contacts of the helix formed by residues 34 - 56 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.3 3.6 - - - -
117A GLN* 3.2 30.2 + - - -
118A MET* 3.6 17.2 + - - -
120A PRO* 4.0 1.8 - - - -
32B ARG 4.0 1.8 + - - -
33B LEU* 1.3 73.9 - - - +
35B VAL* 1.3 62.9 + - - +
36B ASP* 4.1 1.0 - - - +
37B LEU* 2.9 36.1 + - - +
38B SER* 2.7 29.3 + - - -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 3.9 1.1 - - - +
117A GLN* 2.7 31.3 + - - +
120A PRO* 3.7 24.0 - - + +
168A ARG* 3.5 27.8 - - - +
34B SER* 1.3 72.9 - - - +
36B ASP* 1.3 71.2 + - - +
38B SER* 3.6 4.5 - - - -
39B LYS* 3.3 20.4 + - + +
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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
----------------------------------------------------------
40A LYS* 5.8 2.3 + - - -
117A GLN* 2.7 40.3 + - - +
34B SER* 4.1 0.9 - - - +
35B VAL* 1.3 79.3 - - - +
37B LEU* 1.3 60.2 + - + +
39B LYS* 3.3 11.7 + - - +
40B LYS* 2.9 41.3 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 5.3 3.8 - - - -
33B LEU* 3.9 18.5 - - + +
34B SER* 2.9 27.4 + - - +
36B ASP* 1.3 77.0 - - + +
38B SER* 1.3 56.2 + - - +
39B LYS 3.3 0.2 - - - -
40B LYS* 3.7 6.6 - - + +
41B TYR* 2.8 34.0 + - - +
44B TRP* 3.6 34.2 - - + -
114B PRO* 4.4 5.6 - - + +
117B GLN* 4.0 26.0 - - + -
118B MET* 3.6 34.8 - - + -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 4.6 1.1 - - - +
26B PRO* 3.4 30.0 - - - +
28B SER* 2.6 29.2 + - - -
33B LEU* 3.4 13.7 - - - +
34B SER 2.7 24.3 + - - -
35B VAL* 3.6 6.5 - - - -
37B LEU* 1.3 72.7 - - - +
39B LYS* 1.3 65.5 + - - +
41B TYR* 3.5 7.4 - - - +
42B THR* 3.5 6.1 + - - -
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Residues in contact with LYS 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 VAL* 3.3 10.6 + - + +
36B ASP* 3.4 13.7 - - - +
38B SER* 1.3 79.6 - - - +
40B LYS* 1.3 67.1 + - - +
42B THR* 3.2 8.4 + - - -
43B GLU* 2.6 60.9 + - + +
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 2.9 32.7 + - - +
37B LEU* 3.4 8.6 + - + +
39B LYS* 1.3 75.3 - - + +
41B TYR* 1.3 57.7 - - - +
43B GLU* 3.7 17.5 - - - +
44B TRP* 2.7 83.8 + - + +
145B ILE* 4.3 11.9 - - + -
148B ILE* 6.1 5.2 - - - -
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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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16B LYS* 3.7 8.3 - - - +
20B ILE* 3.7 28.0 - - + -
25B LEU* 4.0 12.3 - - + +
26B PRO* 3.5 22.4 - - + -
31B GLN* 3.4 26.9 + - - -
33B LEU* 4.0 11.4 - - + -
37B LEU 2.8 22.5 + - - +
38B SER 3.5 7.4 - - - +
39B LYS 3.2 0.2 - - - -
40B LYS* 1.3 74.8 - - - +
42B THR* 1.3 63.0 + - - +
44B TRP* 3.9 10.8 - + + +
45B HIS* 2.8 39.1 + + - -
82B THR* 3.8 4.0 - - - +
114B PRO* 4.7 17.5 - - + -
2003B PO4 2.4 43.3 + - - -
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Residues in contact with THR 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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20B ILE* 3.9 25.9 - - + +
26B PRO* 3.5 24.1 - - - +
38B SER 3.5 4.4 + - - -
39B LYS* 3.2 10.5 + - - -
41B TYR* 1.3 75.6 - - - +
43B GLU* 1.3 61.3 + - + +
45B HIS* 3.5 2.1 + - - +
46B ARG* 2.9 55.6 + - - +
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Residues in contact with GLU 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 LYS* 2.6 53.6 + - + +
40B LYS* 3.7 25.7 - - - +
42B THR* 1.3 77.5 - - - +
44B TRP* 1.3 56.5 + - - +
46B ARG* 3.3 23.9 + - - +
47B SER* 2.9 31.2 + - - -
145B ILE* 3.7 21.1 - - + +
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Residues in contact with TRP 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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37B LEU* 3.6 26.2 - - + -
40B LYS* 2.7 56.1 + - + +
41B TYR* 3.9 10.8 - + - +
43B GLU* 1.3 72.1 - - - +
45B HIS* 1.3 60.5 + + + +
47B SER* 3.4 4.2 + - - -
48B TYR* 2.8 28.8 + - - +
110B LEU* 3.9 7.4 - - + +
113B LEU* 3.6 30.7 - - + -
114B PRO* 3.6 29.2 - - + -
117B GLN* 5.5 1.1 - - + -
145B ILE* 3.6 30.8 - - + +
146B LEU* 3.8 27.7 - - + +
149B SER* 3.5 29.9 - - - -
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.1 5.8 - - + -
16B LYS* 3.8 13.9 - - + +
17B LEU* 3.7 21.3 - - + +
20B ILE* 3.4 28.8 - - + +
41B TYR* 2.8 54.4 + + - +
42B THR 3.9 2.9 - - - +
44B TRP* 1.3 81.3 - + + +
46B ARG* 1.3 64.0 + - - +
48B TYR* 3.2 4.0 + - - +
49B LEU* 3.1 19.1 + - - +
108B SER 5.5 0.9 - - - -
110B LEU* 3.7 29.1 - - + +
2003B PO4 2.8 31.5 + - - -
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Residues in contact with ARG 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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17B LEU* 4.9 1.3 - - - +
42B THR* 2.9 41.8 + - + +
43B GLU* 3.6 30.2 - - - +
45B HIS* 1.3 74.6 - - - +
47B SER* 1.3 63.8 + - - +
49B LEU* 3.3 10.3 + - + +
50B ILE* 3.0 45.2 + - + +
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Residues in contact with SER 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 GLU 2.9 13.1 + - - -
44B TRP 3.7 3.4 - - - -
46B ARG* 1.3 72.0 - - - +
48B TYR* 1.3 59.9 + - - +
50B ILE* 3.8 9.9 - - - +
51B THR* 2.7 39.8 + - - -
143B SER* 2.6 27.5 + - - -
145B ILE* 3.4 25.7 - - - +
146B LEU* 4.6 1.3 - - - -
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Residues in contact with TYR 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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13B LEU* 4.0 28.7 - - + -
44B TRP 2.8 16.8 + - - +
45B HIS* 3.2 9.6 + - - +
47B SER* 1.3 74.2 - - - +
49B LEU* 1.3 53.0 + - - +
51B THR* 3.7 1.4 - - - -
52B LEU* 2.8 36.7 + - + +
107B GLY 5.1 0.2 - - - -
108B SER* 3.5 30.5 - - - -
110B LEU* 3.8 37.9 - - + -
135B LEU* 5.4 1.2 - - - +
136B LYS* 3.6 34.9 + - + +
139B ILE* 3.4 44.3 - - + +
140B LEU* 4.4 3.8 - - + -
146B LEU* 3.9 9.1 - - + +
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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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13B LEU* 5.2 0.4 - - + -
17B LEU* 3.6 28.2 - - + +
45B HIS 3.1 7.0 + - - +
46B ARG* 3.6 11.9 - - + +
47B SER 3.3 0.2 - - - -
48B TYR* 1.3 78.2 - - - +
50B ILE* 1.3 67.5 + - + +
52B LEU* 3.2 12.8 + - + +
53B LYS 3.1 18.0 + - - -
60B PHE* 3.7 33.2 - - + -
63B VAL* 3.6 20.9 - - + -
64B ASP* 5.1 2.2 - - - +
67B MET* 3.6 26.9 - - + -
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Residues in contact with ILE 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 ARG* 3.0 40.1 + - + +
47B SER* 3.8 8.1 - - - +
49B LEU* 1.3 78.5 - - + +
51B THR* 1.3 64.5 + - - +
53B LYS* 3.3 23.2 + - + +
54B LYS* 3.3 6.1 + - - +
60B PHE* 5.4 2.2 - - + -
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Residues in contact with THR 51 (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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47B SER* 2.7 21.3 + - - -
48B TYR 3.8 2.9 - - - -
50B ILE* 1.3 76.4 - - - +
52B LEU* 1.3 66.4 + - - +
54B LYS* 3.0 19.9 + - + +
55B PHE* 3.1 16.4 + - + -
139B ILE* 3.7 40.4 - - - +
142B GLU* 3.7 25.0 - - + +
143B SER* 3.6 15.5 - - - +
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Residues in contact with LEU 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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10B TYR 5.6 0.7 - - - +
13B LEU* 3.8 16.8 - - + -
48B TYR* 2.8 17.5 + - + +
49B LEU* 3.3 15.0 - - + +
51B THR* 1.3 75.6 - - - +
53B LYS* 1.3 56.1 + - - +
55B PHE* 2.9 3.2 + - - +
56B SER* 2.8 30.4 + - - +
59B ALA* 4.0 21.5 - - + +
60B PHE* 4.2 11.2 - - - +
63B VAL* 3.8 30.3 - - + -
135B LEU* 3.8 24.9 - - + -
139B ILE* 3.7 25.9 - - + +
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Residues in contact with LYS 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 3.1 6.6 + - - +
50B ILE* 3.3 13.7 - - + +
52B LEU* 1.3 75.6 - - - +
54B LYS* 1.3 65.0 + - - +
55B PHE 3.4 0.3 + - - -
56B SER 3.7 11.0 + - - -
57B ARG* 3.9 12.0 + - + +
60B PHE* 3.5 59.8 - - + +
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Residues in contact with LYS 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 ILE 3.3 5.9 + - - +
51B THR* 3.0 18.0 + - - +
53B LYS* 1.3 81.9 - - - +
55B PHE* 1.3 67.9 + - + +
57B ARG 5.5 0.2 + - - -
142B GLU* 3.7 42.6 + - + +
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Residues in contact with PHE 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 THR* 3.1 25.6 + - + +
52B LEU 2.9 5.5 + - - +
54B LYS* 1.3 88.3 - - + +
56B SER* 1.3 62.7 + - - +
57B ARG 4.3 0.2 - - - -
135B LEU* 3.8 22.5 - - + +
138B SER* 3.7 38.6 - - - -
139B ILE* 4.1 7.6 - - + -
142B GLU* 3.5 39.3 - - + -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 2.8 19.4 + - - +
53B LYS 3.9 2.5 - - - -
54B LYS 3.6 0.4 - - - -
55B PHE* 1.3 77.8 - - - +
57B ARG* 1.3 58.9 + - - +
58B ARG* 3.6 12.0 + - - +
59B ALA* 3.1 32.0 + - - +
60B PHE* 2.9 27.7 + - - +
135B LEU* 5.4 5.6 - - - -
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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) + - + + + + + -
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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