Contacts of the helix formed by residues 51 - 63 (chain B) in PDB entry 2VBJ
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 ARG 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.0 26.8 - - - +
135A LEU 5.3 4.9 + - - -
137A ASP* 2.9 40.2 + - - -
47B GLN* 2.8 37.6 + - + +
48B LYS* 2.8 15.4 + - - +
50B GLN* 1.3 97.4 - - + +
52B ARG* 1.3 64.6 + - - +
53B TRP* 3.0 19.3 - - - +
54B PHE* 2.9 21.4 + - + +
55B LEU* 3.8 2.8 + - - +
13E A 4.2 1.0 + - - -
14E A 2.7 27.0 + - - -
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Residues in contact with ARG 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 LYS 3.6 1.9 + - - -
49B THR* 3.0 26.6 + - - +
50B GLN 3.4 0.8 - - - -
51B ARG* 1.3 77.1 - - - +
53B TRP* 1.3 63.4 + - - +
55B LEU* 2.9 21.9 + - - +
56B ASP* 2.9 45.4 + - - -
67B VAL* 3.6 36.9 + - + +
69B ASP* 4.4 15.6 - - - +
74B SER* 3.9 17.5 + - - +
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Residues in contact with TRP 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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96A LYS* 4.3 14.6 - - + -
97A LEU* 3.7 27.6 - - + -
50B GLN 3.8 8.2 + - - -
51B ARG* 3.0 28.9 - - - +
52B ARG* 1.3 78.3 - - - +
54B PHE* 1.3 73.6 + + + +
56B ASP* 3.3 12.2 + - - +
57B LYS* 3.0 37.7 + - + +
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Residues in contact with PHE 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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96A LYS* 4.3 15.5 - - + -
97A LEU* 3.5 34.5 - - + -
12B TYR* 3.6 27.4 - + - -
13B LEU* 5.9 2.2 - - + -
16B PHE* 3.5 45.8 - + - -
45B VAL* 5.3 0.2 - - + -
47B GLN* 5.4 2.7 - - + -
51B ARG* 2.9 14.6 + - + +
53B TRP* 1.3 101.8 - + + +
55B LEU* 1.3 72.8 + - + +
57B LYS* 3.5 5.2 + - - +
58B LEU* 3.1 33.4 + - + +
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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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45B VAL* 3.8 35.0 - - + +
47B GLN* 3.9 22.7 - - + -
51B ARG 4.4 2.0 - - - +
52B ARG* 2.9 10.6 + - - +
54B PHE* 1.3 87.9 - - + +
56B ASP* 1.3 64.3 + - - +
58B LEU* 3.1 9.6 + - + +
59B VAL* 3.0 18.9 + - - +
67B VAL* 3.5 23.2 - - + +
74B SER* 3.6 45.8 - - - +
75B ASN* 3.9 1.1 - - - +
76B TYR* 3.9 18.6 - - + +
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Residues in contact with ASP 56 (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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52B ARG* 2.9 57.9 + - - +
53B TRP* 3.7 11.0 - - - +
55B LEU* 1.3 73.7 - - - +
57B LYS* 1.3 62.1 + - - +
59B VAL* 3.4 7.6 + - - +
60B ASP* 3.3 18.2 + - - +
67B VAL* 3.5 13.3 - - - +
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Residues in contact with LYS 57 (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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53B TRP* 3.0 26.8 + - + +
54B PHE* 3.8 6.1 - - - +
55B LEU 3.3 0.2 - - - -
56B ASP* 1.3 76.9 - - - +
58B LEU* 1.3 62.7 + - - +
60B ASP* 3.1 33.3 + - + +
61B GLU* 3.0 53.8 + - - +
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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
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9B PHE* 4.2 12.1 - - + -
13B LEU* 3.8 28.7 - - + -
43B PHE* 5.1 0.2 - - + -
45B VAL* 4.1 21.5 - - + -
54B PHE* 3.1 24.3 + - + +
55B LEU* 3.1 16.1 + - + +
57B LYS* 1.3 76.3 - - - +
59B VAL* 1.3 58.0 + - - +
61B GLU* 3.1 6.2 + - - +
62B ILE* 2.8 63.3 + - + +
76B TYR* 4.0 33.2 - - + -
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Residues in contact with VAL 59 (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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55B LEU 3.0 6.8 + - - +
56B ASP* 3.5 10.1 - - - +
57B LYS 3.3 0.2 - - - -
58B LEU* 1.3 76.0 - - - +
60B ASP* 1.3 56.0 + - - +
63B GLY* 2.7 33.2 + - - -
64B VAL 3.8 4.3 + - - +
65B GLY 3.9 14.4 - - - +
66B TYR* 3.9 11.2 - - - -
67B VAL* 3.5 32.5 - - + +
76B TYR* 3.6 24.4 - - + -
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Residues in contact with ASP 60 (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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56B ASP 3.3 8.5 + - - +
57B LYS* 3.1 35.8 + - + +
59B VAL* 1.3 84.1 - - - +
61B GLU* 1.3 63.3 + - - +
63B GLY* 3.6 9.3 + - - -
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Residues in contact with GLU 61 (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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96A LYS* 5.9 1.4 + - - -
3B THR* 5.4 1.7 - - - +
5B TYR* 3.6 14.9 - - - -
9B PHE* 3.3 38.7 - - + -
57B LYS* 3.0 52.8 + - - +
58B LEU* 3.1 11.2 + - - +
60B ASP* 1.3 78.8 - - - +
62B ILE* 1.3 62.1 + - - +
63B GLY* 4.6 0.3 - - - -
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Residues in contact with ILE 62 (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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3B THR* 4.7 6.1 + - - +
5B TYR* 2.7 41.5 + - + +
9B PHE* 4.0 11.0 - - + -
13B LEU* 4.2 0.4 - - + -
43B PHE* 4.5 1.1 - - + -
58B LEU* 2.8 47.2 + - + +
61B GLU* 1.3 73.8 - - - +
63B GLY* 1.3 57.8 + - - +
64B VAL* 3.2 17.6 - - + +
76B TYR* 3.3 41.7 - - + +
78B LEU* 4.4 4.3 - - + -
87B PHE* 3.8 35.0 - - + -
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Residues in contact with GLY 63 (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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3B THR* 5.9 2.9 - - - -
59B VAL* 2.7 20.8 + - - -
60B ASP* 3.8 9.2 - - - -
61B GLU 3.4 1.2 - - - -
62B ILE* 1.3 72.2 - - - +
64B VAL* 1.3 62.5 + - - +
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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