Contacts of the strand formed by residues 31 - 36 (chain G) in PDB entry 2VUT
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 HIS 31 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G LYS 5.3 6.5 + - - -
6G LYS 3.6 5.5 + - - +
7G THR* 3.4 27.1 + - + +
8G ILE 3.0 24.2 + - - -
29G GLY 4.8 6.6 + - - -
30G HIS* 1.3 76.8 - - - +
32G VAL* 1.3 62.6 + - - +
33G ARG* 6.1 0.7 - - + -
52G ASN* 3.5 38.8 + - + +
33H ARG* 5.5 10.0 + - - -
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Residues in contact with VAL 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ILE* 3.6 13.0 - - + +
10G VAL* 4.4 6.5 - - + -
21G LEU* 6.4 0.2 - - + -
22G ILE* 4.0 38.1 - - + -
25G ALA* 4.2 24.7 - - + -
26G ALA 4.5 3.1 - - - +
30G HIS 4.3 4.5 - - - +
31G HIS* 1.3 80.8 - - - +
33G ARG* 1.3 70.2 + - - +
34G ALA* 4.0 8.1 - - + -
52G ASN 2.8 10.6 + - - +
53G VAL* 3.9 16.2 - - + -
54G THR* 2.7 34.7 + - - +
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Residues in contact with ARG 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G THR* 3.7 22.7 - - + -
8G ILE 3.0 9.8 + - - +
9G ALA* 3.3 1.8 - - - -
10G VAL* 2.8 25.8 + - - +
31G HIS* 6.1 0.4 - - + -
32G VAL* 1.3 74.3 - - - +
34G ALA* 1.3 58.7 + - - +
54G THR* 3.5 16.2 + - - +
56G PHE* 3.7 28.1 - - + -
69G THR* 2.9 24.9 + - - +
70G LEU* 2.9 40.8 + - + +
72G GLU* 3.2 33.8 + - - +
74G ALA* 4.6 2.7 - - - -
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Residues in contact with ALA 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.2 8.5 - - + +
13G ALA* 3.6 24.9 - - + -
22G ILE* 3.9 16.4 - - + -
32G VAL* 3.8 8.3 - - + -
33G ARG* 1.3 74.3 - - - +
35G GLN* 1.3 61.4 + - - +
53G VAL* 4.8 0.7 - - + -
54G THR 2.9 7.5 + - - -
55G LEU* 3.1 19.2 - - + +
56G PHE* 2.9 25.2 + - - -
70G LEU* 4.1 4.5 - - - -
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Residues in contact with GLN 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL 2.9 8.9 + - - +
11G VAL* 3.5 17.6 - - + +
12G ASN* 2.6 35.6 + - - +
13G ALA* 2.9 25.8 + - - +
34G ALA* 1.3 74.5 - - - +
36G VAL* 1.3 74.1 + - - +
37G HIS* 3.6 6.5 + - - +
56G PHE* 3.4 9.0 - - + +
58G GLY 2.8 21.6 + - - +
59G PRO* 4.5 1.4 - - - +
60G LEU* 3.6 28.8 - - + +
66G LEU* 3.6 30.7 - - + -
70G LEU* 4.1 8.3 - - + +
1355G NAD 5.9 1.6 + - - -
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Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA* 3.3 29.8 - - + -
14G THR* 4.2 15.3 - - + -
35G GLN* 1.3 77.2 - - - +
37G HIS* 1.3 64.1 + - - +
38G SER 3.9 14.4 - - - +
39G LEU* 3.9 26.5 - - + -
44G ALA* 5.1 2.0 - - + -
47G LEU* 5.1 1.8 - - + -
55G LEU* 4.0 20.4 - - + -
56G PHE 3.1 11.2 + - - +
57G GLN* 3.4 6.9 - - - -
58G GLY 3.2 21.8 + - - +
1354G CL 3.7 6.3 - - + -
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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) + - + + + + + -
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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