Contacts of the strand formed by residues 31 - 36 (chain B) in PDB entry 2VUU
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LYS 2.9 7.0 + - - +
7B THR* 3.5 27.1 - - + +
8B ILE* 2.7 32.3 + - - +
29B GLY 4.4 6.3 + - - -
30B HIS* 1.3 80.2 + - - +
32B VAL* 1.3 59.0 + - - +
52B ASN* 3.5 35.7 + - + +
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Residues in contact with VAL 32 (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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8B ILE* 3.4 11.7 - - + +
10B VAL* 3.9 12.3 - - + -
22B ILE* 3.8 34.5 - - + -
25B ALA* 4.4 22.4 - - + -
26B ALA* 4.5 5.6 - - + +
30B HIS 4.4 5.6 - - - +
31B HIS* 1.3 83.3 - - - +
33B ARG* 1.3 69.8 + - - +
34B ALA* 4.2 2.9 - - + -
52B ASN 3.0 8.2 + - - +
53B VAL* 3.5 21.6 - - + -
54B THR* 2.8 31.2 + - - +
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Residues in contact with ARG 33 (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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7B THR* 3.7 25.5 - - + +
8B ILE 2.8 10.6 + - - +
9B ALA* 4.3 0.7 - - - -
10B VAL* 2.8 26.5 + - - +
31B HIS* 6.1 0.2 - - + -
32B VAL* 1.3 76.0 - - - +
34B ALA* 1.3 57.3 + - - +
54B THR* 3.6 20.3 - - + +
56B PHE* 3.3 24.3 - - + -
69B THR* 2.8 25.0 + - - +
70B LEU* 2.9 41.3 + - + +
72B GLU* 3.2 31.6 + - - +
74B ALA* 4.5 3.6 - - - -
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Residues in contact with ALA 34 (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 VAL* 3.3 6.7 - - + +
13B ALA* 3.5 24.2 - - + -
22B ILE* 3.9 15.0 - - + -
32B VAL* 3.8 6.5 - - + -
33B ARG* 1.3 76.1 - - - +
35B GLN* 1.3 56.7 + - - +
53B VAL* 4.9 0.4 - - + -
54B THR 2.8 11.1 + - - +
55B LEU* 3.2 20.5 - - + -
56B PHE* 2.8 32.5 + - - -
70B LEU* 3.9 4.7 - - - +
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Residues in contact with GLN 35 (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 VAL 3.0 14.7 + - - +
11B VAL* 3.6 15.1 - - + +
12B ASN* 2.9 29.6 + - - -
13B ALA* 3.1 23.6 + - - +
34B ALA* 1.3 73.8 - - - +
36B VAL* 1.3 76.9 + - - +
37B HIS* 3.5 6.9 - - - +
56B PHE* 3.5 7.2 - - - +
58B GLY 2.8 24.5 + - - -
59B PRO* 4.7 0.2 - - - +
60B LEU* 3.5 35.2 - - + +
66B LEU* 3.7 21.3 - - + -
70B LEU* 4.1 8.5 - - + +
1353B NAP 5.9 0.8 - - - -
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Residues in contact with VAL 36 (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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12B ASN* 5.5 1.3 - - - +
13B ALA* 3.5 29.4 - - + +
14B THR* 4.3 20.2 - - + +
35B GLN* 1.3 77.2 - - - +
37B HIS* 1.3 59.8 + - - +
38B SER 3.9 10.5 - - - +
39B LEU* 3.6 29.6 - - + -
44B ALA* 5.5 1.1 - - + -
47B LEU* 5.4 1.1 - - + -
55B LEU* 4.1 22.0 - - + -
56B PHE 3.0 13.4 + - - +
57B GLN* 3.2 7.6 - - + -
58B GLY 3.0 25.3 + - - +
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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