Contacts of the strand formed by residues 31 - 36 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LYS 3.1 8.3 + - - +
7F THR* 3.6 26.6 + - + +
8F ILE* 2.7 32.3 + - - +
29F GLY 4.3 8.7 + - - -
30F HIS* 1.3 76.0 - - - +
32F VAL* 1.3 58.4 + - - +
33F ARG* 6.2 0.2 - - + -
52F ASN* 2.6 40.1 + - + +
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 3.4 17.5 - - + +
10F VAL* 4.2 5.4 - - + -
21F LEU* 6.0 0.7 - - + -
22F ILE* 4.1 34.8 - - + -
25F ALA* 4.3 24.0 - - + -
26F ALA* 4.8 5.4 - - + +
30F HIS 4.1 1.5 + - - +
31F HIS* 1.3 81.4 - - - +
33F ARG* 1.3 71.3 + - - +
34F ALA* 4.1 9.6 - - + -
52F ASN 3.1 9.2 + - - +
53F VAL* 3.5 14.9 - - + -
54F THR* 2.8 33.6 + - - +
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Residues in contact with ARG 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F THR* 3.8 24.9 - - + +
8F ILE 2.9 8.3 + - - +
9F ALA* 3.4 1.9 - - - -
10F VAL 2.8 27.4 + - - +
32F VAL* 1.3 74.7 - - - +
34F ALA* 1.3 59.3 + - - +
54F THR* 3.5 13.6 - - - +
56F PHE* 3.8 16.8 - - + -
69F THR* 2.6 37.6 + - - +
70F LEU* 2.7 39.0 + - + +
72F GLU* 3.1 33.4 + - - +
74F ALA* 4.6 4.5 - - - -
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Residues in contact with ALA 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.2 14.1 - - + -
13F ALA* 3.5 25.6 - - + -
22F ILE* 4.0 7.9 - - + -
32F VAL* 3.8 5.1 - - + -
33F ARG* 1.3 75.4 - - - +
35F GLN* 1.3 60.0 + - - +
36F VAL 4.1 0.2 - - - -
53F VAL* 4.7 2.2 - - + -
54F THR 2.8 8.8 + - - +
55F LEU* 3.3 17.5 - - + -
56F PHE* 2.9 29.1 + - - -
70F LEU* 3.8 3.6 - - - -
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Residues in contact with GLN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL 3.0 13.1 + - - +
11F VAL* 3.6 13.6 - - + +
12F ASN* 3.1 24.8 + - - -
13F ALA 3.0 24.3 + - - -
34F ALA* 1.3 74.6 - - - +
36F VAL* 1.3 79.5 + - - +
37F HIS* 3.5 4.9 + - - +
56F PHE* 3.5 4.5 - - - +
58F GLY 2.6 26.9 + - - -
59F PRO* 4.7 0.4 - - - +
60F LEU* 3.7 27.1 - - + +
66F LEU* 3.7 28.7 - - + -
70F LEU* 4.0 13.5 - - + -
1353F NAP 6.2 0.2 - - - -
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASN* 5.5 1.1 - - - +
13F ALA* 3.5 30.1 - - + +
14F THR* 3.9 22.9 - - + +
35F GLN* 1.3 76.9 + - - +
37F HIS* 1.3 61.6 - - - +
38F SER 3.9 10.8 - - - +
39F LEU* 3.8 28.9 - - + -
44F ALA* 5.5 1.3 - - + -
47F LEU* 4.6 1.3 - - + -
55F LEU* 3.7 21.3 - - + -
56F PHE 3.0 15.3 + - - +
57F GLN* 3.1 2.6 - - - -
58F GLY 3.0 24.9 + - - -
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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