Contacts of the strand formed by residues 935 - 939 (chain B) in PDB entry 2XWB
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 VAL 935 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927B PRO* 4.7 0.4 - - - -
931B GLY* 3.3 2.6 - - - -
932B ARG* 2.8 47.8 + - + +
933B GLU* 4.6 8.7 - - + +
934B GLY* 1.3 80.2 - - - +
936B GLN* 1.3 62.6 + - - +
937B LYS* 5.2 16.8 - - + +
1311B THR* 5.0 9.2 - - + -
1312B ALA 3.6 5.8 - - - +
1313B GLU* 3.6 32.1 - - + +
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Residues in contact with GLN 936 (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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923B ARG* 5.9 0.2 - - - +
924B THR 3.2 24.2 + - - -
925B LEU* 3.7 19.7 - - + +
926B ASP* 3.4 34.3 - - - +
927B PRO* 3.5 7.1 - - + -
930B LEU* 3.8 21.4 - - - +
931B GLY* 4.2 5.6 - - - -
932B ARG* 4.5 4.3 - - - +
935B VAL* 1.3 78.2 - - - +
937B LYS* 1.3 70.8 + - - +
938B GLU* 4.1 15.7 + - + +
1310B VAL 3.7 0.9 - - - +
1311B THR* 3.4 7.0 - - - +
1312B ALA* 2.9 37.1 + - + +
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Residues in contact with LYS 937 (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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932B ARG* 3.2 35.2 + - - +
935B VAL* 5.2 14.9 - - + +
936B GLN* 1.3 77.5 - - - +
938B GLU* 1.3 72.0 + - - +
939B ASP* 5.4 4.0 - - - +
1310B VAL 3.7 3.4 - - - -
1311B THR* 4.8 14.4 + - + +
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Residues in contact with GLU 938 (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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923B ARG* 2.8 59.6 + - + +
924B THR 6.1 0.2 - - - -
925B LEU* 5.4 3.1 - - + -
936B GLN* 4.1 20.1 + - - +
937B LYS* 1.3 83.4 - - - +
939B ASP* 1.3 67.2 + - - +
940B ILE* 3.9 2.7 + - + +
1309B THR* 3.6 1.1 - - - -
1310B VAL* 2.9 49.2 + - + +
1320B LEU* 5.0 5.6 - - + -
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Residues in contact with ASP 939 (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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923B ARG* 2.9 30.2 + - - +
937B LYS* 5.3 3.5 - - - +
938B GLU* 1.3 78.3 + - - +
940B ILE* 1.3 61.0 + - - +
941B PRO* 4.1 2.7 - - + -
1308B PHE 4.4 3.4 - - - -
1309B THR* 3.3 24.0 - - + +
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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