Contacts of the strand formed by residues 919 - 925 (chain B) in PDB entry 2WIN
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 THR 919 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917B ASN 3.4 5.7 + - - -
918B LYS* 1.3 72.8 - - - +
920B VAL* 1.3 68.2 + - - +
921B ALA* 4.0 11.0 - - - +
922B VAL* 4.2 24.7 - - + -
1322B VAL 4.1 7.4 - - - +
1323B VAL* 4.6 13.7 - - + +
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Residues in contact with VAL 920 (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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918B LYS 3.5 0.2 + - - -
919B THR* 1.3 75.5 - - - +
921B ALA* 1.3 66.3 + - + +
940B ILE* 4.3 15.9 - - + -
941B PRO* 3.6 24.5 - - + +
942B PRO 5.3 4.0 - - - -
943B ALA* 5.0 6.7 - - + +
956B THR* 4.8 0.9 - - + -
1322B VAL* 3.1 32.4 + - + +
1324B THR* 3.4 40.4 - - + +
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Residues in contact with ALA 921 (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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919B THR* 3.7 3.5 - - - -
920B VAL* 1.3 89.8 - - + +
922B VAL* 1.3 68.9 + - - +
923B ARG* 3.4 34.5 - - + +
940B ILE* 5.4 4.0 - - + -
941B PRO* 5.5 3.4 - - + -
1320B LEU 4.1 1.0 - - - +
1321B SER* 4.0 0.5 - - - -
1322B VAL* 3.3 29.1 + - + +
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Residues in contact with VAL 922 (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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919B THR* 4.2 19.1 - - + -
921B ALA* 1.3 82.4 - - - +
923B ARG* 1.3 65.4 + - - +
1319B THR* 6.3 2.0 - - + -
1320B LEU 3.8 4.3 - - - -
1321B SER* 4.1 21.1 - - - -
1322B VAL 5.0 0.2 - - - +
1323B VAL* 6.0 0.7 - - + -
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Residues in contact with ARG 923 (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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921B ALA* 3.4 28.1 - - - +
922B VAL* 1.3 80.6 - - - +
924B THR* 1.3 65.6 + - - +
925B LEU* 5.5 1.3 - - + -
938B GLU* 2.8 40.4 + - + +
939B ASP 3.0 27.1 + - - -
940B ILE* 3.2 26.1 - - - +
941B PRO* 4.6 6.9 - - - +
1319B THR* 4.3 4.6 - - - +
1320B LEU* 3.2 37.7 + - + +
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Residues in contact with THR 924 (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* 1.3 77.1 - - - +
925B LEU* 1.3 64.9 + - - +
930B LEU* 3.3 26.2 - - + +
936B GLN* 3.1 18.7 + - - -
1317B GLN* 4.1 24.0 - - + +
1318B GLY 3.2 20.2 - - - +
1319B THR* 4.7 7.7 + - - +
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Residues in contact with LEU 925 (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* 4.0 1.7 + - + +
924B THR* 1.3 75.1 - - - +
926B ASP* 1.3 61.1 + - - +
927B PRO* 4.2 3.1 - - - +
936B GLN* 3.7 24.9 - - + +
938B GLU* 4.6 16.6 - - + +
960B LEU* 4.2 19.3 - - + -
1272B LEU* 4.7 6.4 - - + +
1274B VAL* 4.6 8.5 - - + -
1310B VAL* 4.2 14.8 - - + +
1312B ALA* 4.6 15.5 - - + +
1316B GLY 4.6 0.3 - - - +
1317B GLN* 4.1 0.7 - - - -
1318B GLY* 3.0 37.0 + - - +
1319B THR* 4.6 0.4 - - - +
1320B LEU* 3.6 44.2 - - + +
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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