Contacts of the strand formed by residues 1340 - 1347 (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 ASP1340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336B CYS* 6.0 0.5 - - - +
1339B PHE* 1.3 73.6 - - - +
1341B LEU* 1.3 59.4 + - - +
1342B LYS* 4.9 11.0 - - + -
1368B THR* 2.9 32.4 + - - -
1369B ARG* 2.9 51.3 + - + +
1371B ARG* 2.7 40.0 + - - -
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Residues in contact with LEU1341 (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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1336B CYS* 6.5 0.9 - - - -
1339B PHE* 3.7 6.6 + - + +
1340B ASP* 1.3 75.3 - - - +
1342B LYS* 1.3 68.8 + - - +
1343B VAL* 4.2 18.0 + - + +
1366B ILE* 3.7 26.7 - - + -
1367B CYS 3.3 17.7 - - - +
1368B THR* 4.2 9.0 - - - +
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Residues in contact with LYS1342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1340B ASP* 4.9 8.7 - - + -
1341B LEU* 1.3 84.0 - - - +
1343B VAL* 1.3 63.4 + - - +
1344B THR* 4.1 5.6 + - - +
1365B GLU 3.8 3.1 - - - +
1366B ILE* 4.0 0.3 - - - -
1367B CYS* 3.1 52.2 + - + +
1368B THR* 6.1 0.2 - - - +
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Residues in contact with VAL1343 (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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1341B LEU* 4.2 27.3 + - + -
1342B LYS* 1.3 75.0 - - - +
1344B THR* 1.3 67.8 + - - +
1345B ILE* 5.9 0.8 - - + +
1364B LEU* 3.6 27.6 - - + -
1365B GLU 3.6 4.3 - - - +
1366B ILE* 4.8 11.9 - - + -
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Residues in contact with THR1344 (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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1342B LYS* 4.7 6.6 + - - +
1343B VAL* 1.3 77.2 + - - +
1345B ILE* 1.3 65.1 + - - +
1346B LYS* 3.5 41.5 - - + +
1363B ILE 3.5 3.0 - - - +
1364B LEU* 3.6 7.5 - - - +
1365B GLU* 3.1 47.6 + - + +
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Residues in contact with ILE1345 (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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1343B VAL* 5.9 0.7 - - + +
1344B THR* 1.3 78.5 - - - +
1346B LYS* 1.3 63.1 + - - +
1347B PRO* 4.5 1.9 - - - +
1362B MET* 3.5 41.7 - - + -
1363B ILE 3.3 19.3 - - - +
1364B LEU* 4.5 12.3 - - + +
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Residues in contact with LYS1346 (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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1344B THR* 3.5 26.5 - - + +
1345B ILE* 1.3 79.3 - - - +
1347B PRO* 1.3 75.6 - - + +
1362B MET* 3.3 6.5 - - - +
1363B ILE* 2.7 45.1 + - + +
1365B GLU* 5.1 8.5 - - - +
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Residues in contact with PRO1347 (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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1345B ILE 4.5 1.8 - - - +
1346B LYS* 1.3 98.5 - - + +
1348B ALA* 1.3 63.8 + - - +
1349B PRO* 4.3 1.6 - - - +
1360B ASN 5.1 1.1 - - - +
1362B MET* 4.2 20.8 - - + -
1363B ILE* 4.2 8.0 - - - +
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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