Contacts of the strand formed by residues 1325 - 1329 (chain A) in PDB entry 4C2A
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 SER1325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319A VAL* 3.7 13.5 - - - -
1320A GLU 3.8 3.6 - - - -
1321A TYR* 4.5 0.9 - - - +
1324A GLY* 1.3 73.6 - - - -
1326A HIS* 1.3 61.9 + - - +
1327A ALA 3.9 0.4 - - - -
1359A GLU* 4.5 1.4 + - - +
1360A VAL* 3.5 28.6 + - - +
1363A TYR* 3.6 38.3 - - - +
237B LYS 3.6 1.2 - - - +
238B ALA* 3.3 4.2 - - - -
239B VAL* 2.9 34.4 + - - +
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Residues in contact with HIS1326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319A VAL* 3.4 2.8 - - - +
1320A GLU* 2.8 47.6 + - - +
1322A HIS* 3.1 39.2 + + - -
1324A GLY 3.7 8.9 + - - -
1325A SER* 1.3 79.2 - - - +
1327A ALA* 1.3 59.6 + - - +
1328A TYR* 3.3 22.7 + - + -
236B VAL* 4.1 11.0 - - + +
237B LYS 3.4 3.8 - - - -
238B ALA* 3.6 22.7 - - + +
240B THR* 4.5 9.3 + - - -
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Residues in contact with ALA1327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1318A VAL 3.8 4.9 - - - +
1319A VAL* 4.2 14.1 - - + +
1325A SER 3.9 1.4 - - - -
1326A HIS* 1.3 70.1 - - - +
1328A TYR* 1.3 63.4 + - - +
1329A ILE 4.8 7.9 - - - +
1363A TYR* 3.7 23.3 - - + +
235B ASP 4.0 2.6 - - - +
236B VAL* 3.6 4.4 - - - -
237B LYS* 2.7 47.5 + - + +
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Residues in contact with TYR1328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1318A VAL* 2.9 13.6 + - + +
1320A GLU* 4.1 14.9 + - + -
1326A HIS* 3.3 23.3 + - + +
1327A ALA* 1.3 75.9 - - - +
1329A ILE* 1.3 66.9 + - + +
1333A ASP* 4.2 2.5 - - - +
1335A LYS* 4.8 0.3 + - - -
1343A ILE* 3.9 28.8 - - + +
1346A GLN 4.8 2.7 - - - -
1347A VAL* 3.7 48.7 - - + +
1348A LYS* 3.3 33.7 + - + +
235B ASP* 3.8 18.3 - - - +
236B VAL* 3.5 39.4 - - + +
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Residues in contact with ILE1329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304A MET* 4.9 3.8 - - + -
1311A GLN* 4.3 1.3 - - - +
1316A VAL* 3.4 24.0 - - + +
1317A ALA* 3.3 5.5 - - - +
1318A VAL* 3.1 52.6 + - + +
1319A VAL* 5.1 0.5 - - - +
1327A ALA* 4.8 8.3 - - - +
1328A TYR* 1.3 87.7 + - - +
1330A GLY* 1.3 66.3 + - - +
1333A ASP* 3.6 7.2 - - + +
1335A LYS* 6.4 0.7 - - + -
1340A LEU* 3.5 54.1 - - + +
1343A ILE* 3.7 19.5 - - + -
1344A ALA* 4.4 3.4 - - + +
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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