Contacts of the strand formed by residues 1372 - 1376 (chain A) in PDB entry 3AVS
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 PHE1372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1315A LYS* 2.8 29.6 + - - -
1343A PHE* 4.0 5.2 - - + -
1344A VAL 3.4 25.8 - - - +
1345A THR* 3.6 23.1 - - + -
1346A ASN* 3.8 7.8 - - - +
1357A HIS* 3.9 23.6 - + - -
1362A ALA* 3.4 46.2 - - + -
1365A THR* 3.4 19.3 - - - -
1366A SER* 3.6 18.4 - - - -
1369A LEU* 3.1 20.4 + - + +
1370A GLU 3.2 1.7 + - - +
1371A ASN* 1.3 88.4 - - + +
1373A VAL* 1.3 63.1 + - - +
1374A VAL* 5.7 0.2 - - + -
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Residues in contact with VAL1373 (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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1315A LYS* 4.8 3.4 - - - +
1316A GLU* 5.4 5.2 - - + +
1318A ILE* 3.1 37.0 - - + -
1342A LEU 3.5 2.1 - - - +
1343A PHE* 3.5 3.3 - - - -
1344A VAL* 2.8 45.6 + - + +
1346A ASN* 4.0 8.0 + - - +
1349A ASN* 3.9 31.9 - - + +
1372A PHE* 1.3 75.7 - - - +
1374A VAL* 1.3 66.5 + - - +
1375A LEU* 4.0 12.8 - - + -
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Residues in contact with VAL1374 (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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1310A LEU* 3.9 24.7 - - + -
1315A LYS* 4.3 25.8 - - + -
1316A GLU 4.1 11.0 + - - +
1317A ILE* 3.8 5.9 - - + -
1318A ILE* 3.0 28.2 + - - +
1341A LEU* 4.4 25.6 - - + -
1342A LEU 3.3 7.6 - - - +
1343A PHE* 3.8 26.7 - - + -
1369A LEU* 5.1 2.0 - - + -
1372A PHE* 5.3 1.1 - - + +
1373A VAL* 1.3 82.6 - - - +
1375A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU1375 (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 ILE* 3.5 28.0 - - + -
1320A HIS* 3.8 30.7 - - + +
1340A ASP 3.5 0.7 - - - +
1341A LEU* 3.3 5.7 - - - -
1342A LEU* 2.8 49.9 + - + +
1344A VAL* 3.9 17.0 - - + -
1349A ASN* 4.1 9.4 - - - +
1354A TYR* 3.8 32.8 - - + -
1373A VAL* 4.0 20.6 - - + -
1374A VAL* 1.3 74.8 - - - +
1376A GLU* 1.3 61.1 + - - +
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Residues in contact with GLU1376 (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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1307A ARG* 3.1 35.8 + - - -
1317A ILE* 3.6 29.8 - - + +
1318A ILE 2.9 11.1 + - - +
1319A TRP* 3.5 18.1 - - + -
1320A HIS* 3.0 8.9 + - - +
1321A GLY 2.9 21.2 + - - -
1340A ASP* 3.3 12.7 - - - +
1341A LEU* 4.0 5.9 - - + +
1374A VAL 4.0 0.2 + - - -
1375A LEU* 1.3 73.8 - - - +
1377A GLN* 1.3 59.8 + - - +
1378A TYR 3.3 26.1 - - - +
1379A LYS* 5.2 4.6 - - - +
1380A MET* 4.7 5.2 + - - +
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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