Contacts of the strand formed by residues 1342 - 1349 (chain A) in PDB entry 2VZ9
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 GLY1342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1237A MET* 5.2 4.7 - - - -
1313A ASP* 3.2 19.1 - - - -
1338A LEU* 3.0 24.9 - - - +
1339A LYS 3.9 8.6 + - - -
1341A GLY* 1.3 84.5 - - - +
1343A PHE* 1.3 73.0 + - - -
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Residues in contact with PHE1343 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1232A THR* 5.4 4.5 - - + -
1233A ALA* 3.5 42.4 - - + -
1236A ASN* 3.6 36.8 - - + -
1237A MET* 4.5 6.5 - - + -
1313A ASP 2.7 14.1 + - - +
1314A LEU* 3.1 22.0 - - + -
1315A LEU 2.7 31.1 + - - -
1338A LEU* 4.6 0.2 - - - +
1341A GLY 4.4 9.2 - - - -
1342A GLY* 1.3 83.6 - - - -
1344A LEU* 1.3 66.5 + - - +
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Residues in contact with LEU1344 (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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1314A LEU* 4.8 0.7 - - - -
1315A LEU* 3.0 46.9 - - + +
1334A MET* 3.8 36.1 - - + +
1337A THR 6.4 0.4 - - - -
1338A LEU* 5.6 9.0 - - + -
1342A GLY 5.4 1.3 - - - -
1343A PHE* 1.3 92.3 - - - +
1345A LEU* 1.3 66.0 + - - +
1346A LEU* 3.5 31.4 + - + +
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Residues in contact with LEU1345 (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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1226A LEU* 4.5 9.6 - - + +
1229A CYS* 4.3 21.8 - - + -
1230A VAL* 3.9 39.0 - - + +
1258A ILE* 5.3 0.7 - - + -
1314A LEU* 4.3 14.4 - - + +
1315A LEU 2.8 9.0 + - - +
1316A VAL* 3.1 27.5 - - + -
1317A CYS 2.9 24.9 + - - -
1343A PHE 4.3 0.4 - - - -
1344A LEU* 1.3 75.7 - - - +
1346A LEU* 1.3 70.3 + - - +
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Residues in contact with LEU1346 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1317A CYS* 3.3 25.4 - - + +
1319A CYS* 5.7 4.5 - - + -
1331A VAL* 5.8 7.9 - - + -
1334A MET* 5.5 4.0 - - + -
1344A LEU* 3.5 39.5 - - + +
1345A LEU* 1.3 101.5 - - - +
1347A HIS* 1.3 62.6 + - - +
1348A THR* 4.3 2.0 - - - +
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Residues in contact with HIS1347 (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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1219A GLY 4.0 12.7 + - - -
1220A LEU* 6.1 0.7 - - + -
1221A LEU* 3.5 46.4 - - + +
1226A LEU* 5.0 9.5 - - - +
1254A LEU* 6.2 3.8 - - + -
1317A CYS 3.1 10.1 + - - +
1318A ASN* 3.9 19.1 - - - +
1319A CYS* 2.7 30.2 + - - +
1320A ALA* 3.2 8.7 + - + +
1346A LEU* 1.3 76.5 - - - +
1348A THR* 1.3 72.2 + - - +
1349A LEU* 5.6 1.2 - - - -
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Residues in contact with THR1348 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1319A CYS* 3.1 35.4 - - + +
1323A THR* 5.5 4.0 - - + +
1346A LEU* 4.3 1.6 - - - +
1347A HIS* 1.3 84.7 + - - +
1349A LEU* 1.3 64.4 + - - +
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Residues in contact with LEU1349 (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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1320A ALA* 4.6 15.8 - - - +
1347A HIS* 5.4 2.2 - - - -
1348A THR* 1.3 85.4 - - - +
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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