Contacts of the strand formed by residues 1430 - 1436 (chain A) in PDB entry 2VK7
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 TYR1430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1345A THR* 3.5 4.6 - - - +
1346A HIS* 2.8 57.7 + + + +
1348A PRO* 3.9 14.1 - - + -
1360A SER 3.4 18.4 - - - -
1361A GLY* 4.0 3.5 - - - -
1362A PHE* 4.5 0.2 - + - -
1371A LEU* 3.9 21.1 - - + +
1417A ASN* 5.5 0.4 - - - -
1425A ALA* 3.9 7.5 - - + +
1426A LYS* 2.8 44.6 + - - +
1428A THR* 3.4 27.4 - - + +
1429A SER* 1.3 72.4 - - - +
1431A ILE* 1.3 65.7 + - - +
1432A ASN* 3.7 1.9 + - - +
1448A ASN* 3.4 29.4 - - - +
1450A ASN* 3.3 22.2 - - + -
1461A LEU 4.9 0.4 - - - -
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Residues in contact with ILE1431 (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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1343A LEU* 4.2 3.6 - - + -
1344A VAL 3.7 1.6 - - - +
1345A THR* 4.5 1.8 - - - +
1430A TYR* 1.3 74.3 - - - +
1432A ASN* 1.3 66.7 + - - +
1448A ASN* 3.7 4.3 - - - +
1449A ILE* 3.0 55.9 + - + +
1450A ASN* 3.0 17.6 + - - +
1453A VAL* 4.2 14.6 - - + -
1461A LEU* 3.3 34.8 - - + +
1462A GLY* 3.7 16.6 - - - -
1463A ILE* 3.8 31.4 - - + +
1484A VAL* 5.2 2.9 - - + -
1498A ILE* 4.6 4.7 - - + -
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Residues in contact with ASN1432 (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 MET* 4.0 9.0 - - - -
1320A TYR* 2.9 32.5 + - - -
1326A VAL* 4.0 2.0 - - - +
1342A LEU 4.1 0.2 - - - +
1343A LEU* 3.2 7.8 - - - +
1344A VAL* 2.9 45.9 + - + +
1346A HIS* 3.6 26.5 + - - +
1430A TYR* 3.7 3.3 + - - +
1431A ILE* 1.3 79.5 - - - +
1433A LEU* 1.3 61.2 + - - +
1446A PRO* 3.7 18.9 - - + +
1447A GLN 3.3 6.6 - - - +
1448A ASN* 4.1 11.8 + - - +
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Residues in contact with LEU1433 (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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1341A PHE* 3.4 28.3 - - + -
1342A LEU 3.4 8.5 - - - +
1343A LEU* 3.7 20.6 - - + -
1432A ASN* 1.3 75.8 - - - +
1434A VAL* 1.3 92.6 + - - +
1435A TYR* 5.5 0.4 - - + -
1444A SER* 4.5 0.2 + - - -
1445A GLU 3.9 1.4 - - - +
1446A PRO* 3.5 1.7 - - - +
1447A GLN* 2.8 55.1 + - + +
1449A ILE* 4.6 11.4 - - + -
1504A GLY 4.5 3.1 - - - +
1507A TRP* 3.5 44.6 - - + +
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Residues in contact with VAL1434 (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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1317A ILE* 4.1 12.3 - - + +
1318A MET* 4.0 21.1 - - + -
1341A PHE* 3.5 0.5 - - - -
1342A LEU* 2.9 54.3 + - + +
1433A LEU* 1.3 89.9 - - - +
1435A TYR* 1.3 62.0 + - - +
1443A TRP* 3.8 20.4 - - + -
1444A SER* 3.3 29.2 - - - +
1445A GLU 3.8 0.2 - - - -
1446A PRO* 3.6 19.7 - - + -
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Residues in contact with TYR1435 (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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1339A ARG* 3.4 57.8 + - + -
1340A ILE 3.0 13.0 - - - +
1341A PHE* 4.0 11.4 - + + -
1433A LEU* 5.5 0.7 - - + -
1434A VAL* 1.3 77.7 - - - +
1436A SER* 1.3 61.3 + - - +
1437A ASP* 3.8 11.0 - - - -
1443A TRP* 3.4 6.8 - - - -
1444A SER* 2.8 55.5 + - - -
1447A GLN* 3.4 30.7 - - + -
1674B PRO* 4.1 26.3 - - - +
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Residues in contact with SER1436 (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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1338A GLY 4.0 1.4 - - - +
1339A ARG* 3.5 3.8 - - - -
1340A ILE* 2.9 35.2 + - - +
1435A TYR* 1.3 73.9 - - - +
1437A ASP* 1.3 61.3 + - - +
1438A ASP* 2.8 26.3 + - - -
1439A ASP 4.8 0.2 - - - -
1440A GLY* 2.8 24.2 + - - -
1442A THR 2.8 15.8 + - - -
1443A TRP* 3.8 19.1 - - - -
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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