Contacts of the strand formed by residues 1440 - 1449 (chain A) in PDB entry 6PUO
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 ILE1440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339A LEU* 4.9 9.9 - - + -
1345A ASN* 3.7 28.0 - - + +
1347A THR* 4.0 14.4 - - + -
1428A TYR* 3.6 3.3 - - - -
1429A MET* 2.9 58.4 + - + +
1431A ASP* 4.5 12.1 - - + -
1433A ARG* 5.1 17.0 - - + +
1434A ASN* 4.0 18.0 - - - +
1439A TRP* 1.3 85.1 - - - +
1441A GLU* 1.3 67.4 + - - +
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Residues in contact with GLU1441 (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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1312A SER* 2.6 26.4 + - - -
1313A PHE* 2.6 35.6 + - + -
1314A HIS* 3.9 8.4 + - - +
1327A PRO* 5.1 1.0 - - - +
1344A PRO* 3.7 14.8 - - + -
1345A ASN 3.1 10.1 + - - +
1346A HIS* 3.2 26.1 - - + +
1347A THR* 3.0 26.7 + - - +
1427A GLY 3.3 16.6 - - - +
1428A TYR* 3.8 10.0 + - - +
1429A MET 4.5 0.2 - - - +
1439A TRP* 3.4 12.9 + - + -
1440A ILE* 1.3 78.8 - - - +
1442A THR* 1.3 61.6 + - - +
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Residues in contact with THR1442 (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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1313A PHE* 5.3 3.0 - - - -
1347A THR* 3.3 22.3 + - - +
1349A TYR* 3.4 21.9 + - + +
1425A TYR* 4.8 13.9 - - + -
1426A LYS* 3.4 7.6 - - - +
1427A GLY 3.2 31.3 + - - +
1429A MET* 3.8 28.5 - - + -
1441A GLU* 1.3 77.0 - - - +
1443A VAL* 1.3 84.0 + - - +
1444A ALA* 5.7 0.4 - - + -
1491A LEU* 5.4 5.8 - - + -
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Residues in contact with VAL1443 (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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1313A PHE* 4.2 24.5 - - + -
1346A HIS* 6.3 1.1 - - + -
1347A THR 3.2 10.0 + - - +
1348A LEU* 3.6 21.8 - - + +
1349A TYR* 2.8 28.3 + - - +
1423A GLU* 3.8 13.7 - - - +
1425A TYR 3.9 2.0 - - - -
1426A LYS* 3.7 29.6 - - + -
1442A THR* 1.3 85.1 + - - +
1444A ALA* 1.3 62.6 + - - +
1445A VAL* 3.8 0.7 - - + -
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Residues in contact with ALA1444 (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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1349A TYR 3.4 6.5 - - - +
1351A MET* 4.5 7.0 - - + -
1423A GLU* 3.4 5.1 - - - +
1424A VAL* 2.7 41.3 + - + +
1425A TYR* 2.9 33.4 + - + +
1442A THR* 5.7 1.6 - - + -
1443A VAL* 1.3 72.1 - - - +
1445A VAL* 1.3 59.5 + - - +
1491A LEU* 4.2 25.4 - - + -
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Residues in contact with VAL1445 (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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1348A LEU* 4.5 15.3 - - + -
1349A TYR 3.4 3.3 + - - +
1350A PRO* 3.6 26.2 - - + +
1351A MET* 3.1 28.8 + - - +
1419A LYS* 3.8 25.8 - - + +
1421A GLY* 4.1 2.9 - - - +
1422A MET 3.4 13.9 - - - +
1423A GLU* 3.3 31.6 + - - +
1443A VAL 3.8 1.6 - - - -
1444A ALA* 1.3 75.3 - - - +
1446A SER* 1.3 63.7 + - - +
1447A VAL* 4.1 5.8 - - + +
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Residues in contact with SER1446 (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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1351A MET* 3.6 18.4 - - - -
1353A THR* 5.1 6.3 - - - -
1421A GLY* 4.8 0.2 - - - -
1422A MET* 2.5 42.1 + - - +
1424A VAL* 3.7 23.5 - - - +
1445A VAL* 1.3 75.3 - - - +
1447A VAL* 1.3 63.8 - - - +
1448A HIS* 3.7 4.7 + - - +
1495A ALA* 5.9 0.9 - - - -
1499A PHE* 4.8 15.0 - - - -
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Residues in contact with VAL1447 (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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1350A PRO* 6.1 3.8 - - + -
1351A MET 3.2 7.4 + - - +
1352A VAL* 3.6 27.6 - - + -
1353A THR* 3.2 23.9 + - - +
1418A LEU* 3.9 26.2 - - + +
1419A LYS* 5.7 4.0 - - - +
1421A GLY* 5.0 13.7 - - - +
1445A VAL* 4.1 5.6 - - + +
1446A SER* 1.3 74.4 - - - +
1448A HIS* 1.3 65.7 + - - +
1449A PHE* 4.7 17.0 - - + -
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Residues in contact with HIS1448 (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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1353A THR* 2.4 31.7 + - - +
1354A ARG* 4.5 0.2 - - - -
1355A TRP* 3.1 32.0 + + - -
1372A LEU* 4.0 18.2 - - + -
1446A SER 3.7 4.2 + - - +
1447A VAL* 1.3 79.6 - - - +
1449A PHE* 1.3 93.4 + - - +
1450A GLN* 3.1 24.0 + - + -
1499A PHE* 3.3 41.7 - + + -
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Residues in contact with PHE1449 (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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1352A VAL* 6.0 7.4 - - + -
1353A THR 2.9 14.9 + - - +
1354A ARG* 3.9 13.2 - - + -
1355A TRP* 3.7 0.5 - - - -
1418A LEU* 6.6 0.2 - - + -
1447A VAL* 4.7 17.3 - - + -
1448A HIS* 1.3 94.8 + - - +
1450A GLN* 1.3 59.1 + - - +
1451A ASP 4.3 7.9 - - - +
1452A GLN* 2.7 32.0 + - - +
1456A GLU* 3.1 38.6 - - + -
1457A LEU* 3.6 31.4 - - + -
1460A LEU* 4.4 12.1 - - + -
1475A TRP* 5.0 16.4 - + - -
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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