Contacts of the strand formed by residues 1472 - 1477 (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 SER1472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1377A VAL* 3.7 1.3 - - - +
1378A LYS* 2.9 31.6 + - - +
1385A TRP* 4.1 13.7 - - - -
1470A GLY 3.8 0.6 - - - -
1471A ALA* 1.3 84.2 - - - +
1473A ILE* 1.3 77.9 + - - +
1474A ARG* 5.0 3.3 - - - +
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Residues in contact with ILE1473 (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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1375A LEU* 4.8 21.5 - - + -
1376A VAL 3.5 8.5 - - - +
1377A VAL* 3.7 26.9 - - + -
1385A TRP* 4.7 0.2 - - - -
1406A LEU* 5.1 17.9 - - + +
1464A LEU* 5.8 4.9 - - + -
1466A ALA* 3.7 32.3 - - + +
1472A SER* 1.3 85.5 + - - +
1474A ARG* 1.3 67.0 + - - +
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Residues in contact with ARG1474 (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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447A PHE* 4.1 12.7 - - - +
1375A LEU* 3.5 9.6 - - - +
1376A VAL* 3.0 29.9 + - - +
1385A TRP* 3.7 39.7 - - + +
1472A SER* 5.0 3.1 - - - +
1473A ILE* 1.3 76.4 - - - +
1475A TRP* 1.3 66.3 + - - +
1476A GLN* 2.7 39.5 + - - +
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Residues in contact with TRP1475 (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* 3.9 18.6 - - + -
1353A THR 5.3 0.2 - - - -
1354A ARG* 3.2 58.0 - - + +
1373A GLU* 3.6 28.0 - - + +
1374A VAL 3.3 22.4 - - - -
1375A LEU* 3.4 38.7 - - + +
1449A PHE* 5.0 15.0 - + - -
1457A LEU* 6.5 0.9 - - + -
1460A LEU* 6.3 2.5 - - + -
1461A ASN* 6.2 2.2 - - - +
1474A ARG* 1.3 85.1 - - - +
1476A GLN* 1.3 72.0 + - - +
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Residues in contact with GLN1476 (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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447A PHE* 3.4 22.4 - - - +
1373A GLU* 3.3 4.4 - - - -
1374A VAL* 2.5 50.6 + - + +
1376A VAL* 3.7 18.6 - - + +
1385A TRP* 5.3 2.4 - - - -
1474A ARG* 2.7 49.6 + - - +
1475A TRP* 1.3 79.2 - - - +
1477A VAL* 1.3 77.8 + - - +
1482A ILE* 6.1 2.9 - - + -
1483A PRO* 5.1 8.9 - - + +
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Residues in contact with VAL1477 (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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1356A ARG* 4.2 37.0 - - - +
1371A MET* 4.4 12.3 - - + -
1372A LEU 3.4 11.0 - - - +
1373A GLU* 4.3 8.6 - - + +
1374A VAL* 5.3 0.8 - - - +
1476A GLN* 1.3 87.5 + - + +
1478A VAL* 1.3 73.9 + - - +
1479A ASP* 3.7 4.6 + - + +
1482A ILE* 4.9 5.7 - - - +
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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