Contacts of the strand formed by residues 1491 - 1495 (chain B) in PDB entry 1OFD
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 PHE1491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411B VAL* 4.9 0.4 - - + -
1412B VAL 4.6 1.8 - - - -
1413B LEU* 3.9 24.7 - - + -
1430B TYR* 4.4 3.6 - - + -
1431B PHE 3.3 13.9 - - - -
1432B LEU* 3.5 41.7 - - + -
1451B ARG* 3.0 29.7 + - - -
1452B ILE* 3.6 17.6 + - + -
1461B LEU* 3.8 34.3 - - + -
1465B ILE* 4.0 10.5 - - + -
1480B ILE* 4.3 19.5 - - + -
1484B TRP* 5.0 1.8 - + - -
1487B TYR* 3.3 25.1 - - + -
1488B LEU* 3.2 18.7 + - - +
1490B LYS* 1.3 80.0 - - - +
1492B TRP* 1.3 59.7 + - - +
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Residues in contact with TRP1492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429B ALA 3.9 0.3 - - - +
1430B TYR* 3.5 4.5 - - - +
1431B PHE* 2.8 31.6 + - - +
1433B ASP* 4.1 14.2 + - + +
1436B GLY* 5.5 3.6 + - - -
1438B LEU* 3.8 31.2 - - + +
1439B PRO* 4.0 30.4 - - + +
1449B LEU* 3.7 30.3 - - + -
1450B GLN* 3.5 31.9 - - - -
1451B ARG* 3.4 63.2 - - + +
1452B ILE* 5.2 1.1 - - - -
1491B PHE* 1.3 74.9 - - - +
1493B GLN* 1.3 60.9 + - - +
1494B ALA 4.0 0.3 + - - -
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Residues in contact with GLN1493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428B LEU* 4.0 7.5 - - + +
1429B ALA 3.5 6.7 - - - +
1430B TYR* 3.0 37.3 + - + -
1448B THR 3.5 2.3 - - - +
1449B LEU* 3.4 5.5 - - - -
1450B GLN* 2.7 68.7 + - - +
1451B ARG 4.7 4.2 + - - -
1452B ILE* 4.1 19.7 - - + +
1453B THR 5.3 2.0 - - - +
1454B ALA 5.9 0.6 - - - +
1457B GLY* 4.3 0.7 - - - -
1492B TRP* 1.3 72.8 - - - +
1494B ALA* 1.3 63.2 + - - +
1495B VAL* 3.8 12.1 - - + +
1504B GLU 3.0 18.6 + - - +
1505B ALA* 3.8 12.1 + - - +
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Residues in contact with ALA1494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B MET* 3.6 22.0 - - + +
1428B LEU* 3.5 12.5 - - - +
1429B ALA* 2.8 33.5 + - + +
1431B PHE* 4.0 20.6 - - + -
1447B ILE* 4.0 8.1 - - + -
1448B THR 3.5 4.9 - - - -
1449B LEU* 4.0 13.6 - - + +
1492B TRP 4.0 1.2 + - - -
1493B GLN* 1.3 70.7 - - - +
1495B VAL* 1.3 59.4 + - - +
1496B PRO* 3.8 3.8 - - - +
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Residues in contact with VAL1495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428B LEU* 4.0 4.3 - - + -
1447B ILE* 3.7 2.6 - - - +
1448B THR* 2.7 42.1 + - - +
1450B GLN* 3.8 27.4 - - + +
1493B GLN* 3.8 29.2 - - + +
1494B ALA* 1.3 79.0 - - - +
1496B PRO* 1.3 77.0 - - + +
1497B PRO* 4.0 0.9 - - - +
1499B GLU* 3.9 20.9 - - + -
1500B LYS* 4.0 9.8 - - + +
1505B ALA* 4.0 11.7 - - + -
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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