Contacts of the strand formed by residues 1498 - 1504 (chain A) in PDB entry 3ZQK
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 ASP1498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1497A LEU* 1.3 69.7 - - - +
1499A VAL* 1.3 61.2 + - - +
1536A HIS* 3.8 11.1 + - - +
1552A PHE* 3.6 20.8 - - + -
1590A PHE* 3.6 3.1 - - - -
1595A GLY 5.0 0.3 - - - +
1596A ASP* 3.1 7.1 - - - +
1597A ARG* 2.9 50.1 + - - +
1600A ALA* 3.7 5.8 - - - +
1601A PRO 2.9 9.4 + - - +
1602A ASN* 3.5 14.7 - - - +
1603A LEU 3.0 25.8 + - - +
4675A CA 2.4 26.7 - - - -
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Residues in contact with VAL1499 (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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1497A LEU* 4.0 16.2 - - + -
1498A ASP* 1.3 74.2 - - - +
1500A ALA* 1.3 62.4 + - - +
1501A PHE* 3.7 28.9 - - + -
1528A MET* 4.8 8.7 - - - -
1535A ILE* 3.9 22.2 - - + -
1536A HIS 2.9 15.3 + - - +
1537A VAL* 3.2 7.5 - - + +
1538A THR 2.9 24.1 + - - +
1552A PHE* 3.7 4.3 - - - -
1603A LEU* 3.4 18.6 - - + +
1605A TYR* 4.0 25.8 - - + -
1669A CYS* 5.5 1.6 - - + -
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Residues in contact with ALA1500 (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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1498A ASP 4.0 0.4 + - - -
1499A VAL* 1.3 74.8 - - - +
1501A PHE* 1.3 62.3 + - - +
1502A VAL* 4.7 2.5 - - + -
1538A THR* 3.2 25.4 - - + -
1540A LEU* 6.1 0.4 - - + -
1585A LEU* 3.9 18.2 - - + -
1590A PHE* 3.8 19.3 - - + -
1603A LEU 2.8 11.2 + - - +
1604A VAL* 3.4 8.2 - - + +
1605A TYR* 2.9 26.5 + - - +
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Residues in contact with PHE1501 (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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1499A VAL* 3.7 19.5 - - + -
1500A ALA* 1.3 75.4 - - - +
1502A VAL* 1.3 62.1 + - - +
1503A LEU* 4.2 4.5 - - + -
1520A PHE* 4.6 12.6 - + - -
1521A MET* 3.6 38.1 - - + -
1524A VAL* 3.6 39.3 - - + -
1525A ILE* 3.7 20.9 - - + -
1528A MET* 4.0 10.5 - - + -
1537A VAL* 4.1 19.5 - - + -
1538A THR 2.9 8.4 + - - +
1539A VAL* 3.3 4.5 - - + +
1540A LEU 2.9 24.9 + - - +
1605A TYR* 3.4 31.2 - + + +
1665A VAL* 4.9 0.7 - - + -
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Residues in contact with VAL1502 (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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1500A ALA* 4.7 1.6 - - + -
1501A PHE* 1.3 80.2 - - - +
1503A LEU* 1.3 64.0 + - - +
1540A LEU* 3.4 20.2 - - + -
1542A TYR* 3.5 30.3 - - + -
1581A ALA* 4.3 8.1 - - + -
1585A LEU* 3.9 37.7 - - + -
1604A VAL* 4.0 10.3 - - + -
1605A TYR 3.0 6.3 + - - +
1606A MET* 3.3 21.3 - - + +
1607A VAL 2.9 26.7 + - - -
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Residues in contact with LEU1503 (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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1501A PHE* 5.1 2.5 - - + -
1502A VAL* 1.3 79.9 - - - +
1504A GLU* 1.3 63.9 + - - +
1505A GLY 3.5 0.3 + - - -
1514A PHE* 4.1 25.6 - - + -
1517A SER* 4.0 33.0 - - - +
1518A LYS* 4.1 4.0 - - - +
1520A PHE* 4.8 4.9 - - + -
1521A MET* 3.8 39.3 - - + -
1539A VAL* 5.4 1.1 - - + -
1540A LEU 2.9 14.4 + - - +
1541A GLN* 3.3 6.0 - - + +
1542A TYR* 3.0 26.5 + - - -
1605A TYR 5.5 0.4 - - - +
1607A VAL* 3.6 31.2 - - + -
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Residues in contact with GLU1504 (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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1503A LEU* 1.3 72.9 - - - +
1505A GLY* 1.3 61.0 + - - +
1506A SER* 2.7 18.6 + - - +
1509A ILE* 3.5 30.3 - - + +
1514A PHE* 3.8 11.4 - - - -
1517A SER* 5.1 3.3 + - - -
1542A TYR* 3.5 22.1 - - + +
1576A THR* 2.7 39.9 + - + +
1607A VAL* 3.1 21.1 + - + +
1608A THR* 2.8 25.0 + - - -
1609A GLY 2.9 14.6 + - - -
1610A ASN* 2.9 12.7 + - - -
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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