Contacts of the strand formed by residues 1497 - 1504 (chain B) 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 LEU1497 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495B MET 4.2 0.6 + - - +
1496B VAL* 1.3 77.6 - - - +
1498B ASP* 1.3 58.6 + - - +
1499B VAL* 3.5 25.4 - - + -
1534B SER 3.9 1.8 + - - -
1535B ILE* 3.5 21.6 - - + +
1536B HIS 3.0 15.8 + - - +
1597B ARG* 2.9 17.6 + - - +
1600B ALA* 3.8 1.8 - - - +
1601B PRO* 3.3 38.4 - - + +
1602B ASN 4.5 0.2 - - - +
1603B LEU* 4.1 22.4 - - + -
1670B CYS* 3.8 27.6 - - + -
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Residues in contact with ASP1498 (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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1497B LEU* 1.3 70.8 - - - +
1499B VAL* 1.3 61.0 + - - +
1536B HIS* 3.8 10.6 + - - +
1552B PHE* 3.5 21.7 - - + -
1590B PHE* 3.6 4.4 - - + -
1595B GLY 5.0 0.2 - - - +
1596B ASP* 2.8 10.7 - - - +
1597B ARG* 2.9 45.7 + - - +
1600B ALA* 3.7 4.4 - - - +
1601B PRO 2.9 8.3 + - - -
1602B ASN* 3.5 15.2 - - - +
1603B LEU 3.0 24.9 + - - +
4675B CA 2.4 25.2 - - - -
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Residues in contact with VAL1499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497B LEU* 3.5 34.3 - - + -
1498B ASP* 1.3 73.0 - - - +
1500B ALA* 1.3 64.8 + - - +
1501B PHE* 4.0 16.8 - - + -
1528B MET* 4.5 9.2 - - + -
1535B ILE* 3.8 15.7 - - + -
1536B HIS 2.9 12.2 + - - +
1537B VAL* 3.2 7.3 - - + +
1538B THR 2.9 23.9 + - - +
1552B PHE* 3.5 3.3 - - - -
1603B LEU* 3.2 15.5 - - + +
1605B TYR* 3.8 30.5 - - + -
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Residues in contact with ALA1500 (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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1498B ASP 4.1 0.6 + - - -
1499B VAL* 1.3 76.0 - - - +
1501B PHE* 1.3 63.3 + - - +
1502B VAL* 4.7 2.2 - - + -
1538B THR* 3.3 24.2 - - + -
1540B LEU* 6.1 0.4 - - + -
1585B LEU* 3.9 25.4 - - + -
1590B PHE* 3.9 14.1 - - + -
1603B LEU 2.8 8.4 + - - +
1604B VAL* 3.3 6.5 - - + +
1605B TYR 2.9 26.5 + - - +
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Residues in contact with PHE1501 (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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1499B VAL* 4.0 12.6 - - + -
1500B ALA* 1.3 76.1 - - - +
1502B VAL* 1.3 62.5 + - - +
1503B LEU* 4.0 7.9 - - + -
1520B PHE* 4.5 9.9 - + - -
1521B MET* 3.7 47.1 - - + -
1524B VAL* 3.9 26.5 - - + -
1525B ILE* 3.9 27.1 - - + -
1528B MET* 4.2 5.4 - - + -
1537B VAL* 3.8 23.8 - - + -
1538B THR 2.9 8.5 + - - +
1539B VAL* 3.4 2.2 - - + +
1540B LEU 2.9 26.7 + - - +
1605B TYR* 3.5 33.0 - + + +
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Residues in contact with VAL1502 (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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1500B ALA* 4.7 0.9 - - + -
1501B PHE* 1.3 77.5 - - - +
1503B LEU* 1.3 63.2 + - - +
1540B LEU* 3.4 17.0 - - + +
1542B TYR* 3.6 28.0 - - + -
1581B ALA* 4.1 15.7 - - + -
1582B LEU* 6.3 0.7 - - + -
1585B LEU* 3.8 32.8 - - + -
1604B VAL* 4.0 15.9 - - + -
1605B TYR 2.9 10.7 + - - +
1606B MET* 3.3 14.9 - - + +
1607B VAL 2.9 27.0 + - - +
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Residues in contact with LEU1503 (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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1501B PHE* 4.4 14.6 - - + +
1502B VAL* 1.3 82.5 - - - +
1504B GLU* 1.3 63.5 + - - +
1505B GLY 3.4 0.3 + - - -
1514B PHE* 4.1 22.4 - - + -
1517B SER* 4.3 30.1 - - - +
1518B LYS* 4.4 5.2 - - + +
1520B PHE* 5.2 0.2 - - + -
1521B MET* 3.9 33.0 - - + -
1539B VAL* 4.6 5.8 - - + -
1540B LEU 2.9 15.2 + - - +
1541B GLN* 3.3 7.2 - - + +
1542B TYR* 3.0 24.5 + - - -
1568B ILE* 5.9 0.9 - - + -
1607B VAL* 3.7 31.0 - - + -
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Residues in contact with GLU1504 (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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1503B LEU* 1.3 72.4 - - - +
1505B GLY* 1.3 61.8 + - - +
1506B SER* 2.7 25.3 + - - +
1509B ILE* 3.6 27.8 - - + +
1514B PHE* 3.6 11.5 - - - -
1517B SER* 5.1 3.5 + - - -
1542B TYR* 3.5 31.2 - - + +
1576B THR* 2.8 27.1 + - + -
1607B VAL* 3.1 21.4 + - - +
1608B THR* 2.7 24.7 + - - -
1609B GLY 2.8 15.4 + - - -
1610B ASN* 3.0 12.8 + - - -
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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