Contacts of the strand formed by residues 1535 - 1542 (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 ILE1535 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495B MET 4.5 8.3 - - - +
1497B LEU* 3.5 30.3 - - + +
1499B VAL* 3.8 27.4 - - + -
1528B MET* 4.2 13.5 - - + -
1529B ASP* 3.1 40.0 + - + +
1530B VAL* 3.4 20.0 - - + +
1531B GLY 3.0 24.4 + - - +
1534B SER* 1.3 81.5 - - - +
1536B HIS* 1.3 64.2 + - - +
1556B GLN* 4.3 0.2 - - - +
1670B CYS* 4.4 15.3 - - + -
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Residues in contact with HIS1536 (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 3.0 6.7 + - - +
1498B ASP* 3.9 3.1 + - - +
1499B VAL* 2.9 28.4 + - - +
1531B GLY 3.2 19.3 + - - -
1532B GLN* 2.7 36.0 + - - -
1534B SER 3.7 0.9 - - - -
1535B ILE* 1.3 74.8 - - - +
1537B VAL* 1.3 64.0 + - - +
1552B PHE* 3.8 18.7 + - + -
1556B GLN* 3.2 32.6 - - + +
1595B GLY 4.8 5.4 + - - -
1597B ARG* 3.3 44.1 + - + +
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Residues in contact with VAL1537 (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* 3.2 5.2 - - + +
1501B PHE* 3.8 24.5 - - + -
1525B ILE* 4.1 21.3 - - + -
1528B MET* 4.6 4.0 - - + -
1530B VAL* 3.9 30.5 - - + -
1535B ILE* 4.9 0.2 - - + -
1536B HIS* 1.3 77.7 - - - +
1538B THR* 1.3 73.1 + - - +
1539B VAL* 3.9 12.8 - - + -
1550B TYR* 3.8 10.4 - - + -
1551B PRO 4.1 0.9 - - - +
1552B PHE* 3.5 6.3 - - - -
1556B GLN* 2.8 29.1 + - - +
1561B ILE* 4.6 8.7 - - + -
1565B LEU* 4.7 2.9 - - + -
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Residues in contact with THR1538 (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 2.9 6.5 + - - +
1500B ALA* 3.5 20.2 - - + -
1501B PHE 2.9 24.7 + - - -
1537B VAL* 1.3 76.3 - - - +
1539B VAL* 1.3 68.3 + - - +
1540B LEU* 5.4 3.1 - - + +
1548B VAL* 4.8 3.3 - - - +
1550B TYR 2.6 19.8 + - - -
1551B PRO* 3.6 8.5 - - - +
1552B PHE* 3.4 41.4 + - + -
1585B LEU* 5.4 0.4 - - + -
1589B SER* 4.5 17.9 + - - -
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Residues in contact with VAL1539 (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* 3.4 9.0 - - + +
1503B LEU* 4.6 5.8 - - + -
1521B MET* 3.7 33.2 - - + -
1537B VAL* 3.9 13.5 - - + -
1538B THR* 1.3 81.6 + - - +
1540B LEU* 1.3 69.5 + - - +
1548B VAL* 3.8 2.9 - - - +
1549B GLU* 2.8 43.4 + - + -
1550B TYR* 2.9 21.0 + - + +
1565B LEU* 3.8 19.1 - - + -
1568B ILE* 4.1 9.6 - - + -
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Residues in contact with LEU1540 (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* 6.1 0.4 - - + +
1501B PHE 2.9 9.5 + - - +
1502B VAL* 3.4 16.7 - - + -
1503B LEU* 2.9 27.4 + - - +
1538B THR* 5.4 4.9 - - + +
1539B VAL* 1.3 82.7 - - - +
1541B GLN* 1.3 60.3 + - - +
1542B TYR* 5.9 0.2 - - + -
1546B VAL* 3.9 23.8 - - + -
1547B THR 3.4 4.0 - - - +
1548B VAL* 3.6 38.6 - - + -
1549B GLU* 4.5 0.2 - - - -
1581B ALA* 4.2 8.1 - - + +
1584B TYR* 4.0 8.3 - - + -
1585B LEU* 3.6 33.4 - - + -
1589B SER* 3.7 16.2 - - - +
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Residues in contact with GLN1541 (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* 3.3 12.6 - - + +
1505B GLY* 3.7 10.6 - - - -
1514B PHE* 3.4 33.4 - - + -
1539B VAL* 6.1 0.2 - - + -
1540B LEU* 1.3 75.6 - - - +
1542B TYR* 1.3 65.0 + - - +
1546B VAL* 3.5 1.2 - - - +
1547B THR 2.8 32.7 + - - +
1549B GLU* 3.0 31.2 + - + +
1568B ILE* 4.0 0.4 - - - +
1569B ARG 3.1 20.0 + - - -
1570B TYR* 3.6 0.9 - - - -
1571B GLN* 2.8 49.7 + - + +
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Residues in contact with TYR1542 (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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1502B VAL* 3.6 30.1 - - + -
1503B LEU 3.0 12.8 + - - -
1504B GLU* 3.5 25.4 - - + +
1505B GLY 2.8 28.9 + - - -
1540B LEU* 5.9 0.2 - - + -
1541B GLN* 1.3 76.2 - - - +
1543B SER* 1.3 62.8 + - - +
1545B MET 3.3 9.6 - - - +
1546B VAL* 4.2 8.7 - - + -
1571B GLN* 3.8 3.8 - - - +
1576B THR* 3.7 12.9 - - + +
1577B ASN* 3.5 20.6 - - + +
1578B THR* 2.8 43.9 + - + +
1581B ALA* 3.6 16.2 - - + -
1606B MET* 4.7 4.9 - - + -
1607B VAL 4.7 2.5 - - - -
1608B THR* 3.3 24.4 + - - -
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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