Contacts of the strand formed by residues 1535 - 1542 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1495C MET 4.1 12.8 - - - +
1497C LEU* 3.5 29.2 - - + +
1499C VAL* 3.8 18.8 - - + -
1528C MET* 4.2 18.6 - - + -
1529C ASP* 3.4 38.8 - - + +
1530C VAL* 3.3 20.7 - - + +
1531C GLY 3.0 24.1 + - - +
1534C SER* 1.3 81.9 + - - +
1536C HIS* 1.3 69.8 + - - +
1537C VAL* 4.9 0.2 - - + -
1670C CYS* 5.2 7.6 - - - -
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Residues in contact with HIS1536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1560A ASP* 5.9 0.2 - - - -
1497C LEU 2.9 7.3 + - - +
1498C ASP* 3.8 8.8 + - - +
1499C VAL* 2.9 27.0 + - - +
1531C GLY 3.3 17.7 - - - -
1532C GLN* 2.7 46.8 + - - -
1535C ILE* 1.3 75.4 - - - +
1537C VAL* 1.3 66.0 + - - +
1552C PHE* 3.9 17.8 + - + -
1556C GLN* 3.3 23.2 - - + +
1595C GLY 4.6 7.0 + - - -
1597C ARG* 3.3 43.9 + - + +
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Residues in contact with VAL1537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1499C VAL* 3.3 7.6 - - + +
1501C PHE* 3.9 16.4 - - + -
1525C ILE* 3.8 33.7 - - + -
1528C MET* 5.7 1.6 - - - -
1530C VAL* 3.9 25.8 - - + -
1535C ILE* 4.9 0.7 - - + -
1536C HIS* 1.3 80.7 - - - +
1538C THR* 1.3 70.5 + - - +
1539C VAL* 4.0 11.0 - - + -
1550C TYR* 3.9 9.8 - - + -
1552C PHE* 3.6 7.3 - - - -
1556C GLN* 2.8 31.6 + - - +
1561C ILE* 4.3 16.4 - - + -
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Residues in contact with THR1538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1499C VAL 2.9 8.1 + - - +
1500C ALA* 3.4 27.1 - - + -
1501C PHE 2.9 24.8 + - - -
1537C VAL* 1.3 75.9 - - - +
1539C VAL* 1.3 70.0 + - - +
1540C LEU* 5.3 2.8 - - + +
1548C VAL* 4.8 3.8 - - - +
1550C TYR* 2.6 20.5 + - - -
1551C PRO* 3.6 8.0 - - - +
1552C PHE* 3.4 33.6 + - + -
1585C LEU* 5.0 0.9 - - + -
1589C SER* 4.6 17.2 + - - +
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Residues in contact with VAL1539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501C PHE* 3.3 7.0 - - + +
1503C LEU* 4.5 5.8 - - + -
1521C MET* 3.7 27.8 - - + -
1537C VAL* 4.0 15.0 - - + -
1538C THR* 1.3 81.5 + - - +
1540C LEU* 1.3 68.3 + - - +
1548C VAL* 3.7 2.9 - - - +
1549C GLU* 2.8 40.1 + - + -
1550C TYR* 3.0 22.4 + - + +
1565C LEU* 3.7 22.7 - - + -
1568C ILE* 4.0 18.2 - - + -
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Residues in contact with LEU1540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500C ALA* 6.1 0.2 - - + -
1501C PHE 2.8 11.2 + - - +
1502C VAL* 4.2 16.6 - - + -
1503C LEU* 2.9 30.4 + - - +
1538C THR* 5.3 4.9 - - + +
1539C VAL* 1.3 81.6 - - - +
1541C GLN* 1.3 59.9 + - - +
1546C VAL* 3.7 25.8 - - + -
1547C THR 3.3 4.3 - - - +
1548C VAL* 3.6 38.8 - - + -
1549C GLU* 4.5 0.2 - - - -
1581C ALA 4.1 6.5 - - - +
1584C TYR* 4.0 6.7 - - + -
1585C LEU* 3.9 33.4 - - + -
1589C SER* 3.8 15.9 - - - +
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Residues in contact with GLN1541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503C LEU* 3.3 11.0 - - + +
1505C GLY* 3.6 14.2 - - - -
1514C PHE* 3.5 33.2 - - + -
1540C LEU* 1.3 75.3 - - - +
1542C TYR* 1.3 67.2 + - - +
1545C MET 3.9 0.7 - - - +
1546C VAL* 3.6 1.6 - - - +
1547C THR* 2.8 32.9 + - - +
1549C GLU* 2.9 33.4 + - + +
1568C ILE* 4.1 0.2 - - - +
1569C ARG 3.0 19.8 + - - -
1570C TYR* 3.7 0.5 - - - -
1571C GLN* 2.9 40.8 + - - +
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Residues in contact with TYR1542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1502C VAL* 3.6 30.3 - - + -
1503C LEU 2.9 15.5 + - - -
1504C GLU* 3.5 26.2 - - + +
1505C GLY 2.8 29.1 + - - -
1506C SER 4.0 0.3 + - - -
1541C GLN* 1.3 78.9 - - - +
1543C SER* 1.3 63.2 + - - +
1545C MET 3.4 9.9 - - - +
1546C VAL* 4.2 10.3 - - + -
1571C GLN* 5.8 0.4 - - - -
1576C THR* 4.0 8.1 - - + +
1577C ASN* 3.7 24.7 - - + +
1578C THR* 2.9 43.8 + - + +
1581C ALA* 3.7 15.7 - - + -
1606C MET* 4.4 5.1 - - + -
1608C THR* 3.4 24.9 + - - -
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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