Contacts of the strand formed by residues 1497 - 1504 (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 LEU1497 (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 4.0 1.1 + - - +
1496C VAL* 1.3 78.0 - - - +
1498C ASP* 1.3 57.4 + - - +
1499C VAL* 3.6 25.1 - - + -
1528C MET* 5.0 4.5 - - + -
1534C SER 3.9 1.8 + - - -
1535C ILE* 3.5 24.8 - - + +
1536C HIS 2.9 16.8 + - - +
1597C ARG* 2.9 18.2 + - - +
1600C ALA* 3.8 2.2 - - - +
1601C PRO* 3.2 38.6 - - + +
1603C LEU* 4.1 28.3 - - + -
1669C CYS* 5.7 1.6 - - + -
1670C CYS* 5.6 5.4 - - - -
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Residues in contact with ASP1498 (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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1497C LEU* 1.3 70.3 - - - +
1499C VAL* 1.3 60.6 + - - +
1500C ALA 4.0 0.2 + - - -
1536C HIS* 3.8 11.0 + - - +
1552C PHE* 3.4 22.6 - - + -
1590C PHE* 4.1 1.6 - - - -
1595C GLY 5.0 0.2 - - - +
1596C ASP* 2.9 10.6 - - - +
1597C ARG* 2.9 45.6 + - - +
1600C ALA* 3.7 4.4 - - - +
1601C PRO 2.9 9.1 + - - -
1602C ASN* 3.4 15.0 - - - +
1603C LEU 3.0 24.3 + - - +
4675C CA 2.3 26.7 - - - -
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Residues in contact with VAL1499 (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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1497C LEU* 3.6 34.1 - - + -
1498C ASP* 1.3 72.1 - - - +
1500C ALA* 1.3 62.1 + - - +
1501C PHE* 4.0 17.4 + - + -
1528C MET* 4.4 9.0 - - + -
1535C ILE* 3.8 15.9 - - + -
1536C HIS 2.9 11.6 + - - +
1537C VAL* 3.3 9.1 - - + +
1538C THR 2.9 24.8 + - - +
1552C PHE* 3.4 3.0 - - - -
1603C LEU* 3.3 14.4 - - + +
1605C TYR* 3.8 33.0 - - + -
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Residues in contact with ALA1500 (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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1498C ASP 4.0 0.6 + - - -
1499C VAL* 1.3 77.1 - - - +
1501C PHE* 1.3 59.4 + - - +
1502C VAL* 4.0 2.0 - - + -
1538C THR* 3.4 24.5 - - + -
1540C LEU* 6.1 0.2 - - + -
1585C LEU* 3.7 25.4 - - + -
1590C PHE* 4.1 10.1 - - + -
1603C LEU 2.8 12.1 + - - +
1604C VAL* 3.4 7.8 - - + -
1605C TYR* 2.8 31.5 + - - +
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Residues in contact with PHE1501 (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* 4.0 13.7 - - + -
1500C ALA* 1.3 73.8 - - - +
1502C VAL* 1.3 59.2 + - - +
1503C LEU* 4.1 7.0 - - + -
1520C PHE* 4.0 22.4 - + - -
1521C MET* 3.5 42.2 - - + -
1524C VAL* 3.9 26.0 - - + -
1525C ILE* 3.8 27.1 - - + -
1528C MET* 5.3 2.0 - - - -
1537C VAL* 3.9 21.8 - - + -
1538C THR 2.9 11.1 + - - +
1539C VAL* 3.3 1.8 - - + +
1540C LEU* 2.8 32.7 + - - +
1605C TYR* 3.5 33.0 - + + +
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Residues in contact with VAL1502 (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* 4.6 1.3 - - + -
1501C PHE* 1.3 79.8 - - - +
1503C LEU* 1.3 60.5 + - - +
1540C LEU* 3.6 16.4 - - + -
1542C TYR* 3.6 28.0 - - + -
1581C ALA* 4.0 15.9 - - + -
1585C LEU* 3.6 40.4 - - + -
1604C VAL* 4.1 9.4 - - + -
1605C TYR 2.9 10.6 + - - +
1606C MET* 3.3 19.4 - - + +
1607C VAL 2.9 27.4 + - - +
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Residues in contact with LEU1503 (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* 4.6 10.1 - - + -
1502C VAL* 1.3 81.0 - - - +
1504C GLU* 1.3 63.0 + - - +
1505C GLY 3.4 0.5 + - - -
1514C PHE* 3.9 29.4 - - + -
1517C SER* 4.1 26.0 - - - +
1518C LYS* 4.5 2.2 - - + +
1520C PHE* 5.3 0.9 - - + -
1521C MET* 3.4 35.9 - - + -
1539C VAL* 4.5 6.1 - - + -
1540C LEU 2.9 14.8 + - - +
1541C GLN* 3.3 5.1 - - - +
1542C TYR* 2.9 27.2 + - - -
1568C ILE* 5.8 1.1 - - + -
1607C VAL* 3.8 31.6 - - + -
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Residues in contact with GLU1504 (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* 1.3 73.2 - - - +
1505C GLY* 1.3 59.7 + - - +
1506C SER* 2.7 25.9 + - - +
1509C ILE* 3.5 27.2 - - + +
1514C PHE* 3.5 12.3 - - - -
1517C SER* 5.1 3.3 + - - -
1542C TYR* 3.5 24.6 - - + +
1576C THR* 2.8 31.8 + - + -
1607C VAL* 3.1 20.5 + - - +
1608C THR* 2.7 24.3 + - - -
1609C GLY 2.9 13.7 + - - -
1610C ASN* 2.8 14.5 + - - -
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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