Contacts of the helix formed by residues 1481 - 1486 (chain A) in PDB entry 5ZCS
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 MET1481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1477A MET* 3.3 25.8 + - + +
1478A LEU 4.4 4.7 - - - +
1479A GLY 3.4 0.4 - - - -
1480A ARG* 1.3 78.9 - - + +
1482A ARG* 1.3 60.8 + - - +
1483A CYS 3.3 0.4 - - - -
1484A LEU* 3.8 6.4 + - - +
1485A GLU* 3.7 14.3 - - - +
1493A LEU* 3.7 28.6 - - + +
1496A GLN* 4.3 21.3 - - + +
1497A CYS* 3.7 38.6 - - - +
1512A MET* 3.7 37.9 - - - +
1515A MET* 4.4 17.5 - - + -
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Residues in contact with ARG1482 (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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1451A GLU* 3.1 28.0 + - - +
1456A TRP* 3.4 45.5 - - + +
1478A LEU* 3.8 16.3 + - - +
1479A GLY* 3.6 15.8 + - - +
1480A ARG 3.2 1.0 - - - -
1481A MET* 1.3 74.2 - - - +
1483A CYS* 1.3 59.4 + - - +
1484A LEU 3.2 2.5 - - - -
1485A GLU* 3.7 22.3 + - + +
1486A ALA* 3.0 39.6 + - + +
1515A MET* 5.5 0.2 - - - -
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Residues in contact with CYS1483 (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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1456A TRP* 3.6 46.2 - - - +
1460A LEU* 4.0 30.3 - - + -
1463A TYR* 4.6 7.9 - - - -
1479A GLY 4.0 4.5 - - - -
1480A ARG* 3.2 21.1 + - - +
1482A ARG* 1.3 78.0 - - - +
1484A LEU* 1.3 65.8 + - + +
1486A ALA 4.6 0.4 - - - -
1487A LEU* 3.5 27.6 - - + +
1489A GLU* 5.6 0.3 - - - +
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Residues in contact with LEU1484 (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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1480A ARG 5.2 3.4 - - - +
1481A MET 3.8 2.3 + - - +
1482A ARG 3.2 0.6 - - - -
1483A CYS* 1.3 86.6 - - + +
1485A GLU* 1.3 59.5 + - - +
1486A ALA 3.6 0.4 - - - -
1487A LEU 4.4 1.1 - - - -
1488A GLY 3.6 0.3 + - - -
1489A GLU* 2.8 63.0 + - + +
1490A TRP* 4.9 0.2 - - - -
1492A GLN* 3.8 22.2 - - + +
1493A LEU* 3.6 38.4 - - + +
1496A GLN* 3.4 35.9 - - - +
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Residues in contact with GLU1485 (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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1481A MET 3.7 14.7 + - - +
1482A ARG* 3.7 27.8 + - + +
1484A LEU* 1.3 77.1 - - - +
1486A ALA* 1.3 64.6 + - - +
1487A LEU 3.5 0.7 - - - -
1488A GLY 4.2 1.3 - - - -
1490A TRP* 3.6 37.6 - - + -
1493A LEU* 3.8 12.8 - - + +
1514A ARG* 4.3 9.6 + - - -
1515A MET* 3.7 34.0 - - - +
1634A GLN* 3.8 18.5 + - - +
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Residues in contact with ALA1486 (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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1456A TRP* 4.2 22.4 - - + +
1482A ARG* 3.0 27.1 + - + +
1485A GLU* 1.3 77.0 - - + +
1487A LEU* 1.3 57.1 + - + +
1631A GLU* 5.4 2.7 - - + +
1634A GLN* 3.8 5.1 - - - +
1665A ARG* 2.6 32.6 + - - -
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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