Contacts of the helix formed by residues 1485 - 1489 (chain B) in PDB entry 4ZLP
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 ASP1485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474A TYR* 4.3 3.4 - - - +
1484A CYS 4.1 1.8 - - - -
1485A ASP* 3.9 3.1 - - - +
1486A GLN* 3.6 1.3 + - - -
1487A GLY* 2.9 19.2 + - - -
1474B TYR* 2.6 37.0 + - + +
1478B HIS* 3.5 16.3 - - - +
1481B ASP* 3.9 3.3 - - - +
1483B ARG* 3.1 5.4 - - - +
1484B CYS* 1.3 73.6 - - - +
1486B GLN* 1.3 66.0 + - - +
1487B GLY 3.1 2.2 - - - -
1488B CYS* 2.9 16.6 + - + +
1489B ASN* 3.3 7.8 + - - +
1496B ASP* 2.7 20.6 + - - +
1500B CYS* 4.3 2.0 - - - -
5003B CA 2.4 29.8 - - - -
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Residues in contact with GLN1486 (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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1483A ARG* 3.7 47.0 + - + +
1484A CYS* 3.2 36.1 + - + +
1485A ASP* 3.5 1.7 + - - +
1484B CYS* 3.4 22.4 - - - -
1485B ASP* 1.3 71.8 - - - +
1487B GLY* 1.3 58.3 + - - +
1489B ASN* 3.0 51.0 + - - +
1490B THR* 5.4 1.6 - - - +
1500B CYS* 4.2 2.2 - - - +
5005B GOL 5.4 2.0 + - - -
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Residues in contact with GLY1487 (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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1474A TYR* 3.0 19.6 - - - -
1478A HIS* 3.9 21.4 + - - -
1481A ASP* 5.8 0.2 - - - -
1485A ASP* 2.9 13.3 + - - -
1471B TYR* 5.4 4.0 - - - +
1475B CYS* 4.6 1.7 - - - -
1485B ASP 3.0 0.2 + - - -
1486B GLN* 1.3 76.2 - - - +
1488B CYS* 1.3 58.9 + - - +
1489B ASN 3.4 0.2 - - - -
1490B THR* 5.1 6.0 + - - +
1493B CYS* 4.8 6.9 - - - -
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Residues in contact with CYS1488 (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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1474A TYR* 3.6 5.1 + - - -
1474B TYR* 3.6 22.4 - - - -
1475B CYS* 2.0 61.9 - - + +
1478B HIS* 5.7 0.2 - - - -
1485B ASP* 2.9 13.2 + - + +
1487B GLY* 1.3 75.9 - - - +
1489B ASN* 1.3 55.6 + - - +
1490B THR 2.9 12.4 + - - -
1493B CYS* 3.5 16.2 - - + +
1495B TRP 3.8 0.7 + - - -
1496B ASP* 3.4 27.8 + - + +
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Residues in contact with ASN1489 (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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1485B ASP 3.3 3.4 + - - +
1486B GLN* 3.0 44.8 + - - +
1487B GLY 3.4 0.6 - - - -
1488B CYS* 1.3 74.8 - - - +
1490B THR* 1.3 64.6 + - - +
1495B TRP* 3.4 31.0 - - - +
1496B ASP* 4.4 0.7 - - - +
1500B CYS* 3.6 20.9 - - - +
5005B GOL 3.0 40.2 + - - -
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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