Contacts of the helix formed by residues 1498 - 1503 (chain A) in PDB entry 4YOC
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 TRP1498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1455A LEU* 3.8 18.2 - - + -
1475A VAL* 3.2 40.0 + - + +
1476A CYS* 4.0 16.6 - - + -
1486A ASP 5.8 0.4 - - - -
1489A ALA 3.4 6.2 + - - -
1490A ARG* 3.5 41.1 - - + -
1491A GLN* 3.5 46.7 - - + +
1494A THR* 3.7 4.1 + - - +
1496A ILE 3.2 4.2 + - - -
1497A PRO* 1.3 71.4 - - - +
1499A CYS* 1.3 67.9 + - + +
1500A LEU 3.0 0.5 + - - -
1501A PRO* 3.3 4.9 - - - +
1502A HIS* 2.9 75.6 + + - +
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Residues in contact with CYS1499 (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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1497A PRO* 3.2 6.8 - - - -
1498A TRP* 1.3 93.6 - - + +
1500A LEU* 1.3 70.8 + - - +
1502A HIS* 3.6 6.0 - - - +
1503A THR* 3.4 27.6 + - + +
1510A TRP* 4.2 1.2 + - - -
1533A MET* 3.5 32.1 - - - -
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Residues in contact with LEU1500 (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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1436A TRP* 3.5 54.3 - - + -
1497A PRO* 3.2 28.7 + - + +
1498A TRP 3.0 0.8 + - - -
1499A CYS* 1.3 88.6 - - - +
1501A PRO* 1.3 69.0 - - + +
1502A HIS 3.1 0.9 - - - -
1504A GLY* 2.9 29.6 + - - -
1510A TRP* 3.4 31.2 - - + +
1513A LEU* 4.0 17.0 - - + -
1514A TYR* 4.8 1.3 - - + -
1533A MET* 4.3 13.5 - - + -
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Residues in contact with PRO1501 (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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971A GLU* 3.5 38.8 - - + +
974A ARG* 3.8 22.3 + - - +
1436A TRP* 3.8 8.1 - - + -
1455A LEU* 4.2 13.0 - - + -
1457A TYR* 5.1 0.9 - - + -
1473A ARG 5.2 3.0 - - - +
1475A VAL* 4.0 20.3 + - + +
1479A VAL* 5.7 3.8 - - - +
1496A ILE* 4.5 0.7 - - + -
1497A PRO 2.9 27.8 - - - +
1498A TRP 3.3 5.2 - - - +
1500A LEU* 1.3 80.4 - - + +
1502A HIS* 1.3 64.0 + - - +
1503A THR 3.5 0.2 + - - -
1504A GLY 3.6 4.9 + - - -
1505A ASN* 5.5 2.1 + - - -
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Residues in contact with HIS1502 (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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1475A VAL* 3.5 10.5 - - + +
1476A CYS* 3.7 9.0 - - + -
1478A CYS* 3.3 16.0 - - - -
1479A VAL* 5.5 5.1 - - + +
1485A CYS* 4.2 8.5 - - - -
1498A TRP* 2.9 56.7 + + + +
1499A CYS* 3.6 9.0 + - - +
1500A LEU 3.1 0.4 - - - -
1501A PRO* 1.3 78.8 - - - +
1503A THR* 1.3 74.5 + - + +
1505A ASN* 5.5 0.3 + - - -
1701A ZN 2.2 35.8 - - - -
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Residues in contact with THR1503 (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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1499A CYS* 3.4 13.0 + - + +
1500A LEU 3.8 0.2 - - - -
1502A HIS* 1.3 97.8 - - + +
1504A GLY* 1.3 63.0 + - - +
1505A ASN 3.5 2.0 - - - -
1506A ARG* 3.4 10.7 + - - +
1507A HIS* 2.8 32.7 + - + -
1510A TRP* 2.7 31.4 + - - -
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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