Contacts of the helix formed by residues 1473 - 1478 (chain A) in PDB entry 3I08
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 CYS1473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1450A CYS* 2.1 51.6 - - - -
1451A GLU 4.4 2.2 - - - -
1452A LEU 5.4 0.7 - - - -
1455A CYS* 4.0 18.8 - - + +
1459A ALA* 5.1 3.3 - - - +
1467A GLN 5.4 0.2 - - - -
1468A CYS* 3.5 18.2 - - + +
1470A ASN* 3.0 25.0 + - - +
1472A ALA* 1.3 73.7 - - - +
1474A GLY* 1.3 62.3 + - - +
1475A TRP 3.2 2.2 - - - -
1476A ASP* 3.2 3.7 + - - +
1477A GLY* 3.2 17.0 + - - -
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Residues in contact with GLY1474 (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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1471A HIS 3.1 13.4 + - - -
1472A ALA 3.3 1.8 + - - -
1473A CYS* 1.3 77.8 - - - +
1475A TRP* 1.3 74.3 + - - +
1477A GLY* 3.3 3.7 + - - -
1478A GLY* 3.0 19.4 + - - -
1485A ASN* 5.2 0.3 + - - -
1486A ASP* 3.7 27.2 + - - +
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Residues in contact with TRP1475 (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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1468A CYS 3.9 0.9 - - - -
1469A ASN* 3.3 32.3 - - - +
1470A ASN* 3.0 31.5 + - - +
1471A HIS* 3.5 29.2 - - + +
1474A GLY* 1.3 81.9 - - - +
1476A ASP* 1.3 62.4 + - - +
1478A GLY* 3.2 4.5 + - - -
1480A CYS* 3.0 28.0 + - + -
1481A SER* 4.2 16.4 - - - +
1486A ASP* 4.5 1.6 - - - -
1487A PRO* 3.7 21.1 - - + -
1488A TRP* 3.5 24.5 - + - -
1498A TRP* 3.7 26.0 - + + -
1668A CL 3.3 23.0 - - + +
1709B SER* 4.1 19.3 - - - -
1710B LEU* 5.8 4.5 - - + -
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Residues in contact with ASP1476 (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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1A CA 2.3 29.8 - - - -
1455A CYS 4.6 0.5 - - - +
1458A ASP* 3.5 2.4 - - - +
1459A ALA* 3.4 17.2 + - - +
1460A GLY 3.4 1.6 + - - -
1463A VAL 2.6 15.1 - - - +
1464A CYS* 3.8 0.2 - - - -
1465A SER* 3.4 6.5 + - - +
1468A CYS* 3.0 40.4 + - + +
1473A CYS* 3.2 5.0 + - - -
1475A TRP* 1.3 74.9 - - - +
1477A GLY* 1.3 54.4 + - - +
1478A GLY 2.9 4.7 - - - -
1479A ASP* 2.6 34.1 + - + +
1480A CYS* 3.9 11.4 - - - -
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Residues in contact with GLY1477 (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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1459A ALA* 4.0 18.5 - - - +
1460A GLY* 4.2 10.0 - - - -
1473A CYS 3.2 12.7 + - - -
1474A GLY* 3.3 5.8 + - - -
1476A ASP* 1.3 72.8 - - - +
1478A GLY* 1.3 52.4 + - - +
1479A ASP 3.4 0.6 + - - -
1483A ASN* 5.5 1.0 + - - -
1485A ASN* 2.6 29.3 + - - -
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Residues in contact with GLY1478 (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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1474A GLY 3.0 10.0 + - - -
1475A TRP 3.2 2.7 + - - -
1476A ASP 2.9 1.4 - - - -
1477A GLY* 1.3 80.6 - - - +
1479A ASP* 1.3 62.7 + - - +
1480A CYS 3.0 3.2 + - - -
1481A SER* 3.1 21.8 + - - -
1483A ASN* 2.8 34.3 + - - -
1484A PHE 3.8 9.6 - - - -
1485A ASN* 4.0 2.2 - - - -
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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