Contacts of the helix formed by residues 1478 - 1483 (chain D) in PDB entry 4OIR
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 SER1478 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107D VAL 4.9 2.4 + - - -
1108D ARG* 5.7 1.9 - - - -
1217D ILE* 5.1 0.7 - - - +
1218D GLY* 4.0 23.5 + - - -
1473D PRO* 4.2 6.0 + - - -
1474D ALA* 3.7 8.7 + - - +
1475D GLY 3.2 17.7 + - - -
1477D GLY* 1.3 77.9 - - - +
1479D ASP* 1.3 66.7 + - - +
1480D PHE* 2.9 21.2 + - - +
1481D VAL* 3.2 4.7 + - - +
1482D ARG* 3.1 22.0 + - - +
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Residues in contact with ASP1479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473D PRO* 5.8 1.9 - - - +
1477D GLY 3.6 3.0 + - - +
1478D SER* 1.3 72.4 + - - +
1480D PHE* 1.3 63.6 + - - +
1481D VAL 3.6 0.3 + - - -
1482D ARG* 2.7 47.1 + - - +
1483D PHE* 3.4 28.9 - - + -
77E GLU* 5.0 1.4 - - - +
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Residues in contact with PHE1480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108D ARG 5.3 6.7 - - - +
1109D GLU* 5.8 1.6 - - - -
1110D ALA* 5.9 0.9 - - + -
1217D ILE* 4.0 46.9 - - + +
1478D SER* 2.9 14.0 + - - +
1479D ASP* 1.3 81.0 - - - +
1481D VAL* 1.3 74.6 + - + +
14E ASP* 3.1 28.9 - - + -
15E SER* 4.7 3.1 - - - -
18E ARG* 2.9 12.1 + - - -
77E GLU* 2.8 28.3 - - - +
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Residues in contact with VAL1481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217D ILE 4.5 2.7 - - - +
1475D GLY 3.5 25.4 - - - +
1476D THR* 4.4 1.3 - - - -
1478D SER* 3.9 5.2 - - - +
1480D PHE* 1.3 98.4 - - + +
1482D ARG* 1.3 64.1 + - - +
1483D PHE 3.4 2.5 - - - -
1484D THR* 3.0 20.2 + - - -
15E SER* 3.7 17.9 - - - +
17E TYR* 3.8 16.6 - - + +
18E ARG* 3.6 36.9 - - + +
21E VAL* 3.7 14.8 - - + +
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Residues in contact with ARG1482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C HIS* 6.4 0.2 - - + -
4D GLU* 5.5 4.2 + - - -
1471D LEU* 4.9 9.9 - - + +
1476D THR 3.5 18.2 - - - +
1477D GLY* 3.7 23.2 + - - -
1478D SER 3.1 13.5 + - - +
1479D ASP* 2.7 36.4 + - - +
1480D PHE 3.6 1.4 - - - -
1481D VAL* 1.3 78.6 - - - +
1483D PHE* 1.3 97.1 + - + +
1484D THR 3.2 2.2 + - - -
21E VAL* 4.1 7.6 - - + +
25E LYS* 3.5 17.7 + - - -
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Residues in contact with PHE1483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479D ASP* 3.4 31.8 + - + -
1480D PHE 4.9 0.8 + - - -
1481D VAL 3.4 0.6 - - - -
1482D ARG* 1.3 121.6 - - + +
1484D THR* 1.3 65.5 + - - +
1485D GLN* 3.5 12.5 + - - +
25E LYS* 4.0 3.7 + - - +
77E GLU* 4.2 25.5 - - + +
78E ASN 4.8 1.2 + - - -
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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