Contacts of the helix formed by residues 1433 - 1441 (chain D) in PDB entry 4OIN
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 SER1433 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1431D THR* 3.4 16.3 + - - +
1432D LYS* 1.3 77.8 - - - +
1434D TRP* 1.3 60.7 + - - +
1436D SER* 3.2 13.7 + - - -
1437D ALA* 3.3 15.9 + - - +
1457D ASP* 2.8 29.1 + - - +
1460D ILE* 6.3 0.7 - - - -
1464D GLU* 3.1 33.2 - - - +
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Residues in contact with TRP1434 (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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1088C LEU* 6.3 0.2 - - + -
1092C LEU* 5.0 7.2 - - + -
1099C VAL* 4.1 15.7 - - + -
8D VAL* 3.2 43.4 + - + -
9D ARG 4.5 0.2 - - - -
10D ILE* 3.5 30.1 - - + -
614D PHE* 5.4 3.1 - + - -
1431D THR 5.6 0.2 - - - -
1432D LYS 3.4 3.2 + - - -
1433D SER* 1.3 71.2 - - - +
1435D LEU* 1.3 90.5 + - + +
1436D SER 3.3 0.2 - - - -
1437D ALA* 4.6 0.9 - - - -
1438D ALA* 2.9 34.5 + - + +
1446D VAL* 3.8 10.8 - - + +
1447D LEU* 3.7 28.7 - - + -
1450D ALA* 3.8 20.0 - - + -
1455D LYS* 3.5 38.0 + - + +
1456D LYS 4.3 0.2 - - - -
1457D ASP* 3.3 18.5 + - + +
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Residues in contact with LEU1435 (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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1085C PHE* 5.1 3.6 - - + -
1088C LEU* 4.9 6.3 - - + -
8D VAL* 4.4 10.3 - - + -
614D PHE* 4.6 10.3 - - + -
1434D TRP* 1.3 110.0 - - + +
1436D SER* 1.3 51.9 + - - +
1438D ALA* 4.2 1.9 - - - +
1439D SER* 2.7 40.8 + - - -
1457D ASP* 3.0 28.3 + - + +
1459D LEU* 4.0 12.1 - - + -
1464D GLU* 4.1 10.5 - - + -
1467D ILE* 3.9 29.3 - - + +
1468D LEU* 3.9 24.5 - - + -
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Residues in contact with SER1436 (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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1100D ASP* 4.2 6.3 + - - -
1103D HIS* 2.9 31.7 + - - -
1431D THR* 4.4 9.5 - - - +
1433D SER* 3.2 23.7 + - - -
1435D LEU* 1.3 80.1 - - - +
1437D ALA* 1.3 57.7 + - - +
1439D SER* 3.0 4.4 + - - -
1440D PHE* 2.9 25.3 + - - +
1463D LYS* 2.9 25.8 + - - +
1464D GLU* 4.2 6.8 - - - +
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Residues in contact with ALA1437 (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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1428D ALA 4.0 14.4 - - - +
1429D LEU* 3.8 24.3 - - - +
1431D THR* 4.2 3.5 - - + +
1433D SER 3.3 14.0 + - - +
1434D TRP* 4.6 0.7 - - - -
1435D LEU 3.4 0.2 - - - -
1436D SER* 1.3 79.9 - - - +
1438D ALA* 1.3 57.4 + - - +
1440D PHE* 2.9 22.8 + - - +
1441D GLN 3.2 16.1 + - - +
1446D VAL* 3.7 22.0 - - + -
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Residues in contact with ALA1438 (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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614D PHE* 4.1 9.6 - - + -
1434D TRP* 2.9 20.5 + - + +
1435D LEU 4.2 1.6 - - - +
1437D ALA* 1.3 77.1 - - - +
1439D SER* 1.3 60.2 + - - +
1440D PHE 3.6 0.2 + - - -
1441D GLN 4.0 1.7 + - - -
1443D THR* 2.9 36.0 + - + +
1446D VAL* 3.5 15.8 - - + +
1447D LEU* 3.6 33.7 - - + -
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Residues in contact with SER1439 (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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614D PHE* 3.7 34.6 - - - +
615D ARG* 3.9 13.7 - - - +
619D LEU* 3.9 9.2 - - - +
1096D ARG* 3.6 8.8 + - - -
1435D LEU 2.7 23.4 + - - -
1436D SER* 3.0 8.7 + - - -
1438D ALA* 1.3 74.8 - - - +
1440D PHE* 1.3 65.4 + - - +
1443D THR* 5.4 0.2 - - - -
1463D LYS* 3.0 19.8 + - - -
1467D ILE* 3.8 9.7 - - - +
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Residues in contact with PHE1440 (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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615D ARG* 4.8 2.1 + - - -
1096D ARG* 2.7 47.4 + - + +
1097D LYS* 4.1 25.8 - - + -
1100D ASP* 3.2 43.3 - - + +
1425D THR* 3.7 35.7 - - + -
1428D ALA* 4.0 9.0 - - + -
1429D LEU* 3.6 28.0 - - + -
1436D SER 2.9 7.7 + - - +
1437D ALA* 2.9 11.2 + - - +
1439D SER* 1.3 77.2 - - - +
1441D GLN* 1.3 84.2 + - + +
1463D LYS* 3.7 4.9 - - - +
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Residues in contact with GLN1441 (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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615D ARG* 6.0 0.9 - - - +
1093D TYR* 2.3 41.5 + - - -
1096D ARG* 4.6 3.7 - - - +
1425D THR* 3.7 20.7 - - - +
1429D LEU* 3.3 8.1 - - + +
1437D ALA 3.2 12.2 + - - +
1438D ALA 4.0 2.1 + - - -
1439D SER 3.6 1.0 - - - -
1440D PHE* 1.3 106.6 - - + +
1442D ASN* 1.3 84.7 + - - +
1443D THR* 3.2 7.6 + - - -
1446D VAL* 3.9 1.4 - - - +
12G G 3.5 32.1 + - - +
13G A 5.5 0.4 - - - +
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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