Contacts of the helix formed by residues 1435 - 1440 (chain F) in PDB entry 5TWV
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 THR1435 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1434F GLY* 1.3 74.5 - - - +
1436F ILE* 1.3 54.0 + - - +
1437F ARG* 4.0 6.1 - - - -
1438F PHE* 3.8 20.9 - - - +
1439F ASN* 2.5 35.6 + - - +
1471F LEU 4.1 6.3 - - - -
1472F ASP* 4.3 12.1 - - - -
1473F ALA 3.3 7.0 - - - -
1474F ILE* 3.8 5.5 - - - +
1475F ILE 4.3 0.2 - - - -
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Residues in contact with ILE1436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435F THR* 1.3 67.5 - - - +
1437F ARG* 1.3 53.4 + - - +
1439F ASN* 3.6 7.7 - - - +
1440F LEU* 2.7 35.9 + - - +
1470F GLY 3.6 16.2 - - - +
1471F LEU* 3.4 11.8 + - - +
1473F ALA* 2.4 31.6 + - + +
1475F ILE* 4.2 4.2 - - + +
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Residues in contact with ARG1437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435F THR* 3.2 4.5 - - - -
1436F ILE* 1.3 72.9 - - - +
1438F PHE* 1.3 57.7 + - - +
1440F LEU* 3.1 8.9 + - - +
1441F ASP* 2.9 26.7 + - - +
1448F ASP* 5.6 10.8 - - + -
1451F LEU* 6.0 4.5 - - + +
1471F LEU* 2.6 34.8 + - + +
1472F ASP* 5.3 0.4 - - - -
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Residues in contact with PHE1438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516F SER* 5.9 1.4 - - - -
1432F PHE* 5.7 3.1 - - - +
1434F GLY* 4.6 4.9 - - - -
1435F THR* 3.1 26.6 + - - +
1437F ARG* 1.3 75.5 - - - +
1439F ASN* 1.3 66.2 + - - +
1441F ASP* 3.1 24.0 + - - +
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Residues in contact with ASN1439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431F LEU* 4.3 19.1 - - + +
1432F PHE* 4.2 26.4 + - - +
1434F GLY* 4.9 1.0 - - - -
1435F THR 2.5 21.0 + - - +
1436F ILE* 3.6 9.9 - - - +
1438F PHE* 1.3 72.4 - - - +
1440F LEU* 1.3 58.9 + - - +
1441F ASP 3.3 0.9 + - - -
1442F PRO* 3.9 12.1 - - - +
1475F ILE* 4.4 6.5 - - + -
1494F ARG* 6.0 0.7 - - - +
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Residues in contact with LEU1440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436F ILE 2.7 20.5 + - - +
1437F ARG* 3.1 9.4 + - - +
1439F ASN* 1.3 72.2 - - - +
1441F ASP* 1.3 56.8 + - - +
1442F PRO* 3.4 10.0 - - - +
1443F GLU* 5.9 0.5 - - - +
1446F CYS* 5.8 2.8 - - - +
1451F LEU* 5.1 16.4 - - + +
1490F PHE* 5.9 2.9 - - + +
1494F ARG* 5.6 11.9 - - + +
1497F VAL* 5.5 7.3 - - - +
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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