Contacts of the helix formed by residues 1434 - 1440 (chain F) in PDB entry 6C3P
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 THR1434 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433F GLY* 1.3 73.9 - - - -
1435F ILE* 1.3 60.1 + - - +
1436F ARG* 3.8 13.5 - - + -
1437F PHE* 2.8 25.5 + - + +
1438F ASN* 2.4 42.5 + - - +
1470F LEU 3.2 1.6 + - - -
1471F ASP* 3.0 26.0 - - + +
1472F ALA 3.0 19.5 + - - -
1473F ILE* 5.3 1.6 - - - -
1474F ILE 5.0 0.2 - - - +
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Residues in contact with ILE1435 (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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1434F THR* 1.3 78.3 + - - +
1436F ARG* 1.3 58.9 + - - +
1438F ASN* 3.8 4.7 - - + -
1439F LEU* 2.9 49.0 + - + +
1450F LEU* 5.8 0.4 - - + -
1454F LEU* 4.7 11.0 - - + -
1463F VAL* 5.8 4.9 - - + -
1466F LEU* 6.5 1.3 - - + -
1470F LEU* 3.2 49.1 - - + +
1472F ALA* 5.1 8.5 - - + +
1474F ILE* 4.0 28.9 - - + -
1481F PHE* 6.0 1.1 - - + -
1489F PHE* 4.1 22.9 - - + -
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Residues in contact with ARG1436 (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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1434F THR* 3.2 11.0 - - + -
1435F ILE* 1.3 76.7 - - - +
1437F PHE* 1.3 55.5 + - - +
1440F ASP* 2.7 38.8 + - - +
1447F ASP* 2.7 43.3 + - - -
1450F LEU* 3.8 13.5 - - - -
1469F GLY 5.3 0.6 + - - -
1470F LEU* 3.2 22.1 + - + +
1471F ASP* 3.9 24.5 + - - +
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Residues in contact with PHE1437 (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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501F GLU* 5.9 0.7 - - - -
517F ILE* 5.8 0.9 - - + -
518F PHE* 3.5 32.5 - + - -
521F ARG* 3.3 53.8 - - - -
1431F PHE* 4.3 21.1 - + + +
1432F SER 4.1 17.5 - - - -
1433F GLY* 4.4 5.8 - - - -
1434F THR* 2.8 24.7 + - + +
1436F ARG* 1.3 75.6 - - - +
1438F ASN* 1.3 65.3 + - - +
1440F ASP 3.5 19.9 - - - +
1441F PRO* 3.9 14.0 - - + +
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Residues in contact with ASN1438 (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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514F TRP* 4.6 3.1 - - - -
1430F LEU* 5.1 1.0 - - + +
1431F PHE* 2.3 59.3 + - + +
1433F GLY* 3.6 3.9 - - - +
1434F THR* 2.4 50.0 + - - +
1435F ILE* 3.5 7.8 + - + +
1437F PHE* 1.3 70.7 - - - +
1439F LEU* 1.3 64.8 + - + +
1441F PRO* 5.1 0.3 - - - +
1474F ILE* 3.1 29.6 - - + +
1489F PHE* 6.5 0.4 - - + -
1493F ARG* 3.4 23.4 + - - +
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Residues in contact with LEU1439 (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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514F TRP* 3.9 11.4 - - - -
1435F ILE* 2.9 37.1 + - + +
1438F ASN* 1.3 80.8 - - + +
1440F ASP* 1.3 66.4 + - - +
1441F PRO* 3.1 12.0 - - - +
1450F LEU* 3.9 32.8 - - + +
1453F ALA* 5.5 1.8 - - + -
1454F LEU* 4.7 11.9 - - + -
1489F PHE* 4.3 10.1 - - + +
1492F ALA* 4.2 6.5 - - + -
1493F ARG* 3.5 41.4 - - + +
1496F VAL* 4.0 19.0 - - + +
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Residues in contact with ASP1440 (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 ARG* 2.7 27.3 + - + +
1437F PHE* 3.5 12.3 - - - -
1439F LEU* 1.3 75.5 - - - +
1441F PRO* 1.3 64.9 - - - +
1442F GLU 2.9 21.1 - - - +
1443F ARG* 4.8 3.7 - - - -
1445F CYS* 3.2 37.6 - - - +
1450F LEU* 3.2 31.7 - - - +
1496F VAL* 3.8 11.6 - - - +
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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