Contacts of the helix formed by residues 1446 - 1457 (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 SER1446 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445F CYS* 1.3 75.9 - - - +
1447F ASP* 1.3 65.7 + - - +
1448F SER* 3.3 18.4 + - - -
1449F THR* 2.5 37.7 + - - +
1450F LEU* 3.0 12.4 + - - +
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Residues in contact with ASP1447 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1436F ARG* 2.7 47.5 + - - -
1445F CYS 4.4 0.2 + - - -
1446F SER* 1.3 70.3 + - - +
1448F SER* 1.3 66.5 + - - +
1450F LEU* 3.1 15.2 + - + +
1451F TRP* 2.8 46.6 + - + +
1470F LEU* 5.2 1.1 - - - -
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Residues in contact with SER1448 (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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1446F SER* 3.1 14.0 + - - -
1447F ASP* 1.3 78.4 - - - +
1449F THR* 1.3 60.6 + - - +
1451F TRP* 3.4 7.6 + - - +
1452F GLU* 2.9 29.9 + - - +
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Residues in contact with THR1449 (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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1445F CYS* 4.2 7.6 - - - +
1446F SER* 2.5 38.9 + - - +
1448F SER* 1.3 78.2 - - - +
1450F LEU* 1.3 57.7 + - - +
1452F GLU* 3.2 19.5 + - - +
1453F ALA* 2.9 30.5 + - - +
1496F VAL* 5.7 7.2 - - - +
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Residues in contact with LEU1450 (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* 3.8 22.0 - - - +
1439F LEU* 3.9 25.7 - - + +
1440F ASP* 3.2 36.1 - - - +
1445F CYS* 4.5 4.7 - - + -
1446F SER 3.0 17.5 + - - +
1447F ASP* 3.1 32.5 + - - +
1449F THR* 1.3 78.8 - - - +
1451F TRP* 1.3 57.6 + - - +
1453F ALA* 3.2 6.2 + - - +
1454F LEU* 2.9 33.8 + - - +
1470F LEU* 4.5 14.8 - - + -
1496F VAL* 4.7 9.4 - - + -
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Residues in contact with TRP1451 (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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1447F ASP* 2.8 46.7 + - + +
1448F SER* 3.7 6.7 - - - +
1450F LEU* 1.3 72.7 - - - +
1452F GLU* 1.3 56.9 + - - +
1454F LEU* 3.4 14.3 + - + +
1455F GLU* 2.8 30.8 + - - +
1460F LYS* 3.3 54.7 - - + +
1463F VAL* 3.8 32.8 - - + -
1464F LYS* 4.8 9.4 - - + -
1469F GLY* 4.6 10.8 - - - -
1470F LEU* 3.3 29.8 - - + +
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Residues in contact with GLU1452 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1448F SER* 2.9 16.9 + - - +
1449F THR* 3.3 26.6 - - - +
1451F TRP* 1.3 76.2 - - - +
1453F ALA* 1.3 58.2 + - - +
1455F GLU* 3.2 5.8 + - - +
1456F ILE* 2.9 45.1 + - + +
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Residues in contact with ALA1453 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1439F LEU* 5.5 1.3 - - + -
1449F THR 2.9 15.4 + - - +
1450F LEU* 3.7 4.7 - - - +
1452F GLU* 1.3 76.0 - - - +
1454F LEU* 1.3 64.2 + - - +
1456F ILE* 3.3 12.9 - - - +
1457F ALA* 3.2 25.1 + - - +
1492F ALA* 3.9 26.2 - - + +
1495F PHE* 4.4 7.2 - - + +
1496F VAL* 4.2 21.3 - - + +
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Residues in contact with LEU1454 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1435F ILE* 4.7 14.8 - - + -
1439F LEU* 4.7 9.9 - - + -
1450F LEU 2.9 18.9 + - - +
1451F TRP* 3.5 23.8 - - + +
1453F ALA* 1.3 77.2 - - - +
1455F GLU* 1.3 54.6 + - - +
1457F ALA* 3.3 2.3 + - - -
1458F GLN 2.9 7.1 + - - -
1459F LEU* 2.5 51.7 + - + +
1460F LYS* 3.4 12.1 - - - +
1463F VAL* 4.1 21.3 - - + -
1470F LEU* 3.7 30.3 - - + -
1489F PHE* 5.3 7.6 - - + -
1492F ALA* 4.8 6.7 - - + -
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Residues in contact with GLU1455 (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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1451F TRP 2.8 17.9 + - - +
1452F GLU* 3.2 6.9 + - - +
1454F LEU* 1.3 72.5 - - - +
1456F ILE* 1.3 60.8 + - + +
1457F ALA 3.0 4.0 - - - -
1458F GLN* 2.5 33.7 + - - +
1460F LYS* 3.2 27.1 - - + +
1461F LEU* 3.2 33.8 - - - +
1464F LYS* 4.2 1.2 + - - -
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Residues in contact with ILE1456 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1452F GLU* 2.9 38.3 + - + +
1453F ALA* 3.3 17.7 - - - +
1455F GLU* 1.3 74.6 - - + +
1457F ALA* 1.3 56.3 - - - +
1458F GLN* 3.1 14.6 + - - +
1495F PHE* 3.4 39.3 - - + +
1519F LEU* 4.7 5.0 - - - +
1522F VAL* 3.4 32.0 - - + +
1523F VAL* 5.1 7.3 + - + +
1526F ALA* 4.6 17.7 - - + -
1527F PHE* 5.5 6.7 - - + -
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Residues in contact with ALA1457 (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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1453F ALA 3.2 17.6 + - - +
1454F LEU 3.8 0.2 - - - +
1455F GLU 3.0 0.8 - - - -
1456F ILE* 1.3 75.6 - - - +
1458F GLN* 1.3 73.6 + - - +
1459F LEU* 3.2 16.8 - - + +
1488F LEU* 2.9 30.1 - - + +
1492F ALA* 3.9 15.7 - - + +
1495F PHE* 4.2 16.4 - - + -
1519F LEU* 4.6 3.8 - - - -
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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