Contacts of the helix formed by residues 1459 - 1466 (chain H) 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 LEU1459 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1454H LEU* 2.5 38.0 + - + +
1457H ALA* 3.2 35.0 - - + +
1458H GLN* 1.3 75.1 - - - +
1460H LYS* 1.3 66.1 + - - +
1461H LEU 3.1 2.2 - - - -
1462H VAL* 2.8 22.9 + - + +
1463H VAL* 2.8 16.0 + - + +
1485H GLN* 4.4 14.1 - - - +
1488H LEU* 3.4 37.0 - - + +
1489H PHE* 4.1 32.3 - - + -
1492H ALA* 5.0 1.6 - - + -
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Residues in contact with LYS1460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451H TRP* 3.3 50.2 - - + +
1454H LEU* 3.2 14.0 + - + +
1455H GLU* 3.2 35.9 - - + +
1458H GLN 3.8 0.4 - - - -
1459H LEU* 1.3 75.6 - - - +
1461H LEU* 1.3 62.9 + - - +
1463H VAL* 3.7 6.8 - - - +
1464H LYS* 2.9 53.6 + - - +
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Residues in contact with LEU1461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1455H GLU* 3.2 35.0 - - - +
1458H GLN* 5.0 11.4 - - + +
1459H LEU 3.1 1.5 - - - -
1460H LYS* 1.3 77.3 - - - +
1462H VAL* 1.3 64.3 + - + +
1464H LYS* 3.6 31.5 + - + +
1465H ALA* 4.0 3.6 + - - +
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Residues in contact with VAL1462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458H GLN 4.3 12.1 - - - +
1459H LEU* 2.8 22.2 + - + +
1461H LEU* 1.3 71.3 - - + +
1463H VAL* 1.3 60.2 + - + +
1465H ALA* 2.8 26.6 + - + +
1466H LEU* 3.1 26.4 - - + +
1481H PHE* 5.4 6.3 - - + -
1485H GLN* 4.4 23.8 - - - +
1489H PHE* 6.4 1.3 - - + -
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Residues in contact with VAL1463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435H ILE* 5.8 4.3 - - + -
1451H TRP* 3.8 19.6 - - + -
1454H LEU* 4.1 19.3 - - + -
1459H LEU* 2.8 32.0 + - + +
1460H LYS* 3.7 7.9 - - - +
1462H VAL* 1.3 75.0 - - + +
1464H LYS* 1.3 55.2 + - - +
1466H LEU* 2.7 46.8 + - + +
1469H GLY* 4.8 0.9 + - - -
1470H LEU* 3.7 34.1 - - + +
1489H PHE* 5.2 8.7 - - + -
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Residues in contact with LYS1464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451H TRP* 4.9 9.0 - - + -
1455H GLU* 4.2 1.2 + - - -
1460H LYS* 2.9 60.0 + - + +
1461H LEU* 3.6 32.3 - - + +
1462H VAL 3.0 0.2 + - - -
1463H VAL* 1.3 76.4 - - - +
1465H ALA* 1.3 61.7 + - - +
1466H LEU 3.3 5.7 + - - +
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Residues in contact with ALA1465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461H LEU 4.0 3.6 + - - +
1462H VAL* 2.8 17.4 + - + +
1464H LYS* 1.3 74.5 - - - +
1466H LEU* 1.3 63.7 + - + +
1467H PRO* 3.6 8.1 - - - +
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Residues in contact with LEU1466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435H ILE* 6.5 1.8 - - + -
1462H VAL* 3.1 45.5 - - + +
1463H VAL* 2.7 36.6 + - + +
1464H LYS 3.7 5.1 - - - +
1465H ALA* 1.3 77.6 - - + +
1467H PRO* 1.3 70.5 - - + +
1468H GLY* 3.3 4.5 + - - +
1469H GLY* 3.7 7.5 + - - +
1470H LEU 5.8 0.7 - - - +
1472H ALA* 4.8 16.2 - - + -
1481H PHE* 3.5 34.8 - - + -
1489H PHE* 6.0 1.1 - - + -
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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