Contacts of the helix formed by residues 1459 - 1466 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1454E LEU* 2.5 39.2 + - + +
1457E ALA* 3.2 34.1 - - + +
1458E GLN* 1.3 76.8 - - - +
1460E LYS* 1.3 65.3 + - - +
1461E LEU 3.1 2.0 - - - -
1462E VAL* 2.8 24.6 + - + +
1463E VAL* 2.8 16.6 + - + +
1485E GLN* 4.4 14.1 - - - +
1488E LEU* 3.4 38.1 - - + +
1489E PHE* 4.1 31.4 - - + -
1492E ALA* 5.0 1.3 - - + -
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Residues in contact with LYS1460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451E TRP* 3.3 51.1 + - + +
1454E LEU* 3.2 13.6 + - + +
1455E GLU* 3.2 36.3 - - + +
1458E GLN 3.8 0.2 - - - -
1459E LEU* 1.3 77.0 - - - +
1461E LEU* 1.3 63.7 + - - +
1463E VAL* 3.7 6.4 - - - +
1464E LYS* 2.9 55.2 + - - +
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Residues in contact with LEU1461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1455E GLU* 3.2 35.0 - - - +
1458E GLN* 5.0 11.0 - - + +
1459E LEU 3.1 1.5 - - - +
1460E LYS* 1.3 78.0 - - - +
1462E VAL* 1.3 65.0 + - + +
1464E LYS* 3.6 32.5 + - + +
1465E ALA* 4.0 3.5 + - - +
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Residues in contact with VAL1462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458E GLN 4.3 13.2 - - - +
1459E LEU* 2.8 20.6 + - + +
1461E LEU* 1.3 72.2 - - + +
1463E VAL* 1.3 60.8 + - + +
1465E ALA* 2.8 27.0 + - + +
1466E LEU* 3.1 26.6 - - + +
1481E PHE* 5.4 6.1 - - + -
1485E GLN* 4.4 24.7 - - - +
1489E PHE* 6.4 1.1 - - + -
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Residues in contact with VAL1463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435E ILE* 5.8 4.5 - - + -
1451E TRP* 3.8 19.9 - - + -
1454E LEU* 4.1 19.1 - - + -
1459E LEU* 2.8 32.1 + - + +
1460E LYS* 3.7 7.6 - - - +
1462E VAL* 1.3 74.3 - - + +
1464E LYS* 1.3 53.6 + - - +
1466E LEU* 2.7 47.8 + - + +
1469E GLY* 4.8 1.3 + - - -
1470E LEU* 3.8 34.1 - - + +
1489E PHE* 5.2 8.5 - - + -
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Residues in contact with LYS1464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451E TRP* 4.8 9.2 - - + -
1455E GLU* 4.2 0.8 + - - -
1460E LYS* 2.9 60.6 + - + +
1461E LEU* 3.6 32.7 - - + +
1462E VAL 3.0 0.4 + - - -
1463E VAL* 1.3 77.4 - - - +
1465E ALA* 1.3 61.1 + - - +
1466E LEU 3.3 5.7 + - - +
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Residues in contact with ALA1465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461E LEU 4.0 3.0 + - - +
1462E VAL* 2.8 18.6 + - + +
1464E LYS* 1.3 75.2 - - - +
1466E LEU* 1.3 63.4 + - + +
1467E PRO* 3.6 7.6 - - - +
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Residues in contact with LEU1466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435E ILE* 6.5 1.8 - - + -
1462E VAL* 3.1 46.4 - - + +
1463E VAL* 2.7 35.9 + - + +
1464E LYS 3.7 4.7 - - - +
1465E ALA* 1.3 76.1 - - + +
1467E PRO* 1.3 70.6 - - + +
1468E GLY* 3.3 5.3 + - - +
1469E GLY* 3.7 8.3 + - - +
1470E LEU 5.8 0.7 - - - +
1472E ALA* 4.8 15.7 - - + -
1481E PHE* 3.5 34.3 - - + -
1489E PHE* 6.0 1.6 - - + -
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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