Contacts of the helix formed by residues 1758 - 1765 (chain D) in PDB entry 6AH0
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 THR1758 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1468D GLU 5.9 2.5 - - - -
1472D SER* 5.6 3.1 - - - +
1503D TRP* 5.5 6.2 - - - -
1754D TYR 4.2 1.3 + - - -
1755D LEU* 3.1 12.7 + - - +
1756D THR 3.2 3.7 - - - +
1757D TRP* 1.3 82.5 - - - +
1759D PHE* 1.3 63.9 + - - +
1760D LEU 3.3 3.4 - - - +
1761D TYR* 3.7 8.0 + - - +
1762D ARG* 3.7 7.3 + - - -
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Residues in contact with PHE1759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468D GLU* 5.9 3.0 + - - +
1503D TRP* 6.0 4.7 - - - +
1726D SER* 5.5 4.7 + - - -
1758D THR* 1.3 71.2 - - - +
1760D LEU* 1.3 66.5 + - - +
1761D TYR 3.2 0.7 - - - -
1762D ARG* 3.0 4.5 + - - +
1763D ARG* 2.9 19.9 + - - -
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Residues in contact with LEU1760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1726D SER* 5.0 15.8 - - - +
1728D LEU* 6.2 1.8 - - - +
1758D THR* 3.3 1.8 - - - +
1759D PHE* 1.3 76.3 - - - +
1761D TYR* 1.3 63.2 + - - +
1763D ARG* 3.0 2.9 + - - +
1764D MET* 2.9 24.4 + - - -
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Residues in contact with TYR1761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1755D LEU 4.5 14.1 + - - -
1756D THR* 5.4 5.4 - - - +
1758D THR* 3.7 9.2 + - - +
1759D PHE 3.2 0.8 - - - -
1760D LEU* 1.3 74.3 - - - +
1762D ARG* 1.3 63.4 - - - +
1764D MET* 3.7 6.9 + - - +
1765D THR 4.5 2.4 + - - -
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Residues in contact with ARG1762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1499D ASP* 6.1 4.9 - - - +
1758D THR 3.7 6.1 + - - -
1759D PHE* 3.0 11.1 + - - +
1761D TYR* 1.3 79.7 - - - +
1763D ARG* 1.3 61.0 + - - +
1764D MET 3.4 0.2 + - - -
1765D THR* 3.9 5.7 + - - -
1766D GLN* 4.2 4.5 + - - -
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Residues in contact with ARG1763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1759D PHE 2.9 13.3 + - - -
1760D LEU* 3.6 2.2 - - - +
1762D ARG* 1.3 75.0 - - - +
1764D MET* 1.3 65.4 + - - +
1765D THR 3.2 0.2 - - - -
1766D GLN* 2.8 15.2 + - - +
1767D ASN* 3.1 13.0 + - - +
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Residues in contact with MET1764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1760D LEU 2.9 15.1 + - - -
1761D TYR* 3.7 3.0 + - - +
1762D ARG 3.3 1.4 - - - -
1763D ARG* 1.3 76.2 - - - +
1765D THR* 1.3 58.1 + - - +
1767D ASN 5.2 1.1 - - - -
1768D PRO* 3.1 31.9 - - - +
1771D TYR* 6.4 1.8 - - - +
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Residues in contact with THR1765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761D TYR 4.5 3.6 + - - -
1762D ARG 3.9 4.5 + - - -
1763D ARG 3.2 0.4 - - - -
1764D MET* 1.3 75.0 - - - +
1766D GLN* 1.3 62.3 + - - +
1768D PRO* 4.6 2.5 - - - -
1776D ILE* 5.1 18.9 - - - +
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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