Contacts of the helix formed by residues 758 - 763 (chain C) in PDB entry 1RHM
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 LEU 758 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C LEU* 3.8 29.6 - - + -
741C GLY* 3.0 25.7 + - - +
742C ILE 5.1 0.2 - - - +
743C ILE* 3.9 20.0 - - + -
756C VAL 3.6 2.4 + - - -
757C ASP* 1.3 70.3 - - - +
759C LYS* 1.3 63.0 + - - +
761C ILE* 3.1 18.9 + - + +
762C THR* 2.9 33.1 + - - +
780C PHE* 5.5 3.8 - - + -
782C ILE* 3.5 30.1 - - + -
829D TYR* 5.4 6.1 - - + -
831D TYR* 3.7 21.1 - - + +
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Residues in contact with LYS 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PRO 5.1 4.4 + - - -
337B TYR* 4.2 11.9 + - - -
741C GLY 4.9 0.4 + - - -
757C ASP* 3.2 16.5 - - + +
758C LEU* 1.3 76.6 - - - +
760C LYS* 1.3 57.6 + - - +
762C THR* 3.2 7.4 + - + -
763C ASN* 2.9 61.7 + - - +
766C ARG* 5.5 0.6 - - - +
824D GLU* 3.2 27.5 + - - -
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Residues in contact with LYS 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C VAL* 4.3 28.7 - - + -
756C VAL* 4.7 9.0 - - + +
757C ASP* 3.2 27.9 + - - +
758C LEU 3.1 0.8 - - - -
759C LYS* 1.3 79.9 - - - +
761C ILE* 1.3 60.7 + - + +
762C THR 3.6 0.2 + - - -
763C ASN* 3.9 12.0 + - - +
764C PHE* 3.1 28.8 - - + -
769C ARG* 5.3 0.3 + - - -
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Residues in contact with ILE 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C ILE* 4.3 19.1 - - + -
712C VAL* 4.1 30.5 - - + -
715C MET* 3.9 15.8 - - + +
734C LEU* 4.0 18.2 - - + -
743C ILE* 3.9 29.4 - - + -
756C VAL* 5.0 7.2 - - + -
757C ASP 4.8 2.9 - - - +
758C LEU* 3.4 25.3 - - + +
760C LYS* 1.3 78.9 - - + +
762C THR* 1.3 63.4 + - - +
764C PHE* 3.7 11.9 - - + -
765C PHE* 3.5 22.9 - - - -
780C PHE* 4.5 5.3 - - + -
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Residues in contact with THR 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758C LEU* 2.9 24.5 + - - +
759C LYS* 3.7 8.3 - - + +
761C ILE* 1.3 78.6 - - - +
763C ASN* 1.3 67.2 + - - +
764C PHE 3.2 2.5 - - - -
765C PHE* 2.9 30.3 + - - +
766C ARG* 6.2 0.2 - - - -
780C PHE* 4.0 17.3 - - - -
824D GLU* 5.2 4.0 - - - +
827D PHE* 3.8 17.1 - - + -
829D TYR* 3.2 40.0 - - + +
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Residues in contact with ASN 763 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759C LYS* 2.9 58.9 + - - +
760C LYS* 4.0 9.4 + - - +
761C ILE 3.5 0.2 - - - -
762C THR* 1.3 77.9 - - - +
764C PHE* 1.3 56.6 + - - +
765C PHE 2.9 10.9 + - - -
766C ARG* 3.3 34.4 + - - +
769C ARG* 3.0 47.6 + - - +
824D GLU* 4.4 1.2 + - - -
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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