Contacts of the helix formed by residues 867 - 876 (chain C) in PDB entry 3RMD
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 ASP 867 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834C PRO* 2.9 20.0 + - + +
835C LEU 4.1 3.4 - - - +
836C ARG* 3.6 38.3 - - + +
837C GLU 5.0 0.5 + - - -
865C TRP 3.3 1.0 + - - -
866C MET* 1.3 70.4 - - - +
868C TYR* 1.3 66.8 + - - +
869C THR* 3.5 10.9 + - - -
870C VAL* 3.0 42.0 + - + +
871C LEU* 2.9 22.5 + - - +
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Residues in contact with TYR 868 (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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771C PHE* 3.7 19.2 - + + -
772C ARG* 3.6 67.3 + - + +
774C LEU 4.3 8.0 + - - -
776C TYR* 5.2 3.1 - - - +
779C ILE* 3.4 23.7 - - + +
836C ARG* 5.4 1.2 - - - +
863C LEU* 4.7 7.5 + - - +
866C MET* 3.3 43.2 + - + +
867C ASP* 1.3 72.3 + - - +
869C THR* 1.3 64.1 + - - +
871C LEU* 3.1 7.0 + - + +
872C LEU* 2.9 26.1 + - - +
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Residues in contact with THR 869 (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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772C ARG* 2.9 25.1 + - - +
867C ASP* 3.3 10.2 + - - -
868C TYR* 1.3 78.9 - - - +
870C VAL* 1.3 66.9 + - + +
872C LEU* 3.4 5.0 + - - +
873C GLU* 3.1 24.1 + - + +
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Residues in contact with VAL 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C PRO* 4.4 7.0 - - + -
867C ASP* 3.0 36.3 + - + +
869C THR* 1.3 77.6 - - + +
871C LEU* 1.3 66.3 + - - +
873C GLU* 3.3 5.5 + - + +
874C LYS* 2.9 55.8 + - + +
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Residues in contact with LEU 871 (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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771C PHE* 3.7 11.2 - - + -
779C ILE* 3.0 55.9 - - + +
781C SER* 4.4 9.0 - - - +
832C VAL 4.7 0.2 - - - +
833C LEU* 4.0 14.4 - - + -
834C PRO* 3.5 28.0 - - + +
866C MET* 4.5 4.5 - - + -
867C ASP 2.9 17.8 + - - +
868C TYR* 3.5 5.4 - - + +
870C VAL* 1.3 77.2 - - - +
872C LEU* 1.3 57.3 + - - +
874C LYS* 4.9 3.1 - - - +
875C THR* 2.6 53.9 + - + +
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Residues in contact with LEU 872 (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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767C PHE* 3.9 13.7 - - + -
768C GLU* 3.8 36.1 - - + +
771C PHE* 3.7 30.6 - - + -
772C ARG* 5.4 6.7 - - - +
868C TYR 2.9 14.7 + - - +
869C THR* 3.8 5.6 - - - +
871C LEU* 1.3 78.0 - - - +
873C GLU* 1.3 58.2 + - - +
875C THR* 4.2 2.7 - - - -
876C PHE* 2.9 67.5 + - + +
877C ILE* 3.1 16.8 + - + -
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Residues in contact with GLU 873 (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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869C THR* 3.1 19.7 + - + +
870C VAL* 3.7 6.7 - - + +
872C LEU* 1.3 77.9 - - - +
874C LYS* 1.3 66.9 + - + +
877C ILE* 3.5 27.1 + - + +
878C LYS* 2.9 52.9 + - + +
881C GLU* 5.8 0.3 - - - +
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Residues in contact with LYS 874 (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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803C PHE* 3.5 34.4 - - - -
834C PRO* 4.0 18.3 - - - +
870C VAL* 2.9 38.1 + - + +
871C LEU* 4.1 3.4 - - - +
873C GLU* 1.3 84.7 - - + +
875C THR* 1.3 67.4 + - + +
878C LYS* 3.7 18.9 - - + +
879C PRO* 3.7 3.6 - - - +
9I G 5.0 7.8 + - - +
10I A 3.1 33.7 + - - +
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Residues in contact with THR 875 (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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731C GLU* 5.7 1.2 - - - +
737C THR* 5.0 3.0 - - - +
738C PRO* 4.0 23.1 - - + +
741C VAL* 3.5 26.9 - - - +
745C LEU* 4.3 1.2 - - - +
771C PHE* 5.0 0.7 - - - -
781C SER* 3.9 21.3 - - - +
871C LEU* 2.6 39.1 + - + +
872C LEU* 4.1 2.3 + - - -
874C LYS* 1.3 86.4 - - + +
876C PHE* 1.3 58.4 + - - +
879C PRO* 3.2 15.6 - - - +
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Residues in contact with PHE 876 (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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741C VAL* 4.3 8.1 - - + -
744C ALA* 3.6 25.4 - - + -
745C LEU* 3.6 31.0 - - + +
748C CYS* 4.1 13.9 - - - -
763C TYR* 5.0 0.9 - + - -
764C PHE* 3.5 35.4 - + - -
767C PHE* 3.4 34.1 - + + -
768C GLU* 5.0 2.0 - - + -
872C LEU* 2.9 42.5 + - + -
874C LYS 3.7 0.2 - - - -
875C THR* 1.3 75.6 + - - +
877C ILE* 1.3 76.8 + - + +
879C PRO* 3.0 16.2 - - - +
880C LEU* 3.0 16.9 + - + +
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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