Contacts of the helix formed by residues 867 - 876 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834B PRO* 2.8 29.8 + - + +
835B LEU 4.0 2.4 - - - +
836B ARG* 3.6 36.2 - - - +
837B GLU 4.9 0.2 + - - -
865B TRP 3.3 1.0 + - - -
866B MET* 1.3 71.0 - - - +
868B TYR* 1.3 62.0 - - - +
869B THR* 3.5 9.2 + - - -
870B VAL* 2.7 47.4 + - + +
871B LEU* 2.8 24.7 + - - +
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Residues in contact with TYR 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B PHE* 3.4 23.2 - + + -
772B ARG* 3.6 60.3 + - + +
774B LEU 4.9 4.7 + - - -
776B TYR* 6.0 0.7 - - - +
779B ILE* 3.9 23.1 - - + -
836B ARG* 5.4 1.7 - - - +
863B LEU* 4.5 12.6 + - - +
866B MET* 3.3 37.5 + - + +
867B ASP* 1.3 71.2 - - - +
869B THR* 1.3 56.0 + - - +
871B LEU* 3.1 6.7 + - - +
872B LEU* 2.8 31.7 + - - +
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Residues in contact with THR 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772B ARG* 3.8 18.1 + - - +
867B ASP* 3.3 6.9 - - - -
868B TYR* 1.3 78.7 - - - +
870B VAL* 1.3 65.5 + - + +
872B LEU* 3.3 4.0 + - - +
873B GLU* 3.1 22.9 + - + +
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Residues in contact with VAL 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B PHE* 6.3 1.8 - - + -
834B PRO* 4.0 17.9 - - + -
867B ASP* 2.7 45.9 + - + +
869B THR* 1.3 71.8 - - + +
871B LEU* 1.3 67.2 + - - +
873B GLU* 3.2 5.5 + - - +
874B LYS* 2.8 31.9 + - + +
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Residues in contact with LEU 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B PHE* 3.9 8.5 - - + -
779B ILE* 3.4 53.4 - - + +
780B ALA* 5.0 0.2 - - - -
781B SER* 5.1 1.8 - - - +
832B VAL 4.8 4.0 - - - +
833B LEU* 3.6 21.3 - - + -
834B PRO* 3.5 25.8 - - + +
866B MET* 5.1 3.6 - - + -
867B ASP 2.8 18.2 + - - +
868B TYR* 3.2 9.6 - - + +
870B VAL* 1.3 77.3 - - - +
872B LEU* 1.3 54.1 + - - +
874B LYS* 4.8 1.3 - - + -
875B THR* 2.7 55.1 + - + +
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Residues in contact with LEU 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767B PHE* 4.0 3.1 - - + -
768B GLU* 3.8 37.5 - - + +
771B PHE* 3.8 42.5 - - + -
772B ARG* 4.5 11.2 - - - +
868B TYR 2.8 19.2 + - - +
869B THR* 3.7 5.6 - - - +
871B LEU* 1.3 69.8 - - - +
873B GLU* 1.3 60.2 - - - +
875B THR* 4.1 1.1 - - - -
876B PHE* 2.8 65.6 + - + +
877B ILE* 3.0 16.6 + - + -
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Residues in contact with GLU 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869B THR* 3.1 15.3 + - + +
870B VAL* 3.7 5.6 - - - +
872B LEU* 1.3 80.9 - - - +
874B LYS* 1.3 62.4 + - - +
877B ILE* 3.3 39.4 + - - +
878B LYS* 2.9 55.9 + - - +
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Residues in contact with LYS 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870B VAL* 2.8 30.3 + - + +
871B LEU* 4.0 2.2 - - - +
873B GLU* 1.3 78.3 - - - +
875B THR* 1.3 65.1 + - + +
878B LYS* 3.8 9.9 - - - +
879B PRO* 3.6 12.5 - - - +
9G G 5.2 5.6 + - - +
10G A 5.1 13.9 - - - +
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Residues in contact with THR 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B GLU* 5.8 0.9 - - - +
737B THR* 4.8 4.3 - - - +
738B PRO* 4.3 20.3 - - + +
741B VAL* 3.4 28.5 - - - +
745B LEU* 4.1 1.9 - - - +
771B PHE* 5.0 1.0 - - - -
779B ILE 4.9 0.2 + - - -
781B SER* 3.9 19.1 - - - +
871B LEU* 2.7 45.1 + - + +
872B LEU* 3.9 1.9 + - - -
874B LYS* 1.3 82.3 - - + +
876B PHE* 1.3 61.2 + - - +
879B PRO* 3.0 15.7 - - - +
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Residues in contact with PHE 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B VAL* 4.1 9.6 - - + -
744B ALA* 3.8 15.9 - - + -
745B LEU* 3.3 32.3 - - + +
748B CYS* 4.0 17.5 - - - -
764B PHE* 3.7 33.2 - + - -
767B PHE* 3.4 32.8 - + + -
768B GLU* 5.4 0.9 - - - -
872B LEU* 2.8 45.8 + - + +
875B THR* 1.3 78.0 + - - +
877B ILE* 1.3 68.9 + - - +
879B PRO* 3.0 15.1 - - - +
880B LEU* 3.1 28.1 + - + +
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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