Contacts of the helix formed by residues 867 - 876 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834D PRO* 2.8 35.7 + - + +
835D LEU 3.9 4.9 + - - +
836D ARG* 3.8 28.9 - - - +
837D GLU 5.1 0.3 + - - -
865D TRP 3.3 0.6 + - - -
866D MET* 1.3 69.8 - - - +
868D TYR* 1.3 62.8 + - - +
869D THR* 3.0 11.1 + - - -
870D VAL* 3.1 40.7 + - + +
871D LEU* 3.0 25.9 + - - +
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Residues in contact with TYR 868 (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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771D PHE* 3.9 16.9 - + + -
772D ARG* 3.5 73.3 + - + +
774D LEU 5.0 3.1 + - - -
779D ILE* 3.5 27.7 - - + +
836D ARG* 5.7 0.4 - - - +
863D LEU 4.6 4.9 + - - -
864D HIS 6.1 0.4 - - - -
866D MET* 2.9 53.4 + - + +
867D ASP* 1.3 74.5 + - - +
869D THR* 1.3 56.5 + - - +
871D LEU* 3.8 7.6 - - + +
872D LEU* 2.9 34.3 + - - +
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Residues in contact with THR 869 (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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772D ARG* 4.9 11.4 + - - +
867D ASP* 3.0 8.8 + - - -
868D TYR* 1.3 76.1 - - - +
870D VAL* 1.3 63.7 + - + +
871D LEU 2.7 14.4 + - - -
872D LEU* 5.0 1.1 - - - -
873D GLU* 2.8 34.7 + - + +
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Residues in contact with VAL 870 (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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834D PRO* 5.0 9.4 - - + -
867D ASP* 3.1 33.6 + - + +
869D THR* 1.3 85.7 - - + +
871D LEU* 1.3 55.3 + - - +
873D GLU* 4.2 6.5 - - - -
874D LYS* 3.1 47.0 + - + +
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Residues in contact with LEU 871 (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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738D PRO* 5.9 2.5 - - + -
771D PHE* 4.5 2.7 - - + -
779D ILE* 3.1 51.4 - - + +
781D SER* 5.4 7.6 - - - +
832D VAL 5.4 2.7 - - - +
833D LEU* 4.2 5.6 - - + -
834D PRO* 3.7 31.4 - - + +
866D MET* 6.0 2.7 - - + -
867D ASP 3.0 19.3 + - - +
868D TYR* 3.8 8.3 - - + +
869D THR 2.7 2.6 + - - -
870D VAL* 1.3 76.1 - - - +
872D LEU* 1.3 63.8 + - - +
873D GLU 3.1 1.9 + - - -
874D LYS* 6.0 0.9 - - + -
875D THR* 3.0 45.4 + - + +
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Residues in contact with LEU 872 (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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767D PHE* 4.3 7.0 - - + -
768D GLU* 3.4 33.9 - - - +
771D PHE* 3.4 46.4 - - + -
772D ARG* 4.6 9.2 - - - +
868D TYR 2.9 18.6 + - - +
869D THR* 4.1 1.6 - - - +
871D LEU* 1.3 76.7 - - - +
873D GLU* 1.3 58.1 + - - +
875D THR* 4.2 4.5 - - - +
876D PHE* 3.4 28.4 + - + +
877D ILE* 3.1 38.0 + - + +
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Residues in contact with GLU 873 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869D THR* 2.8 27.8 + - + +
870D VAL* 4.4 5.4 - - - +
872D LEU* 1.3 79.3 - - - +
874D LYS* 1.3 64.4 + - + +
877D ILE* 3.6 23.1 - - + +
878D LYS* 2.8 36.3 + - - +
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Residues in contact with LYS 874 (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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803D PHE* 6.1 2.4 - - - -
870D VAL* 3.1 38.5 - - + +
871D LEU* 3.6 0.8 + - + -
873D GLU* 1.3 83.6 - - + +
875D THR* 1.3 70.5 + - + +
876D PHE 3.7 0.2 - - - -
878D LYS* 4.2 9.2 - - + +
879D PRO* 4.2 9.1 - - - +
8K T 5.4 4.1 + - - -
9K G 3.1 41.5 + - - +
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Residues in contact with THR 875 (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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736D SER* 5.9 1.8 - - - +
737D THR* 4.3 29.3 - - + +
738D PRO* 4.6 8.6 - - + +
741D VAL* 3.0 32.4 - - - +
745D LEU* 4.4 1.6 - - - +
771D PHE* 5.7 0.7 - - - -
871D LEU* 3.0 38.8 + - + +
872D LEU* 4.3 1.2 - - - -
874D LYS* 1.3 92.6 - - + +
876D PHE* 1.3 61.7 + - - +
879D PRO* 3.5 12.6 - - - +
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Residues in contact with PHE 876 (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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741D VAL* 3.7 16.6 - - + -
744D ALA* 3.7 22.9 - - + -
745D LEU* 3.5 23.5 - - + +
748D CYS* 4.0 19.3 - - - -
763D TYR* 5.3 1.1 - + - -
764D PHE* 3.4 37.7 - + - -
767D PHE* 3.9 22.7 - + + -
768D GLU* 5.5 3.8 - - - -
872D LEU* 3.4 30.1 + - + +
875D THR* 1.3 85.0 + - - +
877D ILE* 1.3 77.2 + - + +
879D PRO* 3.1 7.5 - - - +
880D LEU* 3.1 29.8 + - + +
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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