Contacts of the helix formed by residues 858 - 866 (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 ILE 858 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B TYR* 3.8 21.1 - - + -
814B ALA* 3.9 24.9 - - + +
815B ILE* 4.7 1.3 - - + -
841B PHE* 3.7 22.2 - - + -
846B ILE* 3.3 33.7 - - + -
854B ILE* 3.9 7.2 - - + -
855B THR* 3.3 14.8 + - + +
857B LEU* 1.3 86.6 - - + +
859B LYS* 1.3 68.2 + - - +
860B ASP 3.4 2.2 - - - -
861B ASP* 3.1 14.5 + - - +
862B VAL* 3.1 29.9 + - + +
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Residues in contact with LYS 859 (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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776B TYR* 4.7 6.5 - - + +
853B GLU* 4.9 12.8 - - + +
854B ILE* 3.6 30.4 - - + +
855B THR 2.8 18.3 + - - +
856B ASP* 3.1 32.7 + - - +
858B ILE* 1.3 77.4 - - - +
860B ASP* 1.3 88.2 + - - +
862B VAL* 3.4 2.3 + - - +
863B LEU* 3.1 51.9 + - + +
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Residues in contact with ASP 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ASP* 4.4 7.8 + - - +
858B ILE 3.4 0.6 - - - -
859B LYS* 1.3 104.4 + - - +
861B ASP* 1.3 64.3 + - - +
863B LEU* 4.1 11.5 - - - +
864B HIS* 3.5 20.1 + - - +
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Residues in contact with ASP 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B PRO* 5.1 10.3 - - + +
841B PHE* 3.5 21.9 - - + -
856B ASP 5.6 0.2 - - - +
857B LEU 4.4 4.6 - - - +
858B ILE* 3.1 26.1 + - - +
860B ASP* 1.3 79.5 + - - +
862B VAL* 1.3 61.7 + - - +
863B LEU 3.1 0.9 - - - -
864B HIS* 2.9 3.8 + - - -
865B TRP* 2.8 42.7 + - + +
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Residues in contact with VAL 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B TYR* 5.5 2.0 - - + -
833B LEU* 4.2 23.3 - - + -
835B LEU* 4.4 8.1 - - + -
841B PHE* 3.6 24.5 - - + -
846B ILE* 3.9 23.6 - - + -
848B TRP* 5.0 0.7 - - + -
854B ILE* 3.7 31.6 - - + -
858B ILE* 3.1 21.0 + - + +
859B LYS* 3.9 4.0 - - - +
861B ASP* 1.3 80.1 - - - +
863B LEU* 1.3 58.8 + - - +
866B MET* 2.8 36.9 + - + +
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Residues in contact with LEU 863 (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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776B TYR* 3.5 44.9 - - + -
859B LYS* 3.1 43.6 + - + +
860B ASP* 4.2 11.4 - - - +
862B VAL* 1.3 79.1 - - - +
864B HIS* 1.3 58.1 + - - +
866B MET* 3.5 22.1 - - + +
868B TYR* 4.5 13.2 + - - +
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Residues in contact with HIS 864 (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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836B ARG* 3.0 27.0 + - - -
860B ASP 3.5 15.9 + - - +
861B ASP* 2.9 6.2 + - - +
863B LEU* 1.3 79.7 - - - +
865B TRP* 1.3 78.8 + + + +
866B MET 5.0 0.2 - - - -
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Residues in contact with TRP 865 (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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835B LEU* 3.3 10.7 - - + -
836B ARG* 2.7 75.4 + - + +
837B GLU 3.8 8.7 - - - -
838B GLY 3.0 28.7 - - - -
839B ASN* 3.7 20.6 - - + -
840B PRO* 3.4 34.6 - - + +
841B PHE* 5.3 1.8 - + + -
861B ASP* 2.8 31.3 + - + +
862B VAL* 5.1 0.2 - - - -
864B HIS* 1.3 94.3 - + + +
866B MET* 1.3 64.0 + - - +
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Residues in contact with MET 866 (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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776B TYR* 3.6 19.1 - - + -
779B ILE* 4.6 9.0 - - - -
833B LEU* 3.6 29.4 - - + -
834B PRO* 3.1 13.2 - - + +
835B LEU* 3.5 4.4 - - + +
836B ARG* 3.5 11.4 + - - +
862B VAL* 2.8 17.5 + - + +
863B LEU* 3.5 48.2 - - + +
864B HIS 5.0 0.4 - - - -
865B TRP* 1.3 79.1 - - - +
867B ASP* 1.3 59.1 + - - +
868B TYR* 3.3 45.7 + - + +
871B LEU* 5.1 2.2 - - + -
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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