Contacts of the helix formed by residues 865 - 876 (chain J) in PDB entry 6C6U
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 HIS 865 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840J LEU* 4.5 5.4 - - - -
841J GLY* 4.9 1.8 - - - +
863J LEU* 3.2 17.2 + - + -
864J LEU* 1.3 77.0 - - - +
866J GLU* 1.3 72.8 + - + +
867J GLN* 3.4 35.9 + - + +
868J TRP* 3.1 38.1 + + - -
869J CYS* 2.9 26.0 + - - -
901J ARG* 4.8 18.4 - - - +
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Residues in contact with GLU 866 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610J ARG* 3.5 43.3 + - - +
836J ARG* 4.4 19.0 + - - +
840J LEU* 4.3 18.5 - - + +
865J HIS* 1.3 82.2 + - + +
867J GLN* 1.3 58.2 + - + +
869J CYS* 3.3 8.3 + - - +
870J ASP* 3.0 35.8 + - - +
901J ARG* 4.3 13.8 + - - +
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Residues in contact with GLN 867 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865J HIS* 3.4 25.1 + - + +
866J GLU* 1.3 78.1 - - + +
868J TRP* 1.3 61.0 + - + +
870J ASP* 3.3 8.2 + - - +
871J LEU* 3.0 37.4 + - + +
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Residues in contact with TRP 868 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857J LEU* 4.1 13.0 - - + -
858J VAL* 3.5 32.0 - - + +
859J PRO* 5.1 9.6 - - + -
862J THR* 5.4 11.6 - - + -
863J LEU 3.7 10.7 + - - -
864J LEU* 3.8 22.9 - - + -
865J HIS* 3.1 47.4 + + - +
867J GLN* 1.3 80.7 + - + +
869J CYS* 1.3 58.1 + - - +
871J LEU* 3.3 22.8 + - + +
872J LEU* 2.9 33.2 + - - +
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Residues in contact with CYS 869 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836J ARG* 3.8 33.1 - - + +
839J VAL 3.6 18.6 - - - -
840J LEU* 3.7 18.4 - - + -
864J LEU* 3.6 19.3 - - - -
865J HIS 2.9 17.0 + - - +
866J GLU* 3.7 9.4 - - - +
867J GLN 3.3 0.4 - - - -
868J TRP* 1.3 74.9 - - - +
870J ASP* 1.3 60.0 + - - +
872J LEU* 3.2 14.1 + - - +
873J GLU* 2.9 27.4 + - - +
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Residues in contact with ASP 870 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836J ARG* 3.2 34.8 + - - -
866J GLU* 3.0 21.7 + - - +
867J GLN* 3.3 7.5 + - - +
869J CYS* 1.3 76.8 - - - +
871J LEU* 1.3 57.0 + - + +
873J GLU* 3.2 13.4 + - - +
874J GLU* 3.0 36.5 + - + +
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Residues in contact with LEU 871 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857J LEU* 4.3 13.6 - - + +
867J GLN* 3.0 26.1 + - + +
868J TRP* 3.6 27.4 - - + +
869J CYS 3.3 0.2 - - - -
870J ASP* 1.3 77.3 - - + +
872J LEU* 1.3 59.0 + - - +
874J GLU* 4.0 11.7 - - + +
875J ASN* 3.3 32.7 + - - +
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Residues in contact with LEU 872 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835J LEU* 3.9 29.2 - - + +
839J VAL* 4.8 2.7 - - + -
848J VAL* 5.0 4.5 - - + -
857J LEU* 4.8 9.9 - - + -
858J VAL* 5.2 11.7 - - + -
864J LEU* 4.1 23.1 - - + -
868J TRP 2.9 19.7 + - - +
869J CYS* 3.4 20.4 - - - +
870J ASP 3.2 0.2 - - - -
871J LEU* 1.3 76.2 - - - +
873J GLU* 1.3 63.9 + - - +
876J SER* 3.3 16.8 + - - -
877J VAL* 3.3 35.3 + - + +
880J VAL* 3.7 22.9 - - + -
990J ARG* 4.5 1.1 + - - -
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Residues in contact with GLU 873 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835J LEU* 6.4 0.7 - - - -
836J ARG* 4.3 21.0 + - + -
869J CYS 2.9 15.0 + - - +
870J ASP* 3.2 20.8 + - - +
872J LEU* 1.3 74.5 - - - +
874J GLU* 1.3 70.9 + - + +
876J SER* 3.6 9.7 + - - -
990J ARG* 4.3 17.0 + - - +
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Residues in contact with GLU 874 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870J ASP* 3.0 23.5 + - + +
871J LEU* 4.3 14.6 - - + +
872J LEU 3.3 0.4 - - - -
873J GLU* 1.3 84.2 - - - +
875J ASN* 1.3 67.8 + - - +
876J SER* 3.2 3.3 + - - -
988J PHE* 5.5 5.5 - - - -
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Residues in contact with ASN 875 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850J LYS* 3.5 35.7 - - + +
851J PRO* 5.1 9.1 - - + +
857J LEU* 3.4 28.9 - - + +
871J LEU* 3.3 22.1 + - - +
872J LEU 3.7 1.6 + - - -
873J GLU 3.5 0.2 - - - -
874J GLU* 1.3 78.8 - - - +
876J SER* 1.3 74.5 + - - +
877J VAL* 4.2 12.3 - - + +
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Residues in contact with SER 876 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851J PRO* 5.8 4.0 - - - +
872J LEU 3.3 4.3 + - - -
873J GLU 3.6 3.1 + - - -
874J GLU 3.2 7.9 - - - -
875J ASN* 1.3 83.1 + - - +
877J VAL* 1.3 66.1 + - - +
878J ASP* 3.5 8.5 + - - +
988J PHE* 2.6 55.4 + - - +
989J GLY* 5.0 0.3 - - - -
990J ARG* 3.6 29.5 + - - +
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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