Contacts of the helix formed by residues 860 - 874 (chain A) in PDB entry 2KE7
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 ASN 860 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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828A TYR* 4.6 1.2 + - - +
859A LEU* 1.3 75.9 - - - +
861A SER* 1.3 54.9 + - - +
862A GLY* 2.8 12.9 + - - +
863A HIS* 2.6 65.3 + - + +
864A ARG* 2.7 32.1 + - - +
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Residues in contact with SER 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859A LEU 2.8 2.7 + - - -
860A ASN* 1.3 71.7 - - - +
862A GLY* 1.3 53.3 + - - +
864A ARG* 2.3 43.9 + - - +
865A GLN* 2.5 49.7 + - - +
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Residues in contact with GLY 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860A ASN* 2.8 11.7 + - - +
861A SER* 1.3 78.5 - - - +
863A HIS* 1.3 50.5 + - - +
865A GLN* 3.3 9.3 + - - +
866A ARG* 2.7 46.8 + - - +
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Residues in contact with HIS 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A LEU* 3.3 34.4 - - + +
828A TYR* 2.4 45.7 + + + +
858A ILE* 3.8 2.5 - - + -
860A ASN* 2.6 39.2 + - + +
862A GLY* 1.3 71.5 - - - +
864A ARG* 1.3 56.1 + - - +
866A ARG* 2.9 12.7 + - - +
867A ILE* 2.5 41.3 + - - +
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Residues in contact with ARG 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A ASP* 2.5 41.5 + - - +
853A LEU* 3.1 31.2 - - + +
854A LEU* 3.7 15.9 - - - +
858A ILE* 2.7 40.6 - - + +
859A LEU 2.9 9.2 + - - -
860A ASN 2.7 18.5 + - - +
861A SER* 2.3 50.2 + - - +
863A HIS* 1.3 72.9 - - - +
865A GLN* 1.3 53.6 + - + +
867A ILE* 3.1 1.2 + - - +
868A LEU* 2.6 32.7 + - - +
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Residues in contact with GLN 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861A SER* 2.5 31.5 + - - +
862A GLY* 3.5 8.1 - - - +
864A ARG* 1.3 74.2 - - + +
866A ARG* 1.3 54.3 + - + +
868A LEU* 3.1 11.2 + - + +
869A GLN* 2.7 44.4 + - + +
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Residues in contact with ARG 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A ILE* 2.4 38.0 + - + +
824A GLY* 2.9 19.8 + - - -
825A LEU* 3.2 29.3 - - + +
862A GLY* 2.7 30.0 + - - +
863A HIS* 3.3 14.2 + - - +
865A GLN* 1.3 72.3 - - + +
867A ILE* 1.3 50.9 + - - +
869A GLN* 3.0 9.5 + - - +
870A ALA* 2.4 37.4 + - - +
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Residues in contact with ILE 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A TRP* 3.8 17.0 - - + -
820A LEU* 3.8 14.8 - - + -
823A ILE* 3.5 21.8 - - + -
825A LEU* 4.1 4.5 - - + -
828A TYR* 3.8 22.0 - - + -
832A LEU* 5.5 2.0 - - + -
843A MET* 6.4 0.4 - - + -
853A LEU* 3.3 24.7 - - + -
856A ILE* 5.5 5.4 - - + -
858A ILE* 4.1 17.0 - - + -
863A HIS 2.5 27.4 + - - +
864A ARG 3.5 4.5 - - - +
866A ARG* 1.3 71.4 - - - +
868A LEU* 1.3 52.9 + - - +
870A ALA* 2.8 5.5 + - - +
871A ILE* 2.7 37.2 + - + +
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Residues in contact with LEU 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848A MET* 4.5 3.4 - - + -
849A GLU* 3.9 38.8 - - - +
850A ASP* 5.5 4.9 - - + +
853A LEU* 4.2 9.8 - - + +
864A ARG 2.6 17.2 + - - +
865A GLN* 3.3 14.6 - - + +
867A ILE* 1.3 71.5 - - - +
869A GLN* 1.3 59.8 + - + +
871A ILE* 2.8 36.7 - - + +
872A GLN* 3.0 34.2 + - - +
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Residues in contact with GLN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865A GLN* 2.7 24.8 + - + +
866A ARG* 3.4 10.8 - - - +
868A LEU* 1.3 69.6 - - + +
870A ALA* 1.3 56.4 + - - +
872A GLN* 2.5 39.4 + - - +
873A LEU* 2.7 48.6 + - + +
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Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A TRP* 2.9 33.2 + - + +
823A ILE* 3.3 38.1 - - + -
866A ARG 2.4 23.5 + - - +
867A ILE* 2.8 13.2 + - - +
869A GLN* 1.3 73.3 - - - +
871A ILE* 1.3 60.0 + - - +
873A LEU* 3.1 20.1 + - - +
874A LEU 3.4 3.1 + - - -
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Residues in contact with ILE 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A TRP* 3.2 28.9 - - + -
840A VAL 4.8 0.7 - - - +
843A MET* 4.7 8.1 - - + -
844A GLY* 3.6 28.9 - - - +
847A VAL 3.4 24.5 - - - +
848A MET* 3.7 26.2 - - + -
849A GLU 4.8 0.2 - - - +
853A LEU* 5.8 3.1 - - + -
867A ILE* 2.7 18.0 + - + +
868A LEU* 2.8 38.8 - - + +
870A ALA* 1.3 69.4 - - - +
872A GLN* 1.3 64.1 + - + +
874A LEU* 2.8 33.9 + - + +
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Residues in contact with GLN 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844A GLY 5.7 0.2 - - - -
848A MET* 5.9 7.6 - - + -
868A LEU* 3.0 49.8 + - - +
869A GLN* 2.5 43.6 + - - +
871A ILE* 1.3 81.2 - - + +
873A LEU* 1.3 64.6 + - + +
874A LEU 3.3 7.3 + - - +
876A LYS* 4.2 21.4 + - - +
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Residues in contact with LEU 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A TRP* 5.3 1.3 - - + +
823A ILE* 6.1 1.8 - - + -
869A GLN* 2.7 27.1 + - + +
870A ALA* 3.2 16.8 - - - +
871A ILE 3.1 0.2 - - - -
872A GLN* 1.3 81.6 - - + +
874A LEU* 1.3 61.8 + - + +
875A PRO* 3.4 7.6 - - - +
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Residues in contact with LEU 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A TRP* 3.6 36.8 - - + +
840A VAL* 3.0 49.4 - - + +
841A GLN* 3.9 17.0 - - + +
844A GLY* 4.3 6.3 - - - +
870A ALA 3.4 9.0 - - - +
871A ILE* 2.8 22.8 + - - +
872A GLN 3.5 7.4 - - - +
873A LEU* 1.3 78.9 - - + +
875A PRO* 1.3 79.2 - - + +
876A LYS* 3.5 5.7 + - - +
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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