Contacts of the helix formed by residues 828 - 835 (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 TYR 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A LEU* 3.3 16.4 - - + -
825A LEU* 3.2 36.3 + - + +
826A PRO* 3.1 5.2 - - - +
827A GLN* 1.3 87.8 - - + +
829A GLU* 1.3 61.2 + - - +
830A ASN 3.5 0.7 - - - -
831A HIS* 3.3 18.5 - + - +
832A LEU* 2.8 37.0 + - + +
857A GLY 5.0 2.2 - - - -
858A ILE* 3.2 45.8 - - + +
859A LEU* 4.7 5.8 + - + +
860A ASN* 4.6 4.2 + - - +
863A HIS* 2.4 52.9 + + + +
867A ILE* 3.8 9.0 - - + -
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Residues in contact with GLU 829 (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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816A VAL* 4.0 19.3 - - - +
817A GLY* 4.7 4.5 - - - -
820A LEU* 3.0 20.5 - - + +
826A PRO* 3.7 3.6 - - - +
827A GLN* 2.7 41.7 + - - -
828A TYR* 1.3 74.1 - - - +
830A ASN* 1.3 102.7 + - - +
832A LEU* 3.0 7.4 + - - +
833A MET* 2.8 36.1 + - + +
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Residues in contact with ASN 830 (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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827A GLN 4.8 2.2 - - - +
829A GLU* 1.3 116.0 + - - +
831A HIS* 1.3 53.0 + - + +
833A MET* 3.4 8.4 - - - +
834A ALA* 2.5 40.2 + - + +
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Residues in contact with HIS 831 (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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827A GLN* 2.4 33.0 + - + -
828A TYR* 3.3 29.9 + + + +
829A GLU 3.1 0.2 - - - -
830A ASN* 1.3 80.0 - - + +
832A LEU* 1.3 63.7 + - - +
834A ALA* 3.1 10.4 + - + +
835A ASN* 2.8 19.6 + - - +
856A ILE* 3.0 39.8 - - + +
857A GLY* 4.3 14.4 + - - -
858A ILE* 5.0 0.2 - - + -
859A LEU* 5.9 2.0 - - - +
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Residues in contact with LEU 832 (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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816A VAL* 3.4 25.8 - - + -
819A TRP* 4.1 10.5 - - + -
820A LEU* 4.4 13.0 - - + -
828A TYR* 2.8 34.5 + - + +
829A GLU 3.4 7.6 - - - +
831A HIS* 1.3 71.7 - - - +
833A MET* 1.3 63.0 + - + +
835A ASN 2.9 7.8 + - - -
837A PHE* 2.5 45.4 + - + +
840A VAL* 4.6 0.2 - - + -
843A MET* 3.3 33.7 - - + -
856A ILE* 3.3 28.4 - - + +
858A ILE* 5.2 2.9 - - + -
867A ILE* 5.5 2.5 - - + -
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Residues in contact with MET 833 (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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815A THR* 6.4 0.2 - - + -
816A VAL* 3.5 34.8 - - + +
829A GLU* 2.8 26.6 + - + +
830A ASN* 3.4 9.6 - - - +
832A LEU* 1.3 71.6 - - + +
834A ALA* 1.3 57.5 + - - +
836A GLY* 2.6 26.0 + - - +
837A PHE 2.9 28.0 - - - +
838A ASP* 3.9 17.9 - - - +
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Residues in contact with ALA 834 (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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830A ASN 2.5 21.8 + - - +
831A HIS* 3.3 11.0 - - + +
833A MET* 1.3 71.9 - - - +
835A ASN* 1.3 57.6 + - - +
836A GLY 3.4 2.4 + - - -
856A ILE 5.9 0.7 - - - +
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Residues in contact with ASN 835 (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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831A HIS 2.8 12.4 + - - +
832A LEU 2.9 7.4 + - - +
834A ALA* 1.3 75.3 - - - +
836A GLY* 1.3 63.4 + - - +
837A PHE* 3.0 28.3 + - + -
855A GLU* 3.0 48.6 + - - +
856A ILE* 3.1 9.0 + - + -
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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