Contacts of the helix formed by residues 817 - 823 (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 GLY 817 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A THR 3.1 3.9 + - - -
816A VAL* 1.3 78.3 - - - +
818A GLN* 1.3 53.3 + - - +
819A TRP 3.0 4.0 - - - +
820A LEU* 2.7 34.7 + - - +
821A GLU* 2.7 27.2 + - - +
829A GLU* 4.7 5.2 - - - -
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Residues in contact with GLN 818 (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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814A GLN* 2.8 40.6 + - + +
815A THR 4.3 3.2 + - - -
817A GLY* 1.3 72.4 - - - +
819A TRP* 1.3 50.3 + - - +
821A GLU* 3.4 21.5 + - - +
822A SER* 2.4 49.0 + - - +
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Residues in contact with TRP 819 (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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814A GLN* 5.7 0.8 - - - +
815A THR 5.2 1.2 + - - +
816A VAL* 4.2 0.9 - - + -
817A GLY 4.0 4.2 - - - +
818A GLN* 1.3 78.4 - - - +
820A LEU* 1.3 90.9 + - + +
822A SER* 3.2 9.5 + - - -
823A ILE* 3.1 25.2 + - + +
832A LEU* 4.1 16.4 - - + -
840A VAL* 3.1 47.1 - - + -
843A MET* 5.1 4.5 - - + -
867A ILE* 3.8 18.4 - - + -
870A ALA* 2.9 46.1 + - + +
871A ILE* 3.2 36.6 - - + -
873A LEU* 5.3 1.3 - - + +
874A LEU* 3.6 26.2 - - + +
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Residues in contact with LEU 820 (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 13.2 - - + -
817A GLY* 2.7 14.4 + - - +
819A TRP* 1.3 101.0 - - + +
821A GLU* 1.3 56.1 + - + +
823A ILE* 2.9 14.1 - - + +
824A GLY 2.9 1.6 + - - -
825A LEU 2.6 43.3 + - - +
826A PRO* 4.7 3.1 - - + -
828A TYR* 3.3 19.5 - - + +
829A GLU* 3.0 49.6 - - + +
832A LEU* 4.4 3.4 - - + -
867A ILE* 3.8 14.6 - - + -
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Residues in contact with GLU 821 (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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817A GLY* 2.7 20.6 + - - +
818A GLN* 3.4 33.2 + - + +
820A LEU* 1.3 70.1 - - + +
822A SER* 1.3 60.0 + - - +
824A GLY* 2.6 25.9 + - - +
825A LEU 4.4 0.9 - - - +
826A PRO* 4.9 19.1 - - + +
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Residues in contact with SER 822 (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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818A GLN* 2.4 49.6 + - - +
819A TRP* 3.3 12.0 - - - -
821A GLU* 1.3 69.4 - - - +
823A ILE* 1.3 62.1 + - - +
824A GLY* 3.0 4.7 + - - -
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Residues in contact with ILE 823 (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* 3.3 11.4 - - + +
820A LEU* 2.9 33.9 - - + +
822A SER* 1.3 78.3 - - - +
824A GLY* 1.3 48.8 + - - +
825A LEU* 3.4 16.6 + - + -
866A ARG* 2.4 43.7 + - + +
867A ILE* 3.5 28.5 - - + -
870A ALA* 3.3 42.0 - - + -
873A LEU* 6.1 2.5 - - + -
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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