Contacts of the helix formed by residues 812 - 824 (chain A) in PDB entry 4KXA
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 LEU 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLN* 5.2 1.1 - - - +
318A THR* 4.3 17.3 - - + +
373A LEU* 4.1 24.0 - - + +
375A ASP* 4.0 17.9 - - + +
378A GLU* 3.7 29.2 - - + +
379A SER* 3.5 21.1 - - - +
810A THR* 3.3 9.0 + - - +
811A SER* 1.3 76.0 - - - +
813A ALA* 1.3 68.7 + - - +
814A GLN* 4.0 5.2 - - + +
815A GLU* 3.1 24.6 + - + +
816A LYS* 3.0 22.2 + - - +
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Residues in contact with ALA 813 (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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369A GLU* 3.6 38.4 + - + +
370A THR* 3.6 17.8 - - + +
373A LEU* 6.3 0.4 - - - +
811A SER 3.3 5.7 + - - -
812A LEU* 1.3 73.5 - - - +
814A GLN* 1.3 57.5 + - - +
816A LYS* 3.2 16.7 + - + +
817A GLU* 2.9 31.4 + - - +
848A GLN* 5.9 4.7 - - - +
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Residues in contact with GLN 814 (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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370A THR* 2.9 44.1 + - - +
373A LEU 3.2 22.7 + - - +
374A TYR* 3.9 2.2 - - - +
379A SER* 2.7 38.4 + - - +
383A ASN* 3.3 38.2 + - - +
387A VAL* 3.5 17.2 - - - +
812A LEU* 3.2 9.1 - - + +
813A ALA* 1.3 75.9 - - - +
815A GLU* 1.3 61.7 + - - +
817A GLU* 3.7 5.0 + - - +
818A LYS* 3.4 30.2 + - - +
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Residues in contact with GLU 815 (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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378A GLU* 4.3 4.3 - - + +
771A TRP* 4.8 3.5 + - - -
783A ARG* 2.9 37.6 + - - +
787A TYR* 2.6 32.7 + - - -
810A THR* 4.0 18.4 - - + +
812A LEU* 3.1 24.7 + - + +
814A GLN* 1.3 76.4 - - - +
816A LYS* 1.3 65.6 + - - +
818A LYS* 3.0 22.9 + - - +
819A LEU* 3.0 29.1 + - + +
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Residues in contact with LYS 816 (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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807A TYR* 2.9 55.3 + - + +
808A GLN* 3.6 11.1 + - - +
810A THR* 2.5 39.7 + - + +
811A SER* 4.8 4.6 - - - +
812A LEU 3.0 11.1 + - - +
813A ALA* 3.3 24.5 - - + +
815A GLU* 1.3 75.2 - - - +
817A GLU* 1.3 59.3 + - - +
819A LEU* 3.0 6.4 + - - +
820A LEU* 2.9 33.1 + - + +
846A LYS* 5.3 16.6 - - + +
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Residues in contact with GLU 817 (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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368A ARG* 5.5 5.2 + - - -
370A THR* 3.9 25.6 + - + +
383A ASN* 5.7 2.9 + - - -
813A ALA 2.9 16.3 + - - +
814A GLN* 3.8 7.1 - - - +
816A LYS* 1.3 75.9 - - - +
818A LYS* 1.3 61.1 + - - +
820A LEU* 3.3 14.4 + - + +
821A TYR* 3.2 16.6 + - - +
849A ASP* 4.8 7.3 - - - +
852A THR* 4.0 18.2 + - + +
856A TYR* 3.7 28.4 + - + +
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Residues in contact with LYS 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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378A GLU 4.8 2.8 + - - -
379A SER* 4.8 3.2 - - - +
380A ALA* 4.3 16.5 - - - +
383A ASN* 2.7 33.7 + - - +
780A VAL 4.6 2.2 - - - -
783A ARG* 4.1 23.6 - - + +
784A LEU* 3.9 35.3 - - + +
787A TYR* 3.8 18.7 - - + -
814A GLN* 3.4 22.2 + - - +
815A GLU* 3.0 21.4 + - - +
817A GLU* 1.3 76.3 - - + +
819A LEU* 1.3 57.8 + - - +
821A TYR* 3.1 6.6 + - - +
822A GLY* 2.9 24.4 + - - -
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Residues in contact with LEU 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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771A TRP* 3.7 33.9 - - + -
787A TYR* 4.0 19.1 - - + -
803A THR* 3.8 17.3 - - + +
806A GLN* 4.0 8.3 - - + -
807A TYR* 3.7 38.1 - - + +
810A THR* 4.0 6.1 - - + -
815A GLU* 3.0 37.2 + - + +
816A LYS 3.0 6.5 + - - +
818A LYS* 1.3 73.4 - - - +
820A LEU* 1.3 58.8 + - - +
822A GLY* 3.2 2.6 + - - +
823A LEU* 2.9 35.6 + - - +
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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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807A TYR* 3.7 36.8 - - + +
816A LYS* 2.9 16.3 + - + +
817A GLU* 3.5 18.2 - - + +
819A LEU* 1.3 78.7 - - - +
821A TYR* 1.3 57.2 + - - +
823A LEU* 3.5 8.1 + - + -
824A ALA* 3.1 20.6 + - - +
835A TYR* 2.8 38.3 + - + +
845A ILE* 4.2 13.7 - - + -
849A ASP* 4.6 19.3 - - + +
852A THR* 5.8 2.2 - - + -
853A VAL* 4.0 16.4 - - + -
856A TYR* 4.0 10.4 - - + -
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Residues in contact with TYR 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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784A LEU* 3.8 26.9 - - + -
788A ARG* 3.3 48.6 + - - -
817A GLU 3.2 4.4 + - - +
818A LYS 3.1 9.8 + - - +
820A LEU* 1.3 76.7 - - - +
822A GLY* 1.3 64.9 + - - +
824A ALA* 3.1 9.8 + - + +
825A SER* 3.0 21.4 + - - -
856A TYR* 3.6 53.7 - + + -
859A TYR* 3.3 34.7 - + + +
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Residues in contact with GLY 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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787A TYR* 3.7 31.6 - - - +
788A ARG* 4.8 0.8 - - - +
791A MET* 3.2 26.3 - - - +
803A THR* 5.1 2.0 - - - -
818A LYS 2.9 14.0 + - - -
819A LEU* 3.2 4.4 + - - -
821A TYR* 1.3 75.1 - - - +
823A LEU* 1.3 55.2 + - - +
825A SER* 2.9 20.1 + - - -
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Residues in contact with LEU 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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791A MET* 4.7 1.1 - - + -
800A TRP* 2.9 71.3 + - + +
803A THR* 3.8 12.7 - - + +
804A LEU* 3.8 36.3 - - + +
807A TYR* 4.7 6.3 - - + -
819A LEU 2.9 24.0 + - - +
820A LEU* 3.7 23.8 - - + +
821A TYR 3.3 0.2 - - - -
822A GLY* 1.3 72.1 - - - +
824A ALA* 1.3 59.7 + - - +
825A SER 3.1 0.9 + - - -
826A VAL* 3.7 9.2 - - - +
832A LEU* 4.1 1.0 - - - +
835A TYR* 3.7 22.0 - - + +
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Residues in contact with ALA 824 (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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820A LEU 3.1 13.2 + - - +
821A TYR* 3.1 12.6 + - + +
823A LEU* 1.3 76.6 - - - +
825A SER* 1.3 57.3 + - - +
826A VAL 3.5 0.4 - - - -
832A LEU* 3.7 7.5 - - - +
835A TYR* 3.5 16.3 - - + -
856A TYR* 3.6 36.4 - - + +
857A ILE* 3.9 3.8 - - + +
860A ASN* 2.9 29.0 + - - +
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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