Contacts of the helix formed by residues 796 - 810 (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 ASN 796 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794A SER 4.2 9.2 + - - +
795A GLY* 1.3 74.8 - - - +
797A GLU* 1.3 59.7 + - - +
798A ILE* 3.2 15.5 + - - +
799A SER* 3.0 26.0 + - - -
800A TRP* 2.8 27.9 + - - +
826A VAL* 4.6 1.1 - - - +
828A ASN* 6.1 1.6 - - - +
831A LEU* 4.0 10.3 - - - -
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Residues in contact with GLU 797 (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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796A ASN* 1.3 75.5 - - - +
798A ILE* 1.3 58.6 + - + +
800A TRP* 3.2 0.8 + - - +
801A ASN* 2.8 36.2 + - - +
831A LEU* 3.9 27.5 - - + +
834A ARG* 4.3 4.7 + - - +
1F NAG 3.0 50.3 + - + +
1G NAG 2.8 33.6 + - - +
2G NAG 4.5 12.3 + - - +
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Residues in contact with ILE 798 (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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796A ASN* 3.2 13.5 + - - +
797A GLU* 1.3 76.6 - - + +
799A SER* 1.3 58.7 + - - +
801A ASN* 3.5 5.6 + - - +
802A TYR* 3.1 26.9 + - + +
1F NAG 4.1 22.9 - - + +
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Residues in contact with SER 799 (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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768A PHE* 4.3 6.7 - - - -
772A LEU* 3.7 33.6 - - - +
791A MET* 4.3 2.3 - - - -
794A SER 4.2 2.1 + - - -
795A GLY* 3.5 10.2 - - - -
796A ASN* 3.0 32.3 + - - -
798A ILE* 1.3 76.1 - - - +
800A TRP* 1.3 55.7 + - - +
802A TYR* 3.7 7.4 - - - +
803A THR* 2.7 37.8 + - - -
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Residues in contact with TRP 800 (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* 4.0 13.9 - - - +
796A ASN 2.8 18.3 + - - +
797A GLU 3.6 3.8 - - - +
799A SER* 1.3 77.8 + - - +
801A ASN* 1.3 67.9 + - - +
803A THR 3.2 1.4 + - - -
804A LEU* 2.9 39.6 + - + +
823A LEU* 2.9 50.0 + - + +
826A VAL* 3.7 31.0 - - + +
831A LEU* 3.8 31.4 - - + -
832A LEU* 5.6 0.2 - - - +
834A ARG* 3.7 32.5 - - + -
835A TYR* 3.7 41.3 - + + -
838A LEU* 4.5 12.3 - - + -
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Residues in contact with ASN 801 (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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797A GLU* 2.8 21.4 + - - +
798A ILE* 3.8 4.3 - - - +
800A TRP* 1.3 76.6 - - - +
802A TYR* 1.3 58.0 + - - +
804A LEU* 3.4 7.3 + - - +
805A GLU* 3.0 32.2 + - + +
834A ARG* 2.9 23.5 + - - -
1F NAG 1.5 67.1 + - - +
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Residues in contact with TYR 802 (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* 3.8 21.8 + + - -
772A LEU* 3.6 39.9 - - + -
774A GLY* 3.5 24.5 + - - -
798A ILE* 3.1 18.8 + - + +
799A SER* 3.7 7.2 - - - +
800A TRP 3.2 0.2 - - - -
801A ASN* 1.3 76.1 - - - +
803A THR* 1.3 57.6 + - - +
805A GLU* 3.1 21.5 + - - +
806A GLN* 2.9 64.6 + - + +
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Residues in contact with THR 803 (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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768A PHE* 4.5 2.2 - - + -
771A TRP* 3.7 24.3 - - + -
787A TYR* 6.1 1.8 - - + -
791A MET* 3.2 20.0 - - + +
799A SER 2.7 22.2 + - - -
800A TRP 3.5 5.4 - - - -
802A TYR* 1.3 76.7 - - - +
804A LEU* 1.3 56.1 + - - +
806A GLN* 3.1 3.0 + - - +
807A TYR* 2.9 28.8 + - - +
819A LEU* 3.8 29.5 - - + +
822A GLY* 5.1 2.0 - - - -
823A LEU* 3.8 21.3 - - + +
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Residues in contact with LEU 804 (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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800A TRP* 2.9 37.3 + - + +
801A ASN* 3.6 9.4 - - - +
803A THR* 1.3 76.3 - - - +
805A GLU* 1.3 61.7 + - - +
807A TYR* 3.4 12.5 + - + +
808A GLN* 3.2 30.8 + - - +
820A LEU* 6.2 0.2 - - + -
823A LEU* 3.8 26.3 - - + +
834A ARG* 4.1 13.5 - - - +
835A TYR* 5.9 1.3 - - + -
838A LEU* 4.0 26.0 - - + -
844A LEU* 4.2 16.2 - - + -
845A ILE* 5.9 1.8 - - + -
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Residues in contact with GLU 805 (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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801A ASN 3.0 16.6 + - - +
802A TYR* 3.3 23.8 - - - +
804A LEU* 1.3 75.5 - - + +
806A GLN* 1.3 59.2 + - - +
808A GLN* 3.2 16.1 + - - +
809A LYS* 3.0 56.6 + - + +
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Residues in contact with GLN 806 (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* 3.9 25.5 - - + +
802A TYR* 2.9 58.4 + - + +
803A THR 3.5 7.4 - - - +
805A GLU* 1.3 77.0 - - - +
807A TYR* 1.3 57.0 + - - +
809A LYS* 3.7 21.9 + - - +
810A THR* 3.0 35.5 + - - +
819A LEU* 4.0 7.6 - - + -
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Residues in contact with TYR 807 (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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803A THR 2.9 13.6 + - - +
804A LEU* 3.6 24.5 - - + +
806A GLN* 1.3 78.9 - - - +
808A GLN* 1.3 67.6 + - + +
810A THR* 3.6 1.8 - - - +
816A LYS* 2.9 71.5 + - + +
819A LEU* 3.7 21.0 - - + +
820A LEU* 3.7 32.7 - - + +
823A LEU* 4.7 3.6 - - + -
844A LEU* 2.7 37.7 + - + -
845A ILE* 3.7 19.1 - - + +
846A LYS* 4.6 4.9 + - - +
849A ASP* 5.0 4.3 + - - -
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Residues in contact with GLN 808 (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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804A LEU* 3.2 26.2 + - - +
805A GLU* 3.2 16.0 + - - +
807A TYR* 1.3 84.3 - - + +
809A LYS* 1.3 63.1 + - + +
810A THR 4.0 0.5 - - - +
816A LYS* 3.6 11.3 + - - +
843A ASN 5.7 1.2 + - - +
844A LEU* 3.6 41.2 - - + +
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Residues in contact with LYS 809 (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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805A GLU* 3.0 43.9 + - - +
806A GLN* 3.2 24.1 + - - +
808A GLN* 1.3 78.4 - - + +
810A THR* 1.3 63.2 + - - +
811A SER* 3.6 4.9 + - - -
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Residues in contact with THR 810 (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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806A GLN* 3.0 18.7 + - - +
807A TYR 3.6 9.4 - - - +
808A GLN 3.5 0.5 - - - +
809A LYS* 1.3 77.8 - - - +
811A SER* 1.3 59.7 + - - +
812A LEU* 3.3 18.2 + - - +
815A GLU* 4.0 15.4 - - + +
816A LYS* 2.5 47.0 + - + +
819A LEU* 4.0 17.9 - - + -
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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