Contacts of the helix formed by residues 862 - 874 (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 TYR 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A LYS* 3.7 50.5 + - + -
828A ASN* 4.0 4.5 - - - -
829A VAL* 4.1 28.0 - - + -
832A LEU* 4.1 9.4 - - + -
860A ASN* 2.8 9.1 + - - +
861A SER* 1.3 81.5 - - - +
863A GLY* 1.3 65.3 + - - +
864A LYS 3.3 1.8 + - - -
865A ASN* 3.5 13.3 + - - +
866A MET* 3.5 13.7 + - - +
1G NAG 5.7 5.0 - - + +
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Residues in contact with GLY 863 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A LEU* 4.0 4.0 - - - +
857A ILE* 3.1 30.5 - - - +
858A SER* 3.4 4.7 - - - -
860A ASN* 3.0 9.1 + - - +
862A TYR* 1.3 77.1 - - - +
864A LYS* 1.3 65.8 + - - +
865A ASN 3.1 2.0 - - - -
866A MET* 3.5 15.7 - - - -
867A ALA* 2.9 19.8 + - - +
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Residues in contact with LYS 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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707A GLU* 4.8 16.3 + - - +
708A ASP* 4.9 9.3 + - - -
858A SER* 3.1 27.1 + - - +
859A TYR 5.5 0.4 - - - -
860A ASN 2.7 16.7 + - - +
861A SER* 4.5 9.6 - - - +
862A TYR 3.3 0.8 - - - -
863A GLY* 1.3 74.4 - - - +
865A ASN* 1.3 75.1 + - - +
867A ALA* 4.3 1.7 - - - +
868A TRP* 3.5 18.9 + - - +
895A ILE* 5.1 8.3 - - - +
898A PRO* 4.4 24.8 + - + +
899A PHE* 4.0 30.1 - - + -
900A ASN* 5.9 0.8 + - - -
904A GLN* 4.0 17.3 - - - +
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Residues in contact with ASN 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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862A TYR 3.5 8.0 + - - +
863A GLY 3.1 0.2 - - - -
864A LYS* 1.3 93.2 - - - +
866A MET* 1.3 58.7 + - - +
868A TRP* 3.4 9.7 + - + +
869A ASN* 2.9 32.6 + - - +
899A PHE* 4.2 19.8 - - - -
904A GLN* 5.0 4.9 + - - +
907A GLN* 5.3 2.8 - - - +
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Residues in contact with MET 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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829A VAL* 3.5 44.9 - - + +
832A LEU* 3.9 29.2 - - + -
833A SER* 3.7 23.3 - - - +
836A LEU* 4.1 16.8 - - + +
857A ILE* 4.8 1.1 - - + -
862A TYR* 3.7 14.1 - - - +
863A GLY* 3.3 10.1 + - - -
865A ASN* 1.3 76.8 - - + +
867A ALA* 1.3 57.1 + - - +
869A ASN* 3.3 5.0 + - - +
870A TRP* 2.8 31.4 + - - +
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Residues in contact with ALA 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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836A LEU* 4.7 4.9 - - + -
854A ILE* 3.5 35.4 - - + +
857A ILE* 4.1 9.1 - - + +
858A SER* 3.9 13.9 - - - +
863A GLY 2.9 16.6 + - - +
866A MET* 1.3 76.2 - - - +
868A TRP* 1.3 62.9 + - - +
870A TRP* 3.3 6.1 + - - +
871A ILE* 3.0 29.8 + - - +
895A ILE* 3.9 3.4 - - + -
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Residues in contact with TRP 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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864A LYS 3.5 18.3 + - - +
865A ASN* 3.4 10.5 + - - +
866A MET 3.3 0.4 - - - -
867A ALA* 1.3 78.5 - - - +
869A ASN* 1.3 60.5 + - - +
871A ILE* 3.3 40.3 - - + +
872A GLN* 3.0 44.2 + - - +
893A VAL* 4.4 11.9 - - + -
895A ILE* 3.8 15.1 - - + +
896A ALA* 4.0 19.1 - - + -
899A PHE* 3.8 24.4 - + + -
907A GLN* 3.4 28.3 + - - +
908A MET* 3.7 42.8 - - + -
911A PHE* 4.1 18.6 - + - -
912A PHE* 4.5 6.5 - + - -
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Residues in contact with ASN 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 ASN 2.9 21.9 + - - +
866A MET* 3.8 5.4 - - - +
868A TRP* 1.3 73.9 - - + +
870A TRP* 1.3 61.2 + - - +
872A GLN* 3.3 15.4 + - - +
873A LEU* 3.0 57.6 + - - +
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Residues in contact with TRP 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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836A LEU* 3.8 56.6 + - + +
837A ASP* 4.8 6.7 + - - +
839A LEU* 3.9 19.1 - - + -
840A LYS* 4.1 22.2 - - + +
850A VAL* 5.3 0.9 - - + -
854A ILE* 3.7 26.7 - - + -
866A MET 2.8 17.5 + - - +
867A ALA 3.3 3.8 + - - +
869A ASN* 1.3 74.9 - - - +
871A ILE* 1.3 70.8 + - + +
873A LEU* 3.4 6.9 + - + -
874A ASN* 2.9 61.3 + - + +
877A TYR* 4.8 4.3 - + - -
878A LEU* 3.9 28.5 - - + -
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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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854A ILE* 3.9 29.8 - - + -
867A ALA 3.0 19.4 + - - +
868A TRP* 3.3 42.6 - - + +
870A TRP* 1.3 86.8 - - + +
872A GLN* 1.3 59.1 + - + +
874A ASN 3.7 0.2 - - - -
875A TRP* 3.0 40.6 + - + +
878A LEU* 4.3 13.5 - - + -
892A ILE* 4.2 25.1 - - + +
893A VAL* 4.7 9.2 - - + -
895A ILE* 4.1 9.2 - - + -
911A PHE* 4.8 4.0 - - + -
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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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868A TRP* 3.0 52.7 + - + +
869A ASN* 3.3 17.5 + - - +
870A TRP 3.2 0.6 - - - -
871A ILE* 1.3 78.4 - - + +
873A LEU* 1.3 66.6 + - + +
874A ASN 3.2 0.5 + - - -
875A TRP* 3.4 14.0 + - - +
907A GLN* 4.7 6.0 - - - +
911A PHE* 3.5 54.1 - - + +
915A TYR* 4.4 9.7 + - - -
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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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869A ASN* 3.0 45.3 + - - +
870A TRP* 3.9 8.5 - - + +
872A GLN* 1.3 77.0 - - + +
874A ASN* 1.3 70.3 + - - +
875A TRP 3.8 0.7 + - - -
876A ASP* 5.3 0.7 + - - +
915A TYR* 5.8 0.2 + - - -
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Residues in contact with ASN 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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840A LYS* 2.9 29.1 - - - +
870A TRP* 2.9 65.8 + - + +
871A ILE 3.7 2.9 - - - -
873A LEU* 1.3 88.5 + - - +
875A TRP* 1.3 64.6 + - - +
876A ASP 3.4 2.7 - - - -
877A TYR* 3.3 13.2 + - + +
878A LEU* 3.0 24.0 + - - +
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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