Contacts of the helix formed by residues 819 - 837 (chain A) in PDB entry 4K6J
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 819 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A ARG 3.3 11.2 + - - -
817A LEU 3.5 1.0 + - - -
818A LEU* 1.3 78.2 - - - +
820A GLY* 1.3 64.7 + - - +
821A LEU 3.3 2.9 - - - -
822A ASP* 3.1 34.0 + - - +
823A HIS* 3.5 18.6 + - - -
871A TYR* 5.3 0.4 - - - -
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Residues in contact with GLY 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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742A ASP* 5.2 2.9 - - - -
745A ILE* 3.4 28.4 - - - +
815A LEU* 2.8 16.6 + - - +
818A LEU 3.3 5.1 + - - -
819A GLY* 1.3 77.1 - - - +
821A LEU* 1.3 62.0 + - - -
823A HIS* 3.2 18.6 + - - +
824A ILE* 3.2 17.0 + - - +
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Residues in contact with LEU 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A LEU* 2.9 35.2 + - + +
816A ARG* 3.8 15.7 - - + +
819A GLY 3.3 0.4 - - - -
820A GLY* 1.3 74.1 - - - +
822A ASP* 1.3 66.8 + - - +
824A ILE* 4.0 13.0 - - + +
825A VAL* 3.1 29.4 + - - +
857A VAL* 5.5 0.2 - - + -
858A LEU* 4.2 10.5 - - + -
861A VAL* 4.1 25.6 - - + -
868A ASN* 3.6 31.9 - - + +
871A TYR* 4.5 12.1 - - + -
872A LEU* 4.2 25.4 - - + -
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Residues in contact with ASP 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ARG 5.0 0.2 - - - +
819A GLY* 3.1 22.5 + - - +
821A LEU* 1.3 77.6 - - - +
823A HIS* 1.3 61.6 + - + +
825A VAL 3.5 0.3 + - - -
826A ASP* 3.0 35.7 + - - +
871A TYR* 2.5 39.7 + - - -
875A TYR* 3.2 36.5 + - - +
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Residues in contact with HIS 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ASP* 4.9 11.6 + - - -
745A ILE* 4.2 12.8 - - + +
749A GLU* 3.1 27.1 - - - +
818A LEU 5.5 1.6 - - - -
819A GLY* 3.5 21.1 + - - -
820A GLY* 3.2 10.6 + - - +
822A ASP* 1.3 80.7 - - + +
824A ILE* 1.3 59.3 + - - +
826A ASP* 3.4 14.1 + - + +
827A LYS* 3.0 23.0 + - - +
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Residues in contact with ILE 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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745A ILE* 4.4 19.3 - - + -
748A LEU* 4.2 18.4 - - + -
749A GLU* 4.8 1.6 - - + -
799A LEU* 4.9 2.2 - - + -
815A LEU* 5.1 3.4 - - + -
820A GLY 3.2 15.0 + - - +
821A LEU* 3.4 18.6 + - + +
822A ASP 3.4 0.2 - - - -
823A HIS* 1.3 77.5 - - - +
825A VAL* 1.3 62.4 + - - +
827A LYS* 3.5 7.1 + - - +
828A VAL* 3.1 21.5 + - - +
854A CYS* 3.5 39.5 - - + +
857A VAL* 3.7 25.8 - - + -
858A LEU* 3.7 14.6 - - + -
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Residues in contact with VAL 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A LEU 3.1 18.4 + - - +
824A ILE* 1.3 74.7 - - - +
826A ASP* 1.3 65.7 + - - +
828A VAL* 3.0 19.1 + - + +
829A LYS* 3.0 11.6 + - - +
858A LEU* 4.1 12.6 - - + -
872A LEU* 3.5 27.1 - - + -
875A TYR* 3.6 33.2 - - + -
879A GLN* 4.1 10.5 - - + -
880A LEU* 4.0 31.0 - - + +
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Residues in contact with ASP 826 (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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822A ASP* 3.0 21.1 + - - +
823A HIS* 3.7 16.6 - - + +
824A ILE 3.4 0.2 - - - -
825A VAL* 1.3 75.4 - - - +
827A LYS* 1.3 57.7 + - - +
829A LYS* 3.2 13.7 + - - +
830A GLU* 3.0 26.2 + - - +
875A TYR* 2.7 30.5 + - - -
876A LYS* 3.8 16.2 + - - +
879A GLN* 5.4 1.6 - - - +
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Residues in contact with LYS 827 (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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748A LEU 4.7 0.2 - - - -
749A GLU* 2.8 51.9 + - + +
751A GLU* 2.8 34.7 + - - +
823A HIS 3.0 16.4 + - - +
824A ILE* 3.6 5.8 - - - +
825A VAL 3.1 0.2 - - - -
826A ASP* 1.3 74.9 - - - +
828A VAL* 1.3 63.9 + - - +
830A GLU* 3.3 27.0 + - - +
831A CYS* 3.1 36.4 + - - -
850A GLY 4.7 3.4 - - - -
853A ARG* 4.6 5.2 - - - +
854A CYS* 3.4 23.3 - - - -
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Residues in contact with VAL 828 (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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824A ILE 3.1 16.4 + - - +
825A VAL* 3.0 10.8 + - - +
827A LYS* 1.3 76.2 - - - +
829A LYS* 1.3 58.4 + - - +
831A CYS* 3.6 4.4 + - - +
832A VAL* 3.0 41.9 + - + +
851A ALA* 4.2 13.0 - - + +
854A CYS* 3.5 21.5 - - + -
855A LEU* 4.2 20.2 - - + -
858A LEU* 4.1 16.8 - - + -
880A LEU* 4.3 11.0 - - + -
883A SER* 4.4 10.5 - - - -
884A SER* 5.2 2.5 - - - +
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Residues in contact with LYS 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A VAL 3.0 11.2 + - - +
826A ASP* 3.4 14.6 - - - +
827A LYS 3.2 0.4 - - - -
828A VAL* 1.3 75.8 - - - +
830A GLU* 1.3 65.3 + - - +
832A VAL* 3.4 0.5 + - - +
833A ASP* 2.7 60.2 + - - +
876A LYS* 6.2 2.0 - - + -
879A GLN* 3.6 42.2 - - + +
883A SER* 3.7 15.9 - - - +
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Residues in contact with GLU 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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751A GLU* 4.9 3.6 - - - +
826A ASP 3.0 12.8 + - - +
827A LYS* 3.3 40.5 + - - +
829A LYS* 1.3 78.9 - - - +
831A CYS* 1.3 69.5 + - - +
833A ASP* 3.1 15.6 + - - +
834A HIS* 3.3 36.0 + - + +
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Residues in contact with CYS 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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751A GLU* 4.8 1.6 - - - -
827A LYS* 3.1 35.6 + - - +
828A VAL 3.9 3.4 - - - +
830A GLU* 1.3 86.6 - - - +
832A VAL* 1.3 63.6 + - - +
834A HIS* 3.1 23.2 + - - +
835A LEU* 3.5 6.7 + - - +
846A ALA 4.7 0.4 - - - -
847A SER* 3.3 33.4 - - - +
850A GLY* 3.6 31.2 - - - -
851A ALA* 3.8 8.5 - - + +
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Residues in contact with VAL 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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828A VAL* 3.0 34.5 + - + +
829A LYS 3.9 2.9 - - - +
831A CYS* 1.3 76.7 - - - +
833A ASP* 1.3 67.3 + - - +
835A LEU* 3.4 23.9 + - + +
836A SER* 3.7 3.5 + - - -
851A ALA* 4.4 12.3 - - + -
855A LEU* 6.2 0.7 - - + -
883A SER* 3.5 29.6 - - - +
884A SER* 5.7 0.2 - - - -
886A LYS* 4.3 11.4 - - + -
887A ALA* 3.5 35.0 - - + +
890A HIS* 4.1 6.1 + - + +
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Residues in contact with ASP 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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829A LYS* 2.7 53.8 + - - +
830A GLU* 3.5 7.9 - - - +
832A VAL* 1.3 82.5 - - - +
834A HIS* 1.3 65.3 + - + +
836A SER* 3.6 20.0 + - - -
837A ARG* 3.9 11.1 + - - +
883A SER* 5.3 1.2 + - - -
886A LYS* 5.1 11.8 + - - +
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Residues in contact with HIS 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 GLU* 3.3 37.1 + - + +
831A CYS* 3.1 7.6 + - - +
833A ASP* 1.3 80.7 - - + +
835A LEU* 1.3 61.9 + - - +
836A SER 3.2 1.3 - - - -
837A ARG* 3.6 39.4 + - - +
839A GLU* 3.0 30.8 - - - +
847A SER* 3.3 22.3 + - - +
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Residues in contact with LEU 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 CYS 3.8 8.5 - - - +
832A VAL* 3.4 22.4 + - + +
834A HIS* 1.3 75.9 - - - +
836A SER* 1.3 57.5 + - - +
837A ARG 2.7 18.2 - - - +
839A GLU* 3.7 3.9 - - - +
844A LEU* 3.9 16.2 - - + +
847A SER* 3.9 17.3 - - - -
848A LEU* 3.7 41.7 - - + +
887A ALA* 4.4 17.7 - - + +
890A HIS* 3.6 33.5 + - + +
891A CYS* 5.2 1.1 - - - -
894A LEU* 4.4 8.6 - - + +
929A CYS* 5.7 2.0 - - - -
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Residues in contact with SER 836 (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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832A VAL 3.7 1.5 + - - -
833A ASP* 3.6 16.5 + - - -
834A HIS 3.2 0.6 - - - -
835A LEU* 1.3 76.4 - - - +
837A ARG* 1.3 65.4 + - - +
890A HIS* 3.3 29.7 + - - -
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Residues in contact with ARG 837 (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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833A ASP 3.9 9.0 + - - +
834A HIS* 3.6 40.5 + - - +
835A LEU 2.7 19.3 - - - +
836A SER* 1.3 79.7 - - - +
838A ASP* 1.3 65.7 + - - +
839A GLU* 4.1 3.5 + - + +
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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
------------------------------------------------------------
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