Contacts of the helix formed by residues 875 - 892 (chain G) in PDB entry 1SOJ
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 ASP 875 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873G HIS 4.1 1.4 + - - -
874G LEU* 1.3 74.6 - - - +
876G HIS* 1.3 66.2 + - + +
877G VAL* 2.9 20.3 + - + +
878G GLU* 2.8 44.6 + - - +
879G PHE* 3.0 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 876 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874G LEU 3.7 1.5 + - - -
875G ASP* 1.3 74.2 - - + +
877G VAL* 1.3 63.4 + - + +
879G PHE* 4.1 6.5 - - - +
880G LYS* 3.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 877 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875G ASP* 2.9 20.3 + - + +
876G HIS* 1.3 78.8 - - + +
878G GLU* 1.3 64.6 + - + +
880G LYS* 3.3 5.9 + - - +
881G ARG* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 878 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713G PHE* 4.8 8.4 - - - -
809G LEU* 4.5 19.5 - - + +
873G HIS 4.6 1.4 - - - +
874G LEU* 3.3 33.0 - - + +
875G ASP* 2.8 39.4 + - - +
877G VAL* 1.3 75.1 - - + +
879G PHE* 1.3 58.9 + - - +
881G ARG* 3.0 8.1 + - - +
882G PHE* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 879 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859G TRP* 3.8 25.4 - + - -
862G TYR* 3.9 18.8 - + - -
863G LEU* 4.9 9.4 - - + -
869G ASN* 5.4 1.8 - - - -
871G LEU* 3.7 42.4 - - + -
874G LEU* 4.2 12.5 - - + +
875G ASP 3.0 14.9 + - - +
876G HIS* 4.1 7.2 - - - +
878G GLU* 1.3 78.1 - - - +
880G LYS* 1.3 69.4 + - + +
882G PHE* 3.2 6.7 + + - +
883G ARG* 3.0 37.8 + - + +
837H ASN* 6.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 880 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876G HIS* 3.0 20.8 + - + +
877G VAL* 3.4 7.4 - - - +
878G GLU 3.2 0.2 - - - -
879G PHE* 1.3 82.4 - - + +
881G ARG* 1.3 61.6 + - - +
883G ARG* 3.5 5.7 + - - +
884G PHE* 3.3 18.8 + - - +
834H VAL* 3.5 35.7 + - - +
835H ALA* 4.1 15.0 + - - +
837H ASN* 4.2 12.7 + - - +
846H ASP* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 881 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G LEU* 4.0 16.3 - - + +
810G GLU* 2.9 32.5 + - - -
877G VAL 3.2 8.4 + - - +
878G GLU* 3.0 9.9 + - - +
880G LYS* 1.3 78.6 - - - +
882G PHE* 1.3 66.1 + - - +
884G PHE* 3.0 16.5 + - + +
885G LEU* 2.8 49.6 + - + +
922G GLU* 3.5 46.4 + - - +
926G LEU* 6.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 882 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G LEU* 4.0 25.5 - - + +
812G MET* 3.6 21.3 - - + -
813G ALA* 3.3 31.0 - - + -
816G VAL* 3.7 30.5 - - + -
859G TRP* 4.0 14.6 - + - -
870G PHE* 5.7 0.7 - + - -
871G LEU* 3.7 31.9 - - + -
874G LEU* 4.8 3.4 - - + -
878G GLU 2.8 20.4 + - - +
879G PHE* 3.5 9.6 - + - +
881G ARG* 1.3 73.1 - - - +
883G ARG* 1.3 65.6 - - - +
885G LEU* 3.2 8.7 + - - +
886G VAL* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 883 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859G TRP* 3.7 54.2 - - + +
863G LEU* 5.4 4.7 - - - +
879G PHE* 3.0 31.6 + - + +
880G LYS* 3.7 5.6 - - - +
882G PHE* 1.3 77.4 - - - +
884G PHE* 1.3 64.0 + - - +
886G VAL* 3.3 2.9 + - - +
887G ILE* 3.0 41.4 + - + +
837H ASN* 5.0 11.2 + - - -
841H ALA 4.3 1.0 + - - -
842H VAL* 3.6 47.7 + - - +
845H ASN* 4.4 1.6 + - - +
846H ASP* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 884 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880G LYS 3.3 10.7 + - - +
881G ARG* 3.0 19.7 + - + +
883G ARG* 1.3 79.3 - - - +
885G LEU* 1.3 90.6 + - + +
887G ILE* 3.1 10.4 + - + +
888G GLU* 2.9 61.9 + - + +
926G LEU* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 885 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G LEU* 5.0 4.3 - - + +
810G GLU* 3.3 41.7 - - + +
813G ALA* 3.6 15.0 - - + -
881G ARG* 2.8 46.5 + - + +
882G PHE* 3.6 9.0 - - - +
884G PHE* 1.3 101.6 - - + +
886G VAL* 1.3 63.2 + - - +
888G GLU* 3.3 5.6 + - - +
889G ALA* 3.0 23.9 + - - +
926G LEU* 4.9 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 886 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G ALA* 3.7 22.2 - - - +
816G VAL* 4.5 2.5 - - + -
817G ALA* 3.9 18.2 - - - +
820G MET* 3.8 22.4 - - - -
859G TRP* 3.7 21.8 - - + +
882G PHE* 2.9 47.3 + - + +
883G ARG 3.6 4.9 - - - +
884G PHE 3.2 0.2 - - - -
885G LEU* 1.3 77.8 - - - +
887G ILE* 1.3 61.7 + - - +
889G ALA* 3.4 2.1 + - - +
890G ILE* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 887 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855G ALA* 4.5 5.6 - - + -
859G TRP* 4.1 13.7 - - + +
883G ARG* 3.0 39.6 + - + +
884G PHE* 3.5 10.3 - - + +
886G VAL* 1.3 72.3 - - - +
888G GLU* 1.3 69.9 + - - +
890G ILE* 3.1 5.3 + - - +
891G LEU* 2.8 47.6 + - + +
845H ASN* 3.5 56.3 - - + +
846H ASP* 5.1 1.1 - - - +
847H ARG* 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 888 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884G PHE* 2.9 57.8 + - + +
885G LEU 3.6 6.7 - - - +
887G ILE* 1.3 78.4 - - - +
889G ALA* 1.3 62.0 + - - +
891G LEU* 3.7 3.6 + - - +
892G ALA* 3.2 14.4 + - - +
926G LEU* 4.0 20.7 - - + +
930G GLN* 3.1 34.4 + - - +
847H ARG* 3.2 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 889 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G ALA 5.1 0.2 - - - +
814G LEU* 4.3 15.9 - - + -
817G ALA* 3.5 25.4 - - + -
885G LEU 3.0 12.6 + - - +
886G VAL 3.6 2.0 - - - +
888G GLU* 1.3 77.6 - - - +
890G ILE* 1.3 63.5 + - - +
892G ALA* 3.2 17.2 + - - +
893G THR* 3.7 5.2 + - - +
926G LEU* 5.3 1.3 - - + +
929G CYS* 5.6 2.0 - - + +
930G GLN* 4.6 6.9 - - + +
933G ILE* 3.8 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 890 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817G ALA* 3.9 18.8 - - + +
820G MET* 3.9 38.1 - - + +
821G HIS* 4.0 23.8 - - + +
851G GLU* 3.8 24.9 - - - +
855G ALA* 3.9 30.7 - - + +
886G VAL* 3.1 20.6 + - + +
887G ILE 3.8 2.5 - - - +
889G ALA* 1.3 76.2 - - - +
891G LEU* 1.3 62.6 + - - +
893G THR* 2.5 32.3 + - - +
933G ILE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 891 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848G SER* 4.5 7.8 + - - +
851G GLU* 3.6 13.9 - - + +
852G ASN* 3.5 50.0 - - - +
855G ALA* 5.1 2.2 - - + -
887G ILE* 2.8 34.2 + - + +
888G GLU* 4.3 2.7 - - - +
890G ILE* 1.3 73.2 - - + +
892G ALA* 1.3 60.6 + - - +
893G THR 3.0 1.2 + - - -
894G ASP* 3.3 19.3 + - - +
897G LYS* 5.8 0.7 - - - +
901G PHE* 4.9 3.7 - - - -
845H ASN* 4.9 2.9 - - - +
847H ARG* 3.1 50.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 892 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888G GLU 3.2 17.9 + - - +
889G ALA 3.2 8.2 + - - +
890G ILE 3.1 1.4 - - - -
891G LEU* 1.3 77.1 - - - +
893G THR* 1.3 57.7 + - - +
894G ASP 3.1 6.7 + - - +
901G PHE* 3.6 32.6 - - + -
930G GLN* 3.8 23.3 - - + +
933G ILE* 4.8 0.2 - - + -
934G LYS* 3.5 30.6 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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