Contacts of the helix formed by residues 876 - 891 (chain J) in PDB entry 4XLN
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 SER 876 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792J ILE 4.6 0.3 + - - -
793J THR 4.3 5.9 + - - -
795J VAL* 3.7 20.9 - - - +
860J LEU 3.4 12.5 + - - -
861J GLN* 3.9 13.1 - - - -
862J ASP 3.2 17.3 - - - -
864J VAL* 5.1 0.9 - - - -
875J THR* 1.3 77.7 - - - +
877J PRO* 1.3 62.6 - - - +
878J GLY* 4.3 0.5 - - - -
879J ARG* 2.9 39.9 + - - +
880J ILE* 3.3 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 877 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843J PHE* 5.3 0.2 - - + -
849J ALA* 5.1 10.5 - - + -
850J LEU* 4.2 14.4 - - + +
853J VAL* 3.7 32.5 - - + -
858J LEU* 4.3 8.7 - - + -
859J ASP 3.9 8.3 - - - +
860J LEU* 3.4 17.3 - - + +
862J ASP 3.1 15.5 - - - +
864J VAL* 4.1 13.9 - - + -
876J SER* 1.3 83.2 - - - +
878J GLY* 1.3 55.0 + - - +
879J ARG 3.3 0.2 - - - -
880J ILE* 3.7 10.5 + - + +
881J LEU* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 878 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792J ILE* 3.4 36.6 - - - +
793J THR* 4.1 0.8 - - - +
860J LEU* 2.8 21.5 + - - +
877J PRO* 1.3 76.6 - - - +
879J ARG* 1.3 59.6 + - - +
881J LEU* 3.3 8.9 - - - +
882J PHE* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 879 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792J ILE 4.5 0.2 + - - -
793J THR* 2.9 42.4 + - - +
795J VAL* 3.4 29.3 - - - +
875J THR* 4.3 11.3 - - + +
876J SER* 2.9 23.4 + - - +
878J GLY* 1.3 74.5 - - - +
880J ILE* 1.3 65.7 + - + +
882J PHE* 2.9 17.9 + - - +
883J ALA* 3.0 15.0 + - - +
901J GLN 4.4 4.5 - - - -
902J MET* 3.2 47.8 + - + +
903J ASP 2.9 21.2 + - - -
904J VAL 2.9 26.9 + - - -
905J PRO* 3.2 7.7 - - - +
906J GLN* 4.9 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 880 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846J PRO* 3.8 36.1 - - + +
849J ALA* 5.8 3.6 - - + -
850J LEU* 5.4 6.5 - - + -
866J VAL* 3.8 25.4 - - + -
868J TYR* 3.7 40.8 + - + -
873J LEU* 5.1 3.1 - - + -
875J THR* 4.0 10.5 - - - +
876J SER 3.3 11.1 + - - +
877J PRO* 3.8 11.7 - - + +
879J ARG* 1.3 81.0 - - + +
881J LEU* 1.3 58.3 + - - +
883J ALA* 3.6 5.1 + - - +
884J ARG* 2.9 29.9 + - + +
902J MET* 5.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 881 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 5.1 6.3 - - - +
792J ILE* 4.4 15.3 - - + -
850J LEU* 4.5 28.0 - - + +
860J LEU* 4.2 24.5 - - + -
877J PRO 2.9 19.8 + - - +
878J GLY* 3.3 6.5 - - - +
880J ILE* 1.3 77.0 - - - +
882J PHE* 1.3 56.7 + - - +
884J ARG* 3.2 12.5 + - - +
885J ILE* 2.9 50.2 + - + +
937J TYR* 5.1 6.3 - - + -
941J LEU* 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 882 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789J LEU* 4.3 29.8 - - + -
792J ILE* 4.5 3.8 - - + +
793J THR* 3.8 16.6 - - + -
878J GLY 2.9 15.0 + - - +
879J ARG* 2.9 10.2 + - + +
881J LEU* 1.3 74.8 - - - +
883J ALA* 1.3 65.8 + - - +
885J ILE* 2.9 21.6 + - + +
886J VAL* 3.0 35.2 + - + +
900J ILE* 3.5 33.0 - - + -
902J MET* 4.8 2.9 - - + -
906J GLN* 3.6 32.1 - - + -
911J LEU* 3.6 24.5 - - + -
914J LEU* 5.1 6.1 - - + -
934J LEU* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 883 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868J TYR* 3.7 23.4 + - + +
879J ARG 3.0 10.7 + - - +
880J ILE* 3.9 4.5 - - - +
882J PHE* 1.3 76.5 - - - +
884J ARG* 1.3 57.2 + - - +
886J VAL* 3.9 0.9 - - - +
887J GLY* 2.9 26.9 + - - -
893J GLU* 4.7 0.9 - - - +
896J ALA* 4.6 4.0 - - - +
897J GLN* 4.8 4.6 + - + -
900J ILE* 4.2 15.7 - - + -
902J MET* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 884 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 3.0 54.3 - - - +
200H TRP* 4.2 12.7 - - - -
846J PRO* 5.4 8.6 - - + +
847J ASP* 4.6 11.7 + - - -
850J LEU* 3.4 22.3 - - + +
868J TYR* 4.0 9.8 + - + +
880J ILE* 2.9 23.7 + - + +
881J LEU* 3.4 13.7 - - - +
883J ALA* 1.3 75.6 - - - +
885J ILE* 1.3 63.1 + - - +
887J GLY 3.9 0.2 - - - -
888J GLU* 2.5 71.1 + - - +
893J GLU* 4.6 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 885 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789J LEU* 5.1 6.7 - - + -
792J ILE* 4.9 2.7 - - + -
881J LEU* 2.9 41.8 + - + +
882J PHE* 2.9 11.9 + - + +
884J ARG* 1.3 79.8 - - - +
886J VAL* 1.3 60.3 + - + +
888J GLU* 3.8 3.2 - - - +
889J ALA* 2.9 31.2 + - + +
933J ALA* 4.8 15.3 - - + +
934J LEU* 5.2 8.3 - - + +
937J TYR* 3.5 57.7 - - + -
941J LEU* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 886 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882J PHE* 3.0 44.9 + - + +
883J ALA 3.9 0.2 - - - +
885J ILE* 1.3 76.5 - - + +
887J GLY* 1.3 57.0 + - - +
889J ALA* 3.2 2.1 + - - +
890J VAL* 2.9 39.7 + - + +
896J ALA* 4.2 8.1 - - + -
899J LEU* 5.2 2.0 - - + -
900J ILE* 3.6 25.1 - - + -
914J LEU* 4.2 15.0 - - + -
930J LEU* 3.8 22.7 - - + -
934J LEU* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 887 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883J ALA 2.9 16.5 + - - -
884J ARG 3.9 0.2 - - - -
886J VAL* 1.3 77.7 - - - +
888J GLU* 1.3 51.1 + - - +
890J VAL* 3.5 0.8 + - - -
891J GLY* 2.7 30.1 + - - -
892J ASP 3.2 11.2 + - - -
893J GLU* 3.6 18.4 - - - -
896J ALA* 3.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 888 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 4.0 6.6 + - - -
198H ARG* 5.8 6.1 + - - +
200H TRP* 4.1 15.6 + - - -
884J ARG* 2.5 60.8 + - - +
885J ILE* 4.0 3.7 - - - +
887J GLY* 1.3 73.7 - - - +
889J ALA* 1.3 64.1 + - - +
891J GLY* 3.7 10.6 + - - +
893J GLU* 4.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 889 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885J ILE* 2.9 19.3 + - + +
886J VAL 3.5 5.8 - - - +
888J GLU* 1.3 77.1 - - - +
890J VAL* 1.3 63.9 + - - +
926J LYS* 5.0 1.4 - - - +
929J ARG* 4.3 25.9 + - - +
930J LEU* 4.1 20.0 + - + -
933J ALA* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 890 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886J VAL* 2.9 28.1 + - + +
887J GLY 4.0 2.7 - - - +
889J ALA* 1.3 76.6 - - - +
891J GLY* 1.3 57.4 + - - +
892J ASP* 3.4 25.5 + - - +
895J VAL* 4.5 2.5 - - + -
896J ALA* 5.2 4.3 - - + -
918J ALA* 6.0 1.1 - - + -
922J LEU* 3.7 37.2 - - + -
926J LYS* 4.0 37.1 + - + +
929J ARG* 4.8 3.1 + - - -
930J LEU* 4.4 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 891 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887J GLY 2.7 13.0 + - - -
888J GLU* 3.7 9.8 + - - -
889J ALA 3.3 2.4 - - - -
890J VAL* 1.3 77.7 - - - +
892J ASP* 1.3 58.1 + - - +
929J ARG* 5.9 1.6 - - - -
----------------------------------------------------------
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