Contacts of the helix formed by residues 860 - 874 (chain A) in PDB entry 2XT6
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 VAL 860 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A VAL* 3.9 14.4 - - + -
857A HIS* 2.9 26.7 + - + +
859A ARG* 1.4 79.2 - - + +
861A ARG* 1.3 65.7 + - - +
862A PRO 3.4 0.4 - - - -
863A VAL* 3.0 25.2 + - + +
864A LEU* 3.4 11.2 + - + +
912A HIS* 3.8 31.2 - - + +
915A ILE* 3.8 32.3 - - + -
916A VAL 6.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 861 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A LEU* 5.0 9.1 - - + +
850A LEU* 4.1 17.6 - - - +
854A PHE 4.7 5.7 + - - -
855A THR* 5.4 0.2 - - - +
856A VAL* 3.4 45.1 + - + +
857A HIS 3.0 13.6 + - - +
858A PRO* 4.2 6.1 - - + +
860A VAL* 1.3 74.4 - - - +
862A PRO* 1.4 69.1 - - + +
863A VAL 3.0 1.7 + - - -
864A LEU* 3.0 18.5 + - + +
865A GLU* 3.2 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A PRO 3.2 22.7 - - - +
859A ARG* 3.6 16.8 - - - +
860A VAL 3.6 0.9 - - - -
861A ARG* 1.4 88.2 - - + +
863A VAL* 1.3 55.5 + - + +
865A GLU* 3.5 12.6 + - + +
866A LYS* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A ARG 4.0 13.5 - - - +
860A VAL* 3.0 13.0 + - + +
862A PRO* 1.3 75.7 - - + +
864A LEU* 1.3 61.2 + - + +
866A LYS* 3.4 6.1 + - - +
867A ARG* 3.0 54.6 + - + +
909A THR 5.7 1.6 - - - +
910A GLN 5.2 0.7 - - - +
912A HIS* 4.0 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A HIS* 3.4 54.6 - - + +
848A LEU* 3.9 12.0 - - + +
850A LEU* 4.4 5.2 - - + -
856A VAL* 3.8 34.1 - - + -
860A VAL* 3.7 12.8 - - + +
861A ARG* 3.0 10.3 + - + +
863A VAL* 1.3 78.4 - - + +
865A GLU* 1.3 61.9 + - - +
867A ARG* 3.3 6.9 + - - +
868A ARG* 3.2 19.9 + - - +
912A HIS* 5.5 3.4 - - + +
915A ILE* 3.9 34.3 - - + -
926A PRO* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A LEU* 4.0 22.5 - - + +
861A ARG* 3.2 42.6 + - - +
862A PRO* 3.7 14.0 - - + +
864A LEU* 1.3 75.9 - - - +
866A LYS* 1.3 63.4 + - - +
868A ARG* 3.3 5.8 + - - +
869A GLU* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A PRO 2.9 18.7 + - - +
863A VAL* 3.4 7.6 + - - +
865A GLU* 1.3 74.0 - - - +
867A ARG* 1.3 53.1 + - + +
869A GLU* 2.8 42.1 + - - +
870A MET* 2.8 72.3 + - + +
874A GLY 5.3 2.2 + - - -
875A ARG* 5.3 8.0 + - - +
877A ASP* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A GLY* 4.4 1.6 - - - -
847A HIS* 3.5 36.9 + - + +
863A VAL* 3.0 31.5 + - + +
864A LEU* 3.5 10.2 - - - +
865A GLU 3.3 0.2 - - - -
866A LYS* 1.3 74.9 - - + +
868A ARG* 1.4 61.9 + - - +
870A MET* 3.5 4.2 + - - -
871A ALA* 3.1 19.4 + - - +
877A ASP* 5.2 2.4 + - - +
879A ALA* 3.8 13.9 - - - +
880A PHE* 3.2 50.1 - - + +
883A LEU* 3.3 21.0 - - - +
910A GLN 2.8 28.9 + - - -
911A ARG 2.8 21.4 + - - -
912A HIS* 4.1 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A GLY* 3.9 17.9 + - - +
845A ASP* 3.6 20.6 + - - +
848A LEU* 3.6 33.4 - - + -
864A LEU 3.2 6.6 + - - +
865A GLU 3.3 6.9 + - - +
867A ARG* 1.4 74.2 - - - +
869A GLU* 1.4 68.7 + - - +
871A ALA* 3.3 5.7 + - - +
872A TYR* 3.0 76.9 - - + +
873A GLU* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLU 3.2 12.6 + - - +
866A LYS* 2.8 44.2 + - - +
868A ARG* 1.4 87.2 - - - +
870A MET* 1.3 52.3 + - - +
872A TYR* 3.2 2.4 + - - -
873A GLU* 2.7 58.0 + - + +
874A GLY 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A LYS* 2.8 55.7 + - + +
867A ARG* 3.7 2.9 - - - +
869A GLU* 1.3 73.1 - - - +
871A ALA* 1.3 59.4 + - - +
874A GLY* 2.9 36.6 + - - +
875A ARG 3.3 24.9 - - - +
876A ILE* 3.6 12.6 - - + +
877A ASP* 3.4 48.0 - - + +
880A PHE* 3.7 26.0 - - + -
1079A VAL* 5.8 0.7 - - + -
1082A ILE* 4.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A LYS* 5.8 0.5 - - - +
840A LEU* 3.3 43.8 - - + +
841A GLN* 3.6 19.0 + - - +
844A GLY* 3.8 11.7 - - - -
867A ARG 3.1 17.1 + - - +
868A ARG 3.6 6.3 - - - +
869A GLU 3.3 0.2 - - - -
870A MET* 1.3 74.8 - - - +
872A TYR* 1.3 59.6 + - + +
876A ILE* 5.0 2.5 - - - -
880A PHE* 3.7 9.6 - - + -
1082A ILE* 3.9 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A GLN* 3.6 53.9 + - + +
845A ASP* 2.6 39.6 + - - -
868A ARG* 3.0 60.8 - - + +
869A GLU 3.2 3.7 + - - +
871A ALA* 1.3 80.5 - - + +
873A GLU* 1.4 69.0 + - + +
1082A ILE* 3.4 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A ARG* 5.5 3.1 - - - +
869A GLU* 2.7 43.3 + - + +
872A TYR* 1.4 83.5 - - + +
874A GLY* 1.3 60.1 + - - +
875A ARG* 5.3 2.8 - - - +
1082A ILE* 3.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A LYS* 5.3 1.7 + - - -
869A GLU* 5.6 0.3 - - - +
870A MET* 2.9 30.9 + - - +
873A GLU* 1.3 81.2 - - - +
875A ARG* 1.3 72.1 + - - +
876A ILE* 3.3 4.3 - - - -
1080A SER 4.4 3.1 - - - -
1081A ASP* 5.0 0.9 - - - -
1082A ILE* 3.4 22.2 - - - +
----------------------------------------------------------
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