Contacts of the helix formed by residues 795 - 813 (chain A) in PDB entry 1KLN
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 795 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ASP* 3.2 21.5 - - - +
722A GLY* 4.5 6.3 - - - -
723A LEU* 3.6 37.4 - - + +
736A ALA* 4.1 1.6 + - - +
737A THR* 3.3 33.1 + - + -
740A GLU* 3.5 21.6 - - + +
741A VAL* 4.2 9.0 - - + -
791A TYR* 2.6 69.9 + + + +
792A PHE* 3.1 15.8 - - - +
794A ARG* 1.3 86.3 - - + +
796A PRO* 1.3 63.9 - - - +
798A VAL* 3.5 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ASP* 3.7 5.6 - - - +
792A PHE 3.0 13.2 - - - +
793A GLU* 3.8 7.4 - - - +
794A ARG 3.6 8.5 - - - +
795A TYR* 1.3 85.5 - - - +
797A GLY* 1.3 57.1 + - - +
799A LEU* 2.8 41.5 + - + +
800A GLU* 2.9 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A SER* 3.1 28.6 - - - +
720A ASP* 2.9 15.4 + - - -
796A PRO* 1.3 79.1 - - - +
798A VAL* 1.3 56.0 + - - +
800A GLU* 3.3 23.6 + - - +
801A TYR* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 4.2 19.5 - - + -
718A SER* 3.9 10.3 - - - +
720A ASP* 3.7 1.3 + - - +
723A LEU* 3.8 29.2 - - + -
764A LEU* 3.7 27.6 - - + -
791A TYR* 3.9 14.6 - - + -
792A PHE* 3.9 9.0 - - + -
795A TYR* 3.5 14.1 + - + +
796A PRO 2.9 1.0 + - - -
797A GLY* 1.3 75.9 - - - +
799A LEU* 1.3 58.6 + - - +
801A TYR* 3.2 7.1 - - + +
802A MET* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A PHE* 3.8 44.8 - - + +
795A TYR 4.3 0.2 + - - -
796A PRO* 2.8 37.5 + - + +
798A VAL* 1.3 73.3 - - - +
800A GLU* 1.3 65.4 + - + +
802A MET* 3.6 14.4 - - + -
803A GLU* 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A SER 4.0 6.6 - - - +
719A ARG* 4.6 14.9 + - - +
796A PRO* 2.9 23.7 + - + +
797A GLY* 3.3 21.8 + - - +
799A LEU* 1.3 81.6 - - + +
801A TYR* 1.3 66.0 + - - +
803A GLU* 3.3 3.9 + - - +
804A ARG* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 4.9 12.3 - - + -
717A LEU* 3.3 49.3 - - + +
718A SER* 3.9 11.2 - - - -
797A GLY 2.9 14.5 + - - +
798A VAL* 3.2 11.7 - - - +
800A GLU* 1.3 76.8 - - - +
802A MET* 1.3 71.6 + - + +
804A ARG* 3.3 18.3 + - - +
805A THR* 2.9 47.1 + - - +
844A ILE* 3.6 29.8 + - + -
847A PRO* 3.3 33.8 - - + +
848A MET* 4.6 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 6.4 0.2 - - - +
764A LEU* 3.7 31.4 - - + +
767A GLY* 5.7 4.7 - - - -
768A MET 6.1 1.3 - - - +
788A MET* 6.3 0.2 - - + -
792A PHE* 4.4 10.5 - - + -
798A VAL* 2.9 25.9 + - + +
799A LEU* 3.1 17.0 + - + +
801A TYR* 1.3 82.3 - - + +
803A GLU* 1.3 59.0 + - + +
805A THR* 3.2 6.2 + - - -
806A ARG* 3.0 36.9 + - + +
844A ILE* 3.8 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU* 2.8 36.6 + - + +
800A GLU* 4.0 3.8 - - - +
802A MET* 1.3 70.8 - - + +
804A ARG* 1.3 55.9 + - - +
806A ARG* 3.1 9.5 + - - +
807A ALA* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU* 3.4 24.8 + - - +
718A SER 5.2 2.8 + - - -
719A ARG* 4.2 28.9 - - - +
800A GLU* 3.1 34.9 + - - +
801A TYR* 3.5 15.5 - - - +
803A GLU* 1.3 75.5 - - - +
805A THR* 1.3 58.2 + - - +
807A ALA* 3.1 8.3 - - - +
808A GLN* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A TYR* 2.9 45.6 + - - +
802A MET* 3.5 6.3 - - - -
804A ARG* 1.3 74.4 - - - +
806A ARG* 1.3 59.7 + - - +
807A ALA 3.0 1.1 - - - -
808A GLN* 3.3 11.6 + - + +
809A ALA* 2.8 31.5 + - - +
815A VAL* 3.9 10.5 - - + -
843A ALA* 3.1 34.8 - - + +
844A ILE* 4.0 9.2 - - + -
847A PRO* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A GLY 5.3 4.2 + - - -
769A SER* 6.1 3.6 - - - +
802A MET* 3.0 22.6 + - - +
803A GLU* 3.7 11.4 - - - +
805A THR* 1.3 75.3 - - - +
807A ALA* 1.3 64.0 + - - +
809A ALA* 3.5 4.6 - - - +
810A LYS* 2.8 40.3 + - - +
837A ALA* 5.2 1.8 + - - +
840A GLU* 3.2 55.9 + - + +
841A ARG* 4.8 3.2 - - - +
843A ALA* 5.1 1.3 - - - -
844A ILE* 3.8 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLU 2.8 12.9 + - - +
804A ARG* 3.1 13.9 - - - +
805A THR 3.0 0.2 - - - -
806A ARG* 1.3 74.5 - - - +
808A GLN* 1.3 67.1 + - - +
809A ALA 3.0 2.4 + - - -
810A LYS* 3.1 8.2 + - - +
811A GLU* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ARG* 2.9 16.2 + - - +
805A THR* 3.8 15.8 + - - +
807A ALA* 1.3 76.8 - - - +
809A ALA* 1.3 63.9 + - - +
811A GLU* 3.9 8.7 - - - -
812A GLN* 2.9 59.6 + - - +
814A TYR 3.3 3.6 - - - +
815A VAL* 3.9 19.1 - - + -
816A GLU* 3.9 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A THR 2.8 19.1 + - - +
806A ARG 3.5 7.9 - - - +
807A ALA 3.0 0.2 + - - -
808A GLN* 1.3 76.4 - - - +
810A LYS* 1.3 63.2 + - - +
813A GLY* 3.0 25.6 + - - -
814A TYR 3.6 10.8 + - - -
815A VAL* 4.3 1.1 - - + -
825A LEU* 3.9 7.1 - - + +
828A ILE* 3.5 29.8 - - + +
843A ALA* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ARG* 2.8 36.5 + - - +
807A ALA* 3.1 7.1 + - - +
809A ALA* 1.3 79.8 - - - +
811A GLU* 1.3 63.7 + - - +
813A GLY* 4.1 3.5 + - - -
828A ILE* 3.6 45.0 - - + +
829A LYS* 5.0 12.2 - - + +
836A ARG* 5.3 7.2 - - - +
840A GLU* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 811 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A ALA 3.0 16.9 + - - +
808A GLN* 3.9 7.9 - - - +
810A LYS* 1.3 81.5 - - - +
812A GLN* 1.3 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A GLN* 2.9 52.5 + - + +
810A LYS 4.8 0.2 - - - -
811A GLU* 1.3 85.5 - - + +
813A GLY* 1.3 60.1 + - - +
814A TYR* 2.9 63.6 + - + -
816A GLU* 4.8 3.3 - - - +
824A TYR* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A ALA 3.0 14.7 + - - -
810A LYS 4.1 3.9 + - - -
811A GLU 3.5 1.4 - - - -
812A GLN* 1.3 78.3 - - - +
814A TYR* 1.3 63.0 + - - +
824A TYR* 3.7 7.9 - - - +
825A LEU* 2.8 34.4 + - - +
828A ILE* 4.8 2.0 - - - -
829A LYS* 4.9 10.5 - - - -
----------------------------------------------------------
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