Contacts of the helix formed by residues 768 - 788 (chain A) in PDB entry 1Q2L
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 768 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A TYR* 1.3 74.6 - - - +
769A GLU* 1.3 59.0 + - - +
770A TYR* 4.0 11.1 + - - +
771A THR* 2.8 36.8 + - - -
772A SER* 2.9 27.4 + - - -
810A ARG 4.6 0.9 - - - -
811A GLN* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A ASP* 1.3 75.2 - - - +
770A TYR* 1.3 79.5 + - + +
772A SER* 3.2 3.0 + - - -
773A SER* 2.9 32.3 + - - -
810A ARG* 3.2 43.4 + - + +
811A GLN* 5.6 0.4 - - - +
812A TRP* 3.7 11.9 + - - +
878A LYS* 5.0 10.0 - - - +
882A ARG* 2.8 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A ASP* 3.5 11.3 + - - +
769A GLU* 1.3 100.5 - - + +
771A THR* 1.3 57.1 + - - +
773A SER* 3.5 2.4 + - - -
774A ALA* 3.1 26.0 + - - +
878A LYS* 5.6 2.7 - - - -
879A ASP* 4.3 1.4 + - - -
882A ARG* 4.5 9.9 + - - -
884A ASN* 3.8 14.9 + - - -
888A ASP* 4.5 0.4 + - - -
889A SER* 3.6 33.7 - - - -
892A LYS* 3.6 53.2 - - + +
893A ILE* 4.0 28.6 - - + +
896A GLN* 4.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A TYR* 4.0 11.0 - - + -
768A ASP* 2.8 33.3 + - - -
770A TYR* 1.3 74.3 - - - +
772A SER* 1.3 65.9 + - - +
774A ALA* 2.9 14.4 + - + +
775A TYR* 2.9 43.0 + - + -
896A GLN* 3.8 31.2 + - + +
900A LEU* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A PRO* 6.1 0.4 - - - -
767A TYR* 3.9 17.6 - - - +
768A ASP 2.9 23.7 + - - -
769A GLU* 3.2 6.1 + - - -
771A THR* 1.3 77.6 - - - +
773A SER* 1.3 58.6 + - - +
775A TYR* 3.7 1.0 - - - +
776A SER* 2.8 35.0 + - - -
811A GLN* 4.0 1.1 - - - -
812A TRP* 2.9 40.3 + - - +
908A PHE* 4.2 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A GLU* 2.9 23.9 + - - -
770A TYR 3.6 5.4 - - - -
772A SER* 1.3 78.6 + - - +
774A ALA* 1.3 61.3 + - - +
776A SER* 4.0 1.1 - - - -
777A SER* 3.0 27.2 + - - -
812A TRP* 3.6 33.9 + - - -
893A ILE* 3.6 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TYR 3.1 13.4 + - - +
771A THR 2.9 9.5 + - - +
773A SER* 1.3 73.8 - - - +
775A TYR* 1.3 65.9 + - - +
777A SER* 3.0 18.9 + - - -
778A LEU* 3.2 9.0 + - - +
893A ILE* 3.8 9.2 - - - +
896A GLN* 3.6 26.5 - - + -
897A ILE* 3.8 19.1 - - + +
900A LEU* 3.7 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A TYR* 3.7 21.2 + + - -
771A THR* 2.9 47.9 + - + -
772A SER 3.7 5.8 - - - +
774A ALA* 1.3 75.8 - - - +
776A SER* 1.3 56.4 - - - +
778A LEU* 3.4 1.9 + - - +
779A LEU* 2.9 35.6 + - - +
900A LEU* 3.7 25.8 - - + +
904A LYS* 3.2 56.5 + - + +
905A LEU* 3.7 16.3 - - + +
908A PHE* 3.4 40.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A SER 2.8 21.6 + - - -
773A SER 4.0 2.5 - - - -
775A TYR* 1.3 75.0 - - - +
777A SER* 1.3 59.8 + - - +
779A LEU* 3.8 8.0 - - - +
780A GLY* 2.9 23.6 + - - -
805A PRO* 3.3 20.9 - - - +
812A TRP* 3.3 11.7 + - - +
813A GLY* 3.1 40.9 + - - -
814A MET* 5.0 2.0 - - - +
908A PHE* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A SER* 3.0 15.6 + - - -
774A ALA* 3.0 17.3 + - - -
776A SER* 1.3 74.1 - - - +
778A LEU* 1.3 63.9 + - - +
780A GLY* 3.5 0.7 + - - -
781A GLN* 3.1 23.4 + - - +
805A PRO* 4.1 13.0 - - - +
858A VAL* 4.0 14.0 - - - +
862A MET* 4.8 6.5 - - - -
893A ILE* 4.9 1.0 - - - +
897A ILE* 3.9 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A ALA 3.2 13.0 + - - +
775A TYR 3.8 3.8 - - - +
777A SER* 1.3 82.4 + - - +
779A LEU* 1.3 57.4 + - - +
781A GLN* 3.2 4.0 + - - +
782A ILE* 2.9 35.9 + - - +
851A PHE* 4.0 18.4 - - + -
854A ILE* 3.5 27.4 - - + -
855A GLN* 4.0 20.4 - - + -
858A VAL* 3.6 18.6 - - + -
897A ILE* 4.3 10.3 - - + -
900A LEU* 3.5 34.5 - - + -
905A LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A TYR* 2.9 20.5 + - + +
776A SER 3.9 3.8 - - - +
778A LEU* 1.3 75.9 - - - +
780A GLY* 1.3 56.4 + - - +
782A ILE* 4.5 2.0 - - - -
783A VAL* 2.7 47.7 + - + +
814A MET* 3.8 22.4 - - + -
843A LEU* 3.5 41.5 - - + -
905A LEU* 4.1 23.8 - - + +
908A PHE* 3.5 35.4 - - + -
909A PHE* 4.2 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A SER 2.9 18.2 + - - -
777A SER 3.5 1.3 + - - -
779A LEU* 1.3 76.9 - - - +
781A GLN* 1.3 62.7 + - - +
784A GLN* 3.1 30.5 + - - +
803A ALA 3.9 6.9 - - - +
805A PRO* 4.2 18.6 - - - -
814A MET* 4.3 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A SER 3.1 14.2 + - - +
778A LEU 3.5 8.5 - - - +
780A GLY* 1.3 76.4 - - - +
782A ILE* 1.3 61.4 + - - +
784A GLN* 4.5 1.0 - - - +
785A PRO* 3.2 19.4 - - - +
854A ILE* 4.1 20.7 - - + +
857A ALA* 4.0 16.6 - - - +
858A VAL* 3.9 20.7 - - + +
861A GLN* 3.3 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A LEU* 2.9 19.7 + - + +
779A LEU 3.9 2.5 - - - +
781A GLN* 1.3 76.3 - - - +
783A VAL* 1.3 58.1 + - - +
785A PRO* 3.2 21.2 - - - +
786A TRP* 3.4 44.9 + - + -
843A LEU* 3.7 12.1 - - + -
846A MET* 3.5 24.7 - - + -
851A PHE* 4.7 2.0 - - + -
854A ILE* 3.6 34.5 - - + -
905A LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A LEU* 2.7 43.6 + - + +
782A ILE* 1.3 77.4 - - + +
784A GLN* 1.3 53.6 + - - +
786A TRP* 3.1 20.0 + - + +
787A PHE* 2.7 31.5 + - - +
803A ALA* 4.2 2.9 - - + -
814A MET* 3.9 15.0 - - + -
816A PHE* 4.1 19.1 - - + -
835A PHE* 3.9 28.0 - - + -
839A ALA* 4.9 3.6 - - + -
843A LEU* 4.6 3.4 - - + -
909A PHE* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A GLY 3.1 20.5 + - - +
781A GLN* 4.5 1.1 - - - +
783A VAL* 1.3 76.6 - - - +
785A PRO* 1.3 73.8 - - + +
787A PHE* 3.2 2.3 + - - +
788A TYR* 3.0 34.2 + - - +
801A VAL 3.9 11.1 - - - +
802A PHE* 3.5 15.9 - - - +
803A ALA* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A GLN 3.2 20.0 - - - +
782A ILE* 3.2 17.0 - - - +
784A GLN* 1.3 97.2 - - + +
786A TRP* 1.3 65.5 + - + +
788A TYR* 3.3 9.8 - - + +
792A ARG* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A ILE* 3.4 42.1 + - + +
783A VAL* 3.1 13.7 + - + +
785A PRO* 1.3 81.0 - - + +
787A PHE* 1.3 60.6 + - - +
789A ASN* 2.9 30.9 - - - +
792A ARG* 4.4 3.6 - - - +
835A PHE* 3.8 16.3 - + + -
839A ALA* 3.5 39.3 - - + -
842A LYS* 3.4 56.7 - - + +
843A LEU* 3.8 11.4 - - + -
846A MET* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A VAL 2.7 19.9 + - - +
784A GLN* 3.6 4.7 - - - +
786A TRP* 1.3 67.4 - - - +
788A TYR* 1.3 51.7 + - - +
789A ASN* 2.6 17.0 + - - +
790A GLN* 2.7 49.6 + - + +
801A VAL* 3.4 29.0 - - + +
802A PHE 3.3 31.4 - - - -
803A ALA* 3.7 11.7 - - + -
816A PHE* 3.6 21.1 - + + -
817A LEU 3.9 7.4 - - - -
818A LEU* 4.8 0.4 - - + -
832A TYR* 3.8 34.3 - + - -
835A PHE* 3.6 35.4 - + + -
836A PHE* 5.3 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A GLN* 3.0 28.0 + - - +
785A PRO* 3.3 17.7 - - + +
786A TRP 3.1 0.4 - - - -
787A PHE* 1.3 74.3 - - - +
789A ASN* 1.3 53.5 + - - +
790A GLN 3.0 3.3 + - - -
791A LEU* 3.2 42.1 + - + +
792A ARG* 3.0 48.7 + - + +
799A TYR* 3.1 44.4 + + - -
801A VAL* 4.4 14.8 - - - -
----------------------------------------------------------
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