Contacts of the helix formed by residues 786 - 802 (chain B) in PDB entry 1QXP
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 PHE 786 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B MET* 3.8 29.8 - - + +
739B GLU* 4.0 2.4 + - - +
740B VAL* 6.3 0.2 - - - -
785B GLY* 1.3 71.6 - - - -
787B GLU* 1.3 82.5 + - - +
789B PHE* 2.8 23.3 + - - +
790B LYS* 2.9 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B PHE* 1.3 94.3 + - - +
788B GLU* 1.4 54.5 + - - +
789B PHE 2.8 5.6 - - - -
790B LYS* 4.3 23.9 + - - +
791B TYR* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B MET* 3.3 49.4 - - + +
777B ASP* 4.9 2.5 - - - +
783B LYS 5.4 0.9 - - - +
784B LEU* 2.6 45.4 - - + +
785B GLY 2.9 13.8 + - - +
786B PHE 3.1 0.6 - - - -
787B GLU* 1.4 73.0 - - - +
789B PHE* 1.3 50.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B ARG* 5.8 9.2 - - - -
740B VAL* 3.1 46.2 - - + -
745B LEU* 5.1 16.4 - - + -
784B LEU* 3.7 4.9 - - + +
785B GLY 3.3 8.3 - - - +
786B PHE* 2.8 12.0 + - - +
787B GLU 2.8 0.2 - - - -
788B GLU* 1.3 80.0 - - - +
790B LYS* 1.4 56.3 - - - +
792B LEU* 2.6 36.0 + - + +
793B TRP* 2.6 53.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ARG* 5.0 28.1 - - + +
786B PHE 2.9 13.5 + - - +
787B GLU* 4.0 23.0 + - - +
789B PHE* 1.4 72.0 - - - +
791B TYR* 1.3 77.0 - - - +
792B LEU 2.8 0.2 - - - -
793B TRP* 2.4 20.2 + - + +
794B ASN* 2.9 15.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B MET* 4.1 26.7 - - + -
787B GLU 3.0 19.2 + - - +
790B LYS* 1.3 86.0 - - - +
792B LEU* 1.3 66.4 + - + +
793B TRP 2.9 0.5 + - - -
794B ASN* 2.9 15.8 + - - +
795B ASN* 3.3 25.7 + - + +
862B ASP* 2.6 29.9 + - - -
866B ARG* 2.8 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 792 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B LEU* 4.1 26.0 - - + -
772B MET* 4.7 21.5 - - + +
776B MET* 3.8 40.2 - - + +
784B LEU* 5.1 6.5 - - + -
788B GLU 5.1 0.2 - - - -
789B PHE* 2.6 26.0 + - + +
790B LYS 2.5 4.0 + - - -
791B TYR* 1.3 79.9 - - + +
793B TRP* 1.3 61.4 + - - +
795B ASN* 3.6 3.9 + - + -
796B ILE* 3.3 23.3 + - + +
859B VAL* 4.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B GLU* 4.0 40.9 - - + +
789B PHE* 2.6 39.1 + + + +
790B LYS* 2.4 22.1 + - + +
792B LEU* 1.3 74.9 - - - +
794B ASN* 1.4 58.0 + - + +
795B ASN 2.7 12.9 + - - -
796B ILE* 3.3 4.4 + - + +
797B LYS* 3.0 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B LYS* 2.9 14.5 + - + +
791B TYR* 3.6 8.3 - - - +
793B TRP* 1.4 81.5 - - + +
795B ASN* 1.3 55.0 + - - +
797B LYS* 3.7 8.2 - - - +
798B LYS* 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B TYR* 3.3 30.9 + - + +
792B LEU* 4.4 5.6 - - + +
793B TRP 2.7 7.9 + - - -
794B ASN* 1.3 72.5 - - - +
796B ILE* 1.3 52.3 + - - +
798B LYS* 4.4 2.5 - - + -
799B TRP* 2.2 63.7 - - + +
862B ASP* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B PHE* 5.4 12.6 - - + -
772B MET* 6.3 2.9 - - + -
792B LEU* 3.3 20.7 + - + +
793B TRP* 4.2 3.8 - - + +
795B ASN* 1.3 71.7 - - - +
797B LYS* 1.4 50.0 + - - +
799B TRP* 2.6 25.0 - - - +
800B GLN* 2.8 22.1 + - - +
851B PHE* 4.6 7.7 - - + -
855B ILE* 5.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B TRP* 3.0 41.9 + - + +
794B ASN* 3.7 9.9 - - - +
795B ASN 3.1 1.8 - - - -
796B ILE* 1.4 69.5 - - - +
798B LYS* 1.4 55.5 - - - +
799B TRP 2.9 3.8 - - - -
800B GLN* 2.6 53.6 + - + +
801B GLY 3.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ASN 3.2 18.3 + - - +
795B ASN* 5.5 2.0 - - + -
797B LYS* 1.4 74.0 - - - +
799B TRP* 1.3 72.3 + - + +
800B GLN 3.5 0.2 + - - -
801B GLY* 4.2 2.1 + - - -
802B ILE* 2.9 37.4 + - + +
825B ALA 3.8 20.0 + - - -
826B ALA* 4.4 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ASN* 2.2 52.0 - - - +
796B ILE* 2.6 11.7 - - - +
798B LYS* 1.3 94.1 - - + +
800B GLN* 1.3 56.4 + - - +
801B GLY 3.5 0.2 - - - -
802B ILE* 2.9 28.9 + - + +
823B PHE* 4.0 22.7 - + - -
826B ALA* 3.7 25.5 + - + +
828B PHE* 3.3 39.9 - + - -
851B PHE* 4.5 7.0 - - + -
854B PHE* 6.4 0.9 - + - -
855B ILE* 5.6 8.7 - - + -
858B LEU* 3.2 41.5 - - + -
859B VAL* 6.1 0.7 - - - -
861B LEU* 5.2 0.2 - - + -
862B ASP* 4.8 6.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ILE 2.8 6.0 + - - +
797B LYS* 2.6 43.7 + - + +
799B TRP* 1.3 68.1 - - - +
801B GLY* 1.4 67.7 + - - +
851B PHE* 3.4 43.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B LYS 3.7 3.0 + - - -
798B LYS 4.4 2.7 - - - -
800B GLN* 1.4 85.0 - - - +
802B ILE* 1.3 63.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B LYS* 2.9 42.4 - - + +
799B TRP* 2.9 23.6 + - + +
801B GLY* 1.3 76.3 - - - +
822B ALA* 2.8 50.2 - - + +
823B PHE 4.4 0.2 - - - +
825B ALA* 3.4 32.5 - - + +
826B ALA* 4.2 12.6 - - + +
----------------------------------------------------------
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