Contacts of the helix formed by residues 915 - 927 (chain A) in PDB entry 1QWN
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 THR 915 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ARG* 4.1 4.3 - - - +
897A GLU* 2.5 44.1 + - + +
898A LYS 5.9 0.2 - - - +
899A VAL* 4.6 7.0 - - + -
902A CYS* 4.6 0.4 - - - -
914A LEU* 1.3 76.0 - - - +
916A SER* 1.3 66.1 + - - +
917A ALA* 3.6 1.7 + - - -
918A ALA* 3.2 12.6 + - - +
919A HIS* 3.0 22.5 + - - +
984A LEU* 4.3 2.2 - - - -
985A MET* 3.8 30.3 - - + +
987A CYS* 4.3 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 916 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A THR* 1.3 73.5 - - - +
917A ALA* 1.3 65.4 + - - +
919A HIS* 3.3 1.2 + - - +
920A LYS* 2.9 31.9 + - - +
955A GLU* 2.7 35.1 + - - -
984A LEU* 4.1 18.7 - - - +
985A MET 5.2 2.8 + - - -
991A GLU* 3.5 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A VAL* 4.5 10.8 - - + +
897A GLU* 3.8 16.2 - - + +
915A THR* 3.2 1.8 + - - -
916A SER* 1.3 79.9 - - - +
918A ALA* 1.3 57.7 + - - +
920A LYS* 3.9 5.3 - - - +
921A ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ARG* 6.0 0.2 - - - +
845A THR* 4.1 22.7 - - + +
847A LEU* 3.6 11.7 - - + +
895A VAL* 4.3 6.0 - - + +
897A GLU* 4.3 3.8 + - - +
914A LEU* 4.0 24.5 - - + -
915A THR* 3.2 19.2 + - - +
917A ALA* 1.3 76.0 - - - +
919A HIS* 1.3 61.0 + - - +
921A ALA* 3.3 7.6 + - - +
922A SER* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 919 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A LEU* 3.8 16.8 - - + +
915A THR 3.0 8.6 + - - +
916A SER* 3.7 3.4 - - - +
918A ALA* 1.3 77.7 - - - +
920A LYS* 1.3 67.5 + - + +
922A SER* 3.1 6.9 + - - -
923A GLN* 3.0 58.6 + - + +
955A GLU* 3.5 22.4 + - + -
956A ASP* 4.5 2.1 - - - -
958A ASP* 6.3 1.6 - - + -
982A THR* 3.8 23.3 + - + +
984A LEU* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 920 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A HIS* 3.4 35.9 + - - +
893A ARG* 5.3 0.2 - - - -
916A SER* 2.9 23.3 + - - +
917A ALA* 4.0 5.8 - - - +
919A HIS* 1.3 79.1 - - + +
921A ALA* 1.3 56.4 + - - +
923A GLN* 3.2 16.1 + - - +
924A SER* 2.9 28.2 + - - -
955A GLU* 3.5 34.3 + - - +
991A GLU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ALA* 5.4 0.4 - - + -
847A LEU* 4.1 2.9 - - + -
893A ARG* 3.7 45.2 - - + +
895A VAL* 4.0 14.6 - - + -
917A ALA 2.9 18.3 + - - +
918A ALA 3.5 5.2 - - - +
919A HIS 3.2 0.4 - - - -
920A LYS* 1.3 78.1 - - - +
922A SER* 1.3 60.7 + - - +
924A SER* 2.7 19.9 + - - -
925A LEU* 3.3 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A SER* 4.7 12.3 + - - -
847A LEU* 3.9 24.9 - - - +
848A THR 5.3 1.4 + - - -
914A LEU* 5.0 5.2 - - - -
918A ALA 2.9 13.9 + - - -
919A HIS* 3.1 12.8 + - - -
921A ALA* 1.3 77.0 - - - +
923A GLN* 1.3 63.0 + - - +
925A LEU* 3.1 7.6 + - - +
926A LEU* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 3.9 36.3 - - + +
562A PRO* 6.2 0.2 - - - +
563A HIS* 3.8 22.0 + - - -
565A ARG* 4.5 2.5 - - - +
919A HIS* 3.0 52.2 + - + +
920A LYS* 3.2 18.3 + - - +
922A SER* 1.3 76.5 - - - +
924A SER* 1.3 57.9 + - - +
926A LEU* 4.5 3.1 - - - +
927A ASP* 2.9 39.5 + - - +
955A GLU 4.7 2.7 + - - +
957A LEU 5.3 1.8 + - - -
958A ASP* 4.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ARG* 3.0 21.5 + - - -
565A ARG* 4.4 11.0 - - - +
567A GLN* 5.0 8.5 - - - +
893A ARG* 2.9 31.9 + - - +
920A LYS 2.9 13.3 + - - -
921A ALA 2.7 18.7 + - - -
923A GLN* 1.3 76.5 - - - +
925A LEU* 1.3 59.9 + - - +
928A PRO* 3.7 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 4.4 7.4 + - - -
530A ARG* 3.8 20.4 + - - +
775A GLU* 4.9 0.9 - - + -
847A LEU* 3.5 43.7 - - + +
848A THR 3.7 13.5 - - - +
849A GLY* 4.2 12.3 - - - -
891A ILE* 3.8 31.7 - - + +
892A TYR* 3.9 12.1 - - - +
893A ARG* 3.7 24.7 - - + +
921A ALA 3.5 10.1 - - - +
922A SER* 3.1 6.4 + - - +
924A SER* 1.3 80.7 - - - +
926A LEU* 1.3 64.7 + - - +
927A ASP 3.6 0.2 - - - -
928A PRO* 3.8 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 3.9 27.8 - - + +
176A ARG* 5.1 1.8 - - - +
427A ARG* 5.6 0.4 - - - +
430A ARG* 4.2 32.9 - - + +
433A MET* 4.2 12.3 - - + +
434A HIS* 3.4 19.8 - - - +
810A GLY* 6.0 0.2 - - - -
832A PRO 5.8 0.2 - - - +
833A SER* 4.4 13.5 - - - -
848A THR 4.0 18.4 - - - +
849A GLY* 4.2 11.2 - - - +
922A SER* 3.0 30.7 + - - +
923A GLN* 4.9 1.6 - - - -
925A LEU* 1.3 76.8 - - - +
927A ASP* 1.3 75.8 + - - +
928A PRO* 3.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 2.8 45.6 + - - -
434A HIS* 2.7 26.5 + - - +
437A ARG* 3.8 15.2 + - - -
560A THR* 3.9 11.9 - - + -
561A LEU* 4.2 11.4 - - + +
565A ARG* 2.8 28.9 + - - -
923A GLN* 2.9 16.6 + - + +
926A LEU* 1.3 85.6 - - - +
928A PRO* 1.3 62.0 - - - +
958A ASP* 5.3 0.5 - - - +
----------------------------------------------------------
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