Contacts of the helix formed by residues 877 - 891 (chain q) in PDB entry 6FF7
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 GLY 877 (chain q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874q LEU* 3.0 19.6 + - - +
875q PRO 3.0 1.5 - - - -
876q GLY* 1.3 81.3 - - - +
878q ASP* 1.3 65.5 + - - +
879q HIS 3.2 2.2 - - - -
880q LEU* 3.1 22.0 + - - +
881q VAL* 3.1 9.2 + - - -
1001q VAL 3.9 3.5 + - - -
1002q LEU* 4.0 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 878 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874q LEU 4.8 0.4 - - - -
877q GLY* 1.3 70.8 - - - +
879q HIS* 1.3 66.0 + - - +
881q VAL* 3.1 18.1 + - - +
882q LEU* 3.3 10.6 + - - +
975q SER* 5.4 10.1 - - - -
1000q GLN* 3.9 14.8 - - + -
1001q VAL 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 879 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844q VAL* 4.7 15.6 - - + +
877q GLY* 3.2 0.6 - - - -
878q ASP* 1.3 80.0 - - - +
880q LEU* 1.3 61.1 + - - +
882q LEU* 3.2 20.5 + - - +
883q LEU* 3.4 5.4 + - - +
944q ILE* 5.7 9.4 - - + -
1000q GLN* 5.6 1.9 - - - +
1001q VAL 4.4 1.8 + - - -
1002q LEU* 4.5 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 880 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874q LEU* 3.6 17.9 - - + -
877q GLY* 3.1 16.1 + - - +
879q HIS* 1.3 76.4 - - - +
881q VAL* 1.3 67.6 + - - +
883q LEU* 2.9 19.5 + - - +
884q ASN* 3.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 881 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872q PHE* 4.0 16.1 - - + +
873q PHE* 4.0 24.2 - - + -
874q LEU* 4.1 4.4 - - - +
877q GLY 3.1 8.0 + - - +
878q ASP* 3.1 14.1 + - - +
880q LEU* 1.3 77.4 - - - +
882q LEU* 1.3 60.9 + - - +
884q ASN* 3.0 3.2 + - - +
885q VAL* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 882 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843q THR 6.0 0.2 - - - -
844q VAL* 5.1 5.6 - - + +
847q MET* 3.7 30.5 - - + +
878q ASP 3.3 6.6 + - - +
879q HIS* 3.2 13.8 + - - +
880q LEU 3.1 0.6 - - - -
881q VAL* 1.3 79.1 - - - +
883q LEU* 1.3 62.7 + - - +
885q VAL* 3.5 4.1 + - - +
886q TYR* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 883 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840q GLU* 5.1 17.3 - - + +
843q THR* 5.0 10.2 - - - -
844q VAL* 5.6 4.7 - - + +
879q HIS 3.4 4.0 + - - +
880q LEU* 2.9 16.0 + - - +
882q LEU* 1.3 79.9 - - - +
884q ASN* 1.3 63.5 + - - +
886q TYR* 3.3 6.1 + - - +
887q THR* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 884 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872q PHE* 3.5 32.5 - - + +
874q LEU* 6.3 0.7 - - + -
880q LEU 3.0 10.9 + - - +
881q VAL 3.0 4.2 + - - +
883q LEU* 1.3 76.9 - - - +
885q VAL* 1.3 64.3 + - - +
887q THR* 3.2 6.7 + - - -
888q GLN* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 885 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854q ILE* 6.2 4.5 - - + -
872q PHE* 4.2 15.0 - - + +
881q VAL 3.0 14.8 + - - +
882q LEU* 4.1 4.3 - - - +
884q ASN* 1.3 77.5 - - - +
886q TYR* 1.3 58.4 + - - +
888q GLN* 3.3 6.5 + - - +
889q TRP* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 886 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843q THR* 4.7 18.4 - - - +
847q MET* 5.6 4.0 - - + -
882q LEU 3.0 19.2 + - - +
883q LEU* 3.7 5.8 - - - +
885q VAL* 1.3 75.8 - - - +
887q THR* 1.3 66.1 + - - +
889q TRP* 3.1 8.9 + - - +
890q ALA* 2.9 20.4 + - - +
912q ALA* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 887 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883q LEU 2.9 17.8 + - - -
884q ASN* 3.2 6.0 + - - -
886q TYR* 1.3 77.6 - - - +
888q GLN* 1.3 63.1 + - - +
890q ALA* 3.0 22.9 + - - +
891q GLU* 3.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 888 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884q ASN 2.9 15.4 + - - +
885q VAL* 3.8 7.0 - - - +
887q THR* 1.3 76.6 - - - +
889q TRP* 1.3 58.6 + - - +
891q GLU* 2.8 35.0 + - - +
892q SER* 3.8 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 889 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885q VAL 2.8 17.9 + - - +
886q TYR* 3.1 9.4 + - - +
888q GLN* 1.3 77.3 - - - +
890q ALA* 1.3 64.2 + - - +
891q GLU 3.4 0.3 + - - -
892q SER* 4.1 12.6 + - - +
895q SER* 5.8 3.6 - - - -
909q MET* 4.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 890 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886q TYR 2.9 10.5 + - - +
887q THR* 3.1 16.8 - - - +
889q TRP* 1.3 81.1 - - - +
891q GLU* 1.3 56.9 + - + +
892q SER 3.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 891 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887q THR 3.4 3.9 + - - +
888q GLN* 2.8 20.0 + - - +
890q ALA* 1.3 79.8 - - + +
892q SER* 1.3 57.7 + - - +
----------------------------------------------------------
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