Contacts of the helix formed by residues 761 - 772 (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 LEU 761 (chain q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759q THR* 3.7 5.4 + - - +
760q SER* 1.3 70.8 - - - +
762q GLY* 1.3 65.1 + - - +
763q ASN 3.3 2.5 - - - -
764q VAL* 3.0 15.9 + - + -
765q VAL* 2.9 23.7 + - + +
785q PRO* 6.3 3.6 - - + -
789q THR* 4.2 19.5 + - - +
790q LEU* 4.6 5.6 - - + -
793q ALA* 3.7 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 762 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760q SER* 3.5 6.1 - - - -
761q LEU* 1.3 76.3 - - - +
763q ASN* 1.3 61.6 + - - +
765q VAL* 3.3 3.3 + - - +
766q LEU* 3.2 21.0 + - - +
793q ALA* 3.7 21.5 - - - +
796q GLN* 6.0 2.2 - - - -
797q LEU* 5.8 3.8 - - - +
823q PRO* 5.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 763 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760q SER 4.8 3.5 + - - +
761q LEU 3.3 0.8 - - - -
762q GLY* 1.3 74.0 - - - +
764q VAL* 1.3 64.5 + - - +
766q LEU* 3.3 8.2 + - - +
767q LEU* 3.1 21.6 + - - +
821q VAL 5.9 1.1 - - - +
822q ASP* 5.3 13.2 - - + -
823q PRO* 5.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 764 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528q LEU* 6.0 7.0 - - + -
760q SER 5.3 0.8 + - - +
761q LEU* 3.0 18.1 + - + +
763q ASN* 1.3 80.4 - - - +
765q VAL* 1.3 57.8 + - - +
767q LEU* 3.2 8.3 + - - +
768q LEU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 765 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761q LEU* 2.9 16.4 + - + +
762q GLY 3.8 4.9 - - - +
764q VAL* 1.3 72.7 - - - +
766q LEU* 1.3 62.6 - - - +
768q LEU* 3.2 7.0 + - - +
769q LYS* 2.9 30.2 + - - +
790q LEU* 5.6 0.9 - - - +
793q ALA* 4.3 20.2 - - + +
794q LEU* 5.1 4.7 - - + +
797q LEU* 5.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 766 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762q GLY 3.2 10.7 + - - +
763q ASN* 3.6 9.9 - - - +
765q VAL* 1.3 79.5 - - - +
767q LEU* 1.3 58.4 + - - +
769q LYS* 3.3 8.2 + - - +
770q SER* 2.9 29.0 + - - -
797q LEU* 6.2 2.9 - - + -
802q ALA* 6.0 6.7 - - + -
813q GLY 6.0 2.2 - - - +
817q ALA* 5.4 9.9 - - + +
823q PRO* 5.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 767 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503q LEU* 6.3 3.1 - - + -
507q LEU* 5.5 2.5 - - - +
763q ASN 3.1 13.1 + - - +
764q VAL* 3.3 12.1 - - - +
765q VAL 3.1 0.2 - - - -
766q LEU* 1.3 76.8 - - - +
768q LEU* 1.3 57.7 + - - +
770q SER* 2.9 10.3 + - - -
771q LEU* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 768 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764q VAL 2.9 16.4 + - - +
765q VAL* 3.2 7.6 + - - +
767q LEU* 1.3 75.8 - - - +
769q LYS* 1.3 64.1 + - - +
771q LEU* 3.0 18.9 + - - +
772q GLY 3.0 9.0 + - - -
773q ILE* 3.0 24.7 + - + +
776q LEU* 5.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 769 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765q VAL 2.9 13.8 + - - +
766q LEU* 3.5 11.9 - - - +
768q LEU* 1.3 75.9 - - - +
770q SER* 1.3 59.0 + - - +
772q GLY* 2.8 21.0 + - - +
773q ILE 4.3 9.8 + - - +
807q GLY 5.2 9.6 - - - +
809q LEU* 5.4 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 770 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507q LEU* 4.0 30.3 - - - +
766q LEU 2.9 13.7 + - - -
767q LEU* 3.3 12.1 - - - -
769q LYS* 1.3 77.2 - - - +
771q LEU* 1.3 60.7 + - - +
772q GLY* 3.3 1.2 + - - -
817q ALA* 4.4 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 771 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506q PHE* 5.6 5.8 - - + -
507q LEU* 5.1 9.1 - - - +
510q PRO* 4.9 13.8 - - - +
536q LEU* 6.5 1.8 - - + -
767q LEU 2.8 12.2 + - - +
768q LEU* 3.1 17.0 - - - +
770q SER* 1.3 75.8 - - - +
772q GLY* 1.3 58.7 + - - +
773q ILE* 4.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 772 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769q LYS 2.8 15.5 + - - -
770q SER 3.1 1.9 - - - -
771q LEU* 1.3 80.1 - - - +
773q ILE* 1.3 61.7 + - - +
774q HIS* 3.6 4.2 + - - +
----------------------------------------------------------
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