Contacts of the helix formed by residues 750 - 763 (chain C) in PDB entry 5Y3R
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 PRO 750 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C VAL* 6.1 3.6 - - + -
719C LYS* 3.0 23.3 + - + -
747C ALA* 5.7 0.7 - - + -
748C TYR* 3.2 10.1 - - - +
749C VAL* 1.3 102.0 - - + +
751C ALA* 1.3 58.4 + - - +
753C GLN* 2.5 32.7 + - + -
754C MET* 2.9 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 751 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715C ALA* 5.8 3.4 - - + -
719C LYS* 3.2 11.2 + - - +
738C HIS* 4.2 13.9 - - + +
748C TYR* 2.6 42.0 + - + +
750C PRO* 1.3 74.0 - - - +
752C LEU* 1.3 53.9 + - + +
755C ALA* 2.3 35.4 + - - +
756C PHE* 4.5 2.0 - - + -
776C TRP* 4.7 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 752 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748C TYR 4.7 4.3 - - - +
749C VAL* 4.2 10.1 - - - +
751C ALA* 1.3 76.3 - - - +
753C GLN* 1.3 86.1 + - - +
755C ALA 3.3 0.9 - - - -
756C PHE* 2.8 58.0 + - + +
757C LYS* 3.5 4.9 + - - +
776C TRP* 3.3 44.2 - - + -
792C ILE* 5.1 8.7 - - + -
795C CYS* 4.1 26.7 - - + -
796C LEU* 5.2 6.1 - - + -
799C TYR* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 753 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C VAL 3.1 17.3 - - - +
750C PRO* 2.5 22.1 + - + +
752C LEU* 1.3 84.6 - - + +
754C MET* 1.3 62.0 + - - +
757C LYS* 3.4 17.0 - - - +
795C CYS* 4.3 9.0 - - - -
799C TYR* 3.1 50.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 754 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C LYS* 3.0 70.7 - - + +
720C GLN* 5.9 0.2 - - - +
750C PRO* 2.9 5.9 + - + +
753C GLN* 1.3 81.1 - - - +
755C ALA* 1.3 66.5 + - - +
757C LYS* 3.5 2.2 - - - +
758C LEU* 2.9 26.1 + - + +
1018C VAL* 3.8 19.1 - - - +
1020C PRO* 3.3 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 755 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C LYS* 4.6 2.7 - - - +
731C THR* 6.0 4.5 - - - -
732C PHE* 3.6 16.8 - - + -
735C SER* 5.5 4.5 - - - -
751C ALA 2.3 32.9 + - - +
752C LEU 3.1 0.6 + - - -
754C MET* 1.3 77.9 - - - +
756C PHE* 1.3 78.3 + - + +
758C LEU* 2.8 27.1 + - - +
759C GLY 2.9 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 756 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735C SER* 4.4 15.3 - - - -
751C ALA* 4.5 1.6 - - + -
752C LEU* 2.8 41.9 + - + +
755C ALA* 1.3 85.6 - - + +
757C LYS* 1.3 55.5 + - - +
759C GLY* 2.4 26.3 + - - -
760C LEU* 3.0 6.9 + - - +
773C LEU* 3.1 63.6 - - + +
774C GLU* 4.7 5.4 - - - +
776C TRP* 3.1 50.9 - + + -
777C SER* 4.8 1.8 - - - -
800C LEU* 5.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 757 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752C LEU 3.5 3.4 + - - +
753C GLN* 3.4 23.3 - - - +
754C MET 3.5 2.2 - - - +
756C PHE* 1.3 76.3 - - - +
758C LEU* 1.3 54.2 + - - +
759C GLY 3.0 0.5 + - - -
760C LEU* 4.6 1.1 + - - +
761C SER* 2.4 65.5 + - - +
799C TYR* 5.5 19.9 - - + +
801C LYS* 4.3 18.8 - - - +
802C THR* 4.6 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C GLU* 4.7 7.2 - - + -
727C ALA* 5.4 2.7 - - + -
728C SER* 3.1 37.0 - - - +
731C THR* 4.5 6.1 - - + +
732C PHE* 3.5 21.5 - - + -
754C MET* 2.9 17.3 + - + +
755C ALA* 2.8 16.7 + - - +
757C LYS* 1.3 72.4 - - - +
759C GLY* 1.3 64.7 + - - +
761C SER* 3.1 5.5 + - - -
762C TYR* 3.5 40.7 + - + -
763C THR* 3.7 7.6 + - + +
1020C PRO* 5.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 759 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732C PHE* 3.6 11.6 - - - -
755C ALA 2.9 6.9 + - - -
756C PHE 2.4 21.1 + - - -
758C LEU* 1.3 73.9 - - - +
760C LEU* 1.3 55.4 + - - -
763C THR* 2.8 26.7 + - - +
770C LEU* 2.9 19.5 - - - +
773C LEU* 3.4 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 760 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C PHE 3.0 10.1 + - - +
757C LYS* 3.1 2.8 + - - -
759C GLY* 1.3 71.0 - - - -
761C SER* 1.3 61.3 + - - +
764C PRO* 3.1 33.6 - - + +
770C LEU* 3.4 28.0 - - + -
773C LEU* 4.0 6.5 - - + +
774C GLU* 6.0 1.1 - - - +
802C THR* 3.5 24.8 + - - +
803C SER* 3.5 40.4 - - - +
806C SER* 3.1 27.6 - - - +
848C LEU* 6.3 0.4 - - + -
851C ILE* 4.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 761 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C LYS* 2.4 79.3 + - - +
758C LEU* 3.1 7.4 + - - -
760C LEU* 1.3 68.2 - - - +
762C TYR* 1.3 81.4 + - - +
763C THR 3.5 0.2 - - - -
764C PRO* 3.1 13.9 - - - +
918C ALA 4.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 762 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C GLU* 3.4 35.5 - - + +
758C LEU* 3.5 28.0 + - + -
761C SER* 1.3 99.4 + - - +
763C THR* 1.3 68.8 + - + +
764C PRO* 3.5 2.3 - - - +
765C LEU* 5.3 2.1 - - - +
920C THR* 5.1 6.4 + - - -
971C ARG* 5.0 11.8 + - - -
972C LEU* 5.2 21.3 - - + -
1019C ASP* 5.7 1.7 - - - +
1020C PRO* 4.2 30.3 - - + +
1021C VAL* 4.6 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 763 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C GLU* 4.0 15.3 - - + +
728C SER* 6.5 1.3 - - - -
732C PHE* 4.8 6.6 - - - -
758C LEU* 3.7 5.9 + - + +
759C GLY* 2.8 20.1 + - - +
762C TYR* 1.3 86.2 - - + +
764C PRO* 1.3 58.7 - - - +
765C LEU* 2.9 9.2 - - + +
766C ALA* 2.7 53.9 + - + +
768C VAL* 5.6 0.5 - - - +
770C LEU* 3.0 8.0 - - - +
----------------------------------------------------------
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