Contacts of the helix formed by residues 768 - 777 (chain C) in PDB entry 6CIM
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 SER 768 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767C GLU* 1.3 78.1 - - - +
769C VAL* 1.3 55.1 + - - +
770C GLU* 2.6 27.1 + - - -
771C GLU* 3.1 27.3 + - - +
772C LEU* 2.7 33.2 + - - +
63D SER 5.7 0.7 - - - -
64D LYS* 4.5 21.2 - - - +
68D TYR* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 769 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760C TRP* 3.9 16.1 - - + -
768C SER* 1.3 73.7 - - - +
770C GLU* 1.3 80.4 + - + +
772C LEU* 3.7 4.7 - - - +
773C ARG* 2.9 28.8 + - + +
39D ARG* 5.5 3.8 - - - +
42D PRO* 3.9 20.0 - - + -
43D THR* 5.9 1.3 - - + -
61D ILE* 5.5 15.5 - - + -
68D TYR* 3.2 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 770 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C SER* 2.6 30.5 + - - -
769C VAL* 1.3 94.9 + - + +
771C GLU* 1.3 65.2 + - + +
773C ARG* 3.4 7.5 + - - +
774C ASP* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 771 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767C GLU* 3.6 33.1 - - + +
768C SER* 3.1 30.1 + - - +
770C GLU* 1.3 77.4 - - + +
772C LEU* 1.3 57.3 - - - +
774C ASP* 3.2 7.8 + - - +
775C ARG* 2.9 28.2 + - - +
64D LYS* 4.7 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 772 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759C VAL* 3.9 29.6 - - + +
760C TRP* 3.5 46.0 - - + +
763C ASN* 4.0 23.6 - - - +
764C PRO* 5.4 0.4 - - + -
767C GLU* 4.2 6.4 - - + +
768C SER 2.7 21.1 + - - +
769C VAL* 3.7 5.6 - - - +
771C GLU* 1.3 73.8 - - - +
773C ARG* 1.3 62.0 + - - +
775C ARG* 3.0 21.3 + - - +
776C VAL* 3.0 14.3 + - + +
68D TYR* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 773 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C GLU* 2.8 40.3 + - - +
723C SER* 3.3 13.1 + - - +
724C VAL* 3.5 32.5 - - - +
725C TYR* 3.5 13.6 + - + -
760C TRP* 3.9 17.8 - - + -
769C VAL* 2.9 19.3 + - + +
770C GLU* 3.7 7.0 - - - +
772C LEU* 1.3 75.9 - - - +
774C ASP* 1.3 57.5 + - - +
776C VAL* 3.4 4.2 + - + -
777C LYS* 2.9 26.0 + - - -
778C GLY* 3.7 4.7 + - - +
780C SER* 5.3 0.9 - - - +
39D ARG* 3.4 45.9 - - - +
10J T 5.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 774 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C TYR* 3.2 15.5 + - - +
733C THR* 5.8 1.2 - - - +
770C GLU 2.9 18.3 + - - +
771C GLU* 3.7 6.7 - - - +
773C ARG* 1.3 77.0 - - - +
775C ARG* 1.3 61.5 + - - +
777C LYS* 2.5 58.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 775 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C ARG* 4.5 8.8 + - - +
759C VAL* 3.4 31.6 - - + -
764C PRO* 5.5 0.7 - - - -
765C TYR* 3.4 37.2 - - - +
767C GLU* 2.5 41.3 + - - +
771C GLU 2.9 13.8 + - - +
772C LEU* 3.0 12.5 + - + +
774C ASP* 1.3 78.9 - - - +
776C VAL* 1.3 59.1 + - - +
777C LYS* 3.6 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 776 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C ARG* 3.2 42.1 - - + +
759C VAL* 3.6 24.9 - - + -
760C TRP* 3.7 24.2 - - + +
772C LEU* 3.0 19.0 + - + +
773C ARG* 3.8 6.1 - - + +
775C ARG* 1.3 75.3 - - + +
777C LYS* 1.3 71.9 + - - +
778C GLY 2.9 3.8 + - - +
779C VAL* 3.1 41.0 + - - +
780C SER* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 777 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C TYR* 3.2 49.6 - - + +
731C ASP* 3.5 39.7 - - + +
733C THR* 5.7 0.4 - - - -
736C GLU* 5.2 7.6 - - - -
748C ARG* 2.7 26.6 + - - +
756C ARG* 3.9 18.4 - - - +
773C ARG 2.9 7.1 + - - -
774C ASP* 2.5 49.7 + - - +
775C ARG* 3.3 6.1 + - - +
776C VAL* 1.3 79.2 - - - +
778C GLY* 1.3 53.5 + - - +
----------------------------------------------------------
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