Contacts of the helix formed by residues 770 - 780 (chain X) in PDB entry 3II6
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 ASP 770 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.4 12.3 - - - +
769X THR* 1.3 81.4 + - - +
771X LEU* 1.3 59.5 + - - +
772X ASN* 3.9 14.6 - - - +
773X GLN* 3.5 32.3 - - + +
774X LEU* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 771 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 5.1 14.8 - - + +
177A TYR* 3.5 39.7 - - + -
178A LYS* 5.5 8.7 - - + -
181A ILE* 3.5 11.3 - - + +
770X ASP* 1.3 78.9 + - - +
772X ASN* 1.3 69.3 + - - +
774X LEU* 3.8 1.0 - - - +
775X LYS* 3.0 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 772 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770X ASP* 3.9 13.8 - - - +
771X LEU* 1.3 82.8 - - - +
773X GLN* 1.3 66.6 + - - +
775X LYS* 3.1 20.6 - - - +
776X GLU* 3.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 773 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 4.5 1.6 - - - +
763X ASP* 5.0 1.9 + - - +
764X SER* 4.3 11.9 + - - +
767X ILE* 3.7 13.5 + - - +
768X ASP 2.9 25.5 + - - +
769X THR* 3.2 31.1 - - - +
770X ASP* 3.5 20.5 - - + +
771X LEU 3.5 0.2 - - - -
772X ASN* 1.3 79.3 + - + +
774X LEU* 1.3 61.0 + - - +
776X GLU* 3.4 8.3 + - - +
777X VAL* 3.2 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 774 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 3.3 33.0 - - + -
180A PHE* 4.4 11.2 - - + -
181A ILE* 4.3 13.2 - - + -
184A LEU* 4.0 20.9 - - + -
183B VAL* 4.7 3.6 - - + -
763X ASP* 5.0 2.9 - - - +
769X THR* 3.4 13.6 + - + +
770X ASP 2.8 25.6 + - - +
771X LEU 3.9 1.6 - - - +
773X GLN* 1.3 72.7 - - - +
775X LYS* 1.3 59.6 + - - +
777X VAL* 3.8 16.8 - - + -
778X PHE* 2.9 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 775 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 4.4 16.9 + - - +
174A THR* 4.8 8.9 + - - -
177A TYR* 3.8 38.8 + - + +
771X LEU* 3.0 45.4 + - + +
772X ASN* 3.1 13.7 - - - +
774X LEU* 1.3 75.5 - - - +
776X GLU* 1.3 54.6 + - - +
778X PHE* 3.2 3.1 + - - +
779X SER* 2.8 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 776 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741X ARG* 3.6 49.8 + - + +
772X ASN* 3.1 10.5 + - - +
773X GLN* 3.4 13.5 - - - +
775X LYS* 1.3 80.2 - - - +
777X VAL* 1.4 64.5 + - + +
779X SER* 3.1 24.6 + - - -
780X GLY 3.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 777 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 4.1 26.5 - - + -
761X TYR* 4.1 24.9 - - + +
762X GLY 3.9 26.9 - - - +
763X ASP* 4.0 13.0 - - + +
769X THR* 6.0 0.2 - - - +
773X GLN* 3.2 14.7 + - + +
774X LEU* 3.7 15.5 - - + +
776X GLU* 1.4 80.9 - - + +
778X PHE* 1.3 69.1 + - + +
779X SER 3.1 0.7 + - - -
780X GLY 3.4 8.1 + - - +
781X ILE* 3.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 778 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 3.3 31.9 - + - +
180A PHE* 3.8 21.8 - + - -
184A LEU* 5.3 0.4 - - + -
176B LEU* 3.6 27.8 - - + -
179B ARG* 2.5 58.9 + - + +
180B PHE* 3.2 33.0 - + - -
183B VAL* 4.0 9.9 - - + -
774X LEU* 2.9 50.6 + - + +
775X LYS 3.2 5.4 + - - +
777X VAL* 1.3 83.6 - - + +
779X SER* 1.3 59.8 + - - +
780X GLY 3.4 1.4 + - - -
781X ILE* 3.7 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 779 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 4.9 0.4 - - - -
775X LYS 2.8 18.1 + - - -
776X GLU* 3.1 20.2 + - - -
777X VAL 3.1 0.2 - - - -
778X PHE* 1.3 76.5 - - - +
780X GLY* 1.4 55.4 + - - +
781X ILE 4.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 780 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722X LYS* 6.3 0.9 - - - -
761X TYR* 5.4 0.2 - - - -
776X GLU 3.6 4.6 + - - -
777X VAL 3.4 8.4 + - - +
779X SER* 1.4 74.3 - - - +
781X ILE* 1.4 73.6 + - - +
----------------------------------------------------------
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