Contacts of the helix formed by residues 862 - 868 (chain A) in PDB entry 3OPY
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 862 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A THR* 6.2 0.2 - - + -
748A LEU* 3.8 28.0 - - + -
751A TYR* 3.6 44.1 - - + +
769A VAL* 4.1 8.5 - - + -
770A GLU 3.4 19.5 - - - +
860A ALA 3.6 6.1 - - - +
861A VAL* 1.4 87.8 - - - +
863A GLY* 1.3 62.2 + - - +
864A HIS 3.6 0.9 + - - -
865A VAL* 3.4 32.8 + - + +
866A GLN* 4.4 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLU 4.7 0.4 + - - -
772A GLN* 3.4 36.0 - - - +
861A VAL* 3.2 6.2 - - - +
862A PRO* 1.3 75.7 - - - +
864A HIS* 1.3 57.0 + - - -
865A VAL 3.0 10.4 + - - -
866A GLN* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PRO* 5.8 2.9 - - + -
772A GLN* 4.2 16.7 + - - -
862A PRO 3.6 1.8 + - - -
863A GLY* 1.3 69.4 - - - -
865A VAL* 1.3 55.6 + - - +
866A GLN* 3.2 1.1 - - - -
867A GLN* 3.1 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A THR* 3.3 23.7 - - + +
751A TYR* 4.5 11.7 - - + -
862A PRO* 3.4 37.1 + - + +
863A GLY 3.0 0.8 + - - -
864A HIS* 1.3 73.0 - - - +
866A GLN* 1.3 65.6 + - - +
867A GLN 3.1 3.1 - - - -
868A GLY* 3.1 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A VAL* 3.8 9.1 - - + +
744A CYS* 3.2 39.9 + - - +
747A THR* 4.2 9.1 - - - -
748A LEU* 3.6 29.8 - - + +
770A GLU 3.9 3.3 - - - +
771A VAL* 3.9 6.2 - - - -
772A GLN* 2.8 55.4 + - - +
779A LEU* 3.7 11.7 - - - +
862A PRO* 4.6 2.5 - - + -
863A GLY 3.0 27.8 + - - +
864A HIS* 4.8 0.4 - - - -
865A VAL* 1.3 76.2 - - - +
867A GLN* 1.4 61.1 + - - +
868A GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA* 5.3 2.6 - - - +
609A PRO* 3.2 55.2 - - + +
610A THR* 4.1 9.2 - - - +
611A SER* 3.1 26.4 + - - +
728A VAL* 4.5 11.7 - - + +
740A GLY 5.2 1.2 - - - +
743A THR* 3.4 6.1 - - - +
864A HIS* 3.1 43.9 + - - +
866A GLN* 1.4 78.9 - - - +
868A GLY* 1.3 63.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A SER* 4.0 6.7 - - - -
662A GLY* 4.9 2.3 - - - -
663A GLY 5.4 0.7 + - - -
743A THR* 4.0 6.7 - - - -
747A THR* 3.8 17.7 - - - -
865A VAL* 3.1 15.5 + - - -
866A GLN 3.3 1.0 - - - -
867A GLN* 1.3 84.2 - - - +
869A LYS* 1.4 65.2 + - - +
870A SER 3.7 1.3 - - - -
----------------------------------------------------------
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