Contacts of the helix formed by residues 826 - 833 (chain A) in PDB entry 3J0A
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 GLY 826 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A ASP 2.8 0.8 + - - -
825A VAL* 1.3 74.6 - - - +
827A TRP* 1.3 62.7 + - - +
828A PHE 3.1 2.8 - - - +
829A LEU* 3.4 21.2 + - - +
830A HIS* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A PRO* 5.9 0.9 - - + -
824A ASP* 3.2 16.4 + - + +
826A GLY* 1.3 77.6 - - - +
828A PHE* 1.3 61.1 + - - +
830A HIS* 3.5 8.1 - - + +
831A LYS* 3.1 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 828 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TRP* 4.1 11.4 - + - -
790A VAL* 3.6 22.9 - - + -
816A LEU* 3.2 42.2 - - + -
817A ARG 3.7 14.1 - - - -
818A TRP* 3.5 37.7 - + + -
819A PRO* 3.9 21.7 - - + +
824A ASP 4.0 2.8 + - - +
825A VAL* 5.5 1.1 - - - -
826A GLY 3.1 1.2 - - - +
827A TRP* 1.3 81.0 - - - +
829A LEU* 1.3 70.4 + - + +
830A HIS 3.1 1.3 - - - -
831A LYS* 3.6 3.5 + - + +
832A LEU* 2.9 55.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 829 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A HIS* 3.9 40.2 - - + +
715A LEU* 4.9 1.8 - - + -
818A TRP* 5.2 4.0 - - + -
825A VAL* 3.9 17.9 - - + +
826A GLY* 3.4 30.0 + - - +
828A PHE* 1.3 87.3 - - + +
830A HIS* 1.3 63.8 + - - +
832A LEU* 3.8 21.3 - - + +
833A SER* 3.1 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A GLY 3.1 16.5 + - - +
827A TRP* 3.5 11.4 - - + +
829A LEU* 1.3 77.4 - - - +
831A LYS* 1.3 63.4 + - + +
833A SER* 3.0 7.9 + - - -
834A GLN* 3.0 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A LEU* 3.6 19.5 - - + +
827A TRP* 3.1 53.6 + - + +
828A PHE* 4.2 3.1 - - + +
830A HIS* 1.3 80.1 - - + +
832A LEU* 1.3 57.9 + - - +
833A SER 3.0 5.2 - - - -
834A GLN* 3.0 14.0 + - - +
835A GLN* 2.7 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LEU* 4.1 15.0 - - + -
715A LEU* 3.6 34.3 - - + +
725A PHE* 4.7 1.7 - - - -
755A VAL* 4.1 26.0 - - + -
757A LEU* 6.1 0.2 - - + -
788A ILE* 5.5 2.2 - - + -
790A VAL* 4.5 12.6 - - + -
816A LEU* 3.9 9.1 - - + +
828A PHE* 2.9 43.4 + - + +
829A LEU* 3.9 15.5 - - + +
830A HIS 3.2 0.2 - - - -
831A LYS* 1.3 77.9 - - - +
833A SER* 1.3 57.3 - - - +
834A GLN 3.4 0.2 - - - -
835A GLN* 5.7 0.7 - - - -
836A ILE* 3.1 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ASP* 4.8 1.7 + - - -
715A LEU* 6.4 1.1 - - - -
718A GLN* 4.3 19.3 + - - -
725A PHE* 4.4 9.9 - - - -
829A LEU 3.1 18.0 + - - -
830A HIS* 3.0 6.8 + - - -
831A LYS 3.0 0.8 - - - -
832A LEU* 1.3 78.0 - - - +
834A GLN* 1.3 58.6 + - - +
837A LEU* 3.1 41.8 - - - +
----------------------------------------------------------
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