Contacts of the helix formed by residues 831 - 836 (chain A) in PDB entry 3H0G
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 ILE 831 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A ARG* 3.6 28.9 - - + +
828A GLU* 2.9 21.0 + - + +
830A LEU* 1.3 84.3 - - + +
832A ASP* 1.3 62.0 + - - +
833A THR 3.0 5.8 - - - -
834A ALA* 2.8 27.8 + - + +
835A VAL* 3.1 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A GLU* 2.9 41.7 + - - +
829A GLY* 4.0 8.7 + - - -
830A LEU 3.8 0.2 - - - +
831A ILE* 1.3 86.3 - - - +
833A THR* 1.3 56.7 + - - +
835A VAL* 4.1 10.0 - - - +
836A LYS 3.8 11.8 + - - -
1084A LEU* 3.4 25.6 - - + +
1087A PHE* 4.1 24.1 - - + +
1088A HIS 5.3 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A GLY 3.5 18.6 + - - +
830A LEU* 4.0 18.8 - - + +
831A ILE 3.0 0.4 - - - -
832A ASP* 1.3 77.8 - - - +
834A ALA* 1.3 65.4 + - + +
835A VAL 3.3 2.0 + - - -
836A LYS* 4.4 5.4 - - - +
837A THR* 3.3 21.0 + - - -
1084A LEU* 5.0 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A LEU 4.1 5.2 - - - +
831A ILE* 2.8 25.5 + - + +
833A THR* 1.3 83.3 - - + +
835A VAL* 1.3 61.1 + - + +
837A THR* 3.5 15.6 - - - +
838A ALA* 4.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ILE* 3.1 15.2 + - + +
832A ASP* 4.3 10.8 - - - +
833A THR 3.3 0.4 - - - -
834A ALA* 1.3 75.2 - - + +
836A LYS* 1.3 54.5 + - - +
837A THR 2.3 19.1 + - - -
838A ALA* 2.4 19.4 + - - -
839A GLU* 3.1 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 6.5 0.9 - - - -
832A ASP 3.8 14.7 + - - +
833A THR* 4.3 5.4 + - - +
835A VAL* 1.3 78.1 - - - +
837A THR* 1.3 54.1 + - - +
839A GLU* 5.1 0.2 - - - -
840A THR* 2.2 58.9 + - + +
1080A THR* 3.7 32.0 + - - -
1081A GLN* 4.6 5.1 - - - +
1083A THR* 4.3 8.3 - - + -
1084A LEU* 3.4 40.1 - - + +
----------------------------------------------------------
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