Contacts of the helix formed by residues 825 - 831 (chain A) in PDB entry 5LOH
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 825 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A TRP* 4.1 19.1 - - - -
824A ALA* 1.3 75.1 - - - +
826A MET* 1.3 66.4 + - - -
827A LYS 3.3 2.5 - - - -
828A GLU* 3.1 15.9 + - - +
829A LEU* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 826 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ALA* 4.0 10.5 - - - +
142A LEU* 3.6 40.2 - - + +
145A ASP* 3.5 33.0 - - + +
761A TRP* 3.6 29.7 - - + -
825A GLY* 1.3 70.8 - - - -
827A LYS* 1.3 61.2 + - + +
829A LEU* 3.3 4.1 + - - -
830A LYS* 2.9 47.4 + - + +
840A TRP* 3.6 28.3 - - + -
902A CL 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 6.0 4.3 - - - +
825A GLY 3.3 0.4 - - - -
826A MET* 1.3 79.0 - - + +
828A GLU* 1.3 70.7 + - - +
830A LYS* 3.4 11.5 + - + +
831A ARG* 3.2 39.8 + - - +
753B ARG* 5.8 5.4 - - - +
819B ASP* 5.3 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 828 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A ILE* 4.5 8.1 - - + -
823A ARG 4.4 6.0 - - - +
824A ALA* 3.8 19.7 - - + -
825A GLY* 3.1 33.0 + - - +
826A MET 3.2 0.6 - - - -
827A LYS* 1.3 83.3 + - - +
829A LEU* 1.3 62.1 + - - +
831A ARG* 3.4 36.7 + - - +
832A HIS* 3.2 22.6 + - - +
821B THR* 4.7 12.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
141A ALA* 4.1 11.7 - - + -
761A TRP* 3.6 32.1 - - + -
764A LEU* 3.8 16.2 - - + -
811A ALA* 5.4 2.5 - - + -
814A ILE* 4.5 9.2 - - + -
815A LEU* 4.0 30.1 - - + -
824A ALA* 4.5 6.5 - - + -
825A GLY 3.2 13.5 + - - +
826A MET* 3.9 4.3 - - - +
828A GLU* 1.3 73.2 - - - +
830A LYS* 1.3 67.9 + - - +
832A HIS* 3.1 15.5 + - + +
835A PHE* 3.3 46.4 - - + +
840A TRP* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 5.3 3.6 - - - +
145A ASP* 5.6 1.6 - - - -
826A MET* 2.9 40.8 + - + +
827A LYS* 3.6 13.7 - - + +
828A GLU 3.3 0.2 - - - -
829A LEU* 1.3 78.8 - - - +
831A ARG* 1.3 57.0 + - - +
832A HIS 3.4 5.0 + - - +
835A PHE 4.4 5.0 - - - +
836A SER* 5.4 1.2 - - - -
840A TRP* 3.4 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A LYS* 3.3 35.3 + - - +
828A GLU* 3.5 39.4 + - - +
830A LYS* 1.3 75.9 - - + +
832A HIS* 1.4 59.5 + - - +
833A PRO* 4.0 4.5 - - - +
----------------------------------------------------------
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