Contacts of the helix formed by residues 794 - 802 (chain D) in PDB entry 5LPI
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 SER 794 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790D VAL* 5.5 1.1 - - - -
791D GLU* 3.0 32.1 + - - +
793D SER* 1.3 83.4 + - - +
795D LEU* 1.3 57.1 + - - +
796D THR 3.4 2.0 - - - -
797D GLU* 3.4 16.7 + - - +
798D HIS* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 795 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781D THR* 4.4 11.9 - - + -
783D CYS* 5.0 6.7 - - + -
790D VAL* 3.6 22.9 - - + -
791D GLU 3.1 7.5 + - - +
792D ILE* 3.1 17.6 + - - +
793D SER 3.6 0.8 - - - -
794D SER* 1.3 75.5 - - - +
796D THR* 1.3 61.5 + - - +
798D HIS* 3.1 11.1 + - + +
799D LEU* 2.9 58.8 + - + +
846D PRO* 4.0 22.2 - - + +
847D LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 796 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D SER 3.4 0.6 - - - -
795D LEU* 1.3 77.3 - - - +
797D GLU* 1.3 63.3 + - - +
799D LEU* 3.2 11.4 + - - +
800D LEU* 3.0 34.9 + - + +
811D LYS* 5.8 0.2 - - - -
816D SER* 3.3 27.1 - - - +
817D GLU* 3.9 10.4 - - - +
818D ALA 3.8 16.9 + - - +
844D ARG* 6.1 0.9 - - - +
846D PRO* 3.7 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 797 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D SER* 3.4 17.2 + - - +
795D LEU 3.3 0.2 - - - -
796D THR* 1.3 77.9 - - - +
798D HIS* 1.3 62.4 + - - +
800D LEU* 4.6 5.2 - - - +
801D THR* 2.8 47.9 + - + +
802D GLU* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 798 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783D CYS* 3.6 9.2 - - + +
786D CYS* 3.6 7.8 - - - -
788D GLN* 4.8 4.5 - - + -
790D VAL* 3.4 32.8 - - + +
794D SER* 2.8 16.0 + - - +
795D LEU* 3.1 14.3 + - + +
797D GLU* 1.3 76.8 - - - +
799D LEU* 1.3 68.4 + - + +
802D GLU* 2.9 41.1 + - + +
803D CYS* 2.8 43.5 + - + +
902D ZN 2.1 37.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783D CYS* 3.9 17.5 - - - -
785D HIS* 3.7 31.2 - - + +
795D LEU* 2.9 45.0 + - + +
796D THR* 3.7 6.5 - - - +
798D HIS* 1.3 77.5 - - + +
800D LEU* 1.3 58.6 + - - +
803D CYS* 4.0 2.9 - - - -
806D LYS* 3.2 28.2 - - - +
809D PHE* 3.6 25.2 - - + -
818D ALA* 3.8 26.2 - - + +
902D ZN 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 800 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796D THR* 3.0 36.6 + - + +
797D GLU* 4.2 3.1 - - - +
799D LEU* 1.3 78.6 - - - +
801D THR* 1.3 70.0 + - + +
802D GLU 3.9 0.2 - - - -
806D LYS* 3.7 15.9 - - - +
809D PHE* 4.2 8.1 - - + +
810D GLY* 3.7 27.4 - - - -
811D LYS* 3.8 33.9 - - + +
818D ALA* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 801 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D GLU* 2.8 36.9 + - + +
800D LEU* 1.3 88.8 - - + +
802D GLU* 1.3 63.5 + - - +
806D LYS* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 802 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A LYS* 6.0 1.4 - - - -
790D VAL* 6.1 0.2 - - - -
797D GLU* 5.4 1.0 - - - +
798D HIS* 2.9 35.8 + - + +
801D THR* 1.3 84.7 - - - +
803D CYS* 1.3 71.2 + - - +
804D ASP* 3.5 3.1 + - - +
806D LYS* 3.8 3.7 + - - +
----------------------------------------------------------
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