Contacts of the helix formed by residues 787 - 794 (chain D) in PDB entry 4PE5
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 787 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 4.9 11.2 - - - -
696A GLN* 4.9 0.7 - - - -
783D LEU 3.2 5.8 + - - -
784D PHE 3.4 9.6 + - - -
785D GLY 3.2 3.6 - - - -
786D ASP* 1.3 78.8 - - - +
788D GLU* 1.3 62.6 + - - +
789D MET* 3.1 3.8 - - - -
790D GLU* 3.3 20.3 + - - +
791D GLU* 3.6 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 788 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 4.9 15.0 - - - +
783D LEU* 3.4 16.0 + - + +
786D ASP* 3.3 10.8 + - + -
787D GLY* 1.3 77.0 - - - +
789D MET* 1.3 60.0 + - - +
791D GLU* 3.1 11.4 + - + +
792D LEU* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 789 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A ARG* 6.5 0.7 - - + -
460D PHE* 3.6 29.1 - - + -
464D ILE* 3.7 21.8 - - + -
529D PHE* 3.9 24.2 - - + +
530D ILE* 5.3 2.0 - - + -
780D ILE* 4.2 5.8 - - + -
783D LEU* 3.5 34.8 + - + +
784D PHE* 3.4 40.4 - - + -
787D GLY* 3.1 1.1 - - - -
788D GLU* 1.3 79.2 - - - +
790D GLU* 1.3 56.8 + - - +
792D LEU* 3.4 6.8 + - - +
793D GLU* 2.9 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 790 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A LEU 5.9 1.1 - - - +
753A PHE* 5.7 7.2 - - + -
754A PHE 5.5 9.2 - - - +
787D GLY* 3.3 13.2 + - - +
788D GLU 3.2 0.4 - - - -
789D MET* 1.3 78.4 - - - +
791D GLU* 1.3 57.7 + - - +
793D GLU* 3.3 8.0 + - - +
794D ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 791 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787D GLY 3.6 3.8 + - - +
788D GLU* 3.1 18.7 + - + +
790D GLU* 1.3 78.6 - - - +
792D LEU* 1.3 62.6 + - + +
794D ALA* 3.3 6.3 + - - +
795D LEU* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 792 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D PHE* 3.4 26.9 - - + +
463D ASP* 4.0 33.2 - - + +
464D ILE* 3.7 27.6 - - + -
467D LYS* 4.2 30.3 - - + +
783D LEU* 5.0 3.6 - - + -
788D GLU* 2.9 23.5 + - + +
789D MET* 3.8 4.3 - - - +
791D GLU* 1.3 77.7 - - + +
793D GLU* 1.3 61.3 + - - +
795D LEU* 4.1 14.4 - - + -
796D TRP* 3.2 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 793 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D PHE* 3.6 13.4 - - + -
530D ILE* 5.1 4.7 - - + -
789D MET* 2.9 18.0 + - + +
790D GLU* 3.6 9.6 - - - +
791D GLU 3.2 0.2 - - - -
792D LEU* 1.3 78.1 - - - +
794D ALA* 1.3 55.9 + - - +
795D LEU 3.2 0.9 - - - -
797D LEU* 3.2 44.8 + - + +
798D THR* 4.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 794 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C ARG* 5.7 2.8 - - - +
790D GLU 3.0 16.7 + - - +
791D GLU* 3.6 7.2 - - - +
792D LEU 3.3 0.4 - - - -
793D GLU* 1.3 76.0 - - - +
795D LEU* 1.3 58.7 + - - +
798D THR* 3.4 23.0 - - - +
----------------------------------------------------------
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