Contacts of the helix formed by residues 713 - 724 (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 713 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D VAL* 4.7 7.9 - - - +
711D GLN 3.9 3.2 + - - +
712D ARG* 1.3 76.5 - - - +
714D VAL* 1.3 60.9 + - - -
715D ASP* 3.3 11.4 - - - -
716D ASP* 3.4 2.6 + - - -
717D ALA* 3.0 27.5 + - - +
1J NAG 5.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D GLU* 4.5 13.5 - - - +
686D VAL* 4.7 4.0 - - + -
713D GLY* 1.3 69.0 - - - -
715D ASP* 1.3 61.4 + - - +
717D ALA* 3.2 6.7 + - - +
718D LEU* 2.9 29.7 + - + +
729D PHE* 3.9 19.6 - - + -
731D TYR* 3.3 46.9 - - + +
735D VAL* 4.6 9.9 - - + -
736D LEU* 5.0 4.3 - - + -
739D MET* 5.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 715 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713D GLY* 3.8 10.6 - - - -
714D VAL* 1.3 77.6 + - - +
716D ASP* 1.3 75.0 + - - +
718D LEU* 3.4 6.5 + - - +
719D LEU* 2.9 29.3 + - - +
739D MET* 5.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 716 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711D GLN* 5.7 2.5 - - + -
712D ARG 3.5 24.2 - - - +
713D GLY 3.6 0.4 - - - +
714D VAL 3.2 0.6 - - - -
715D ASP* 1.3 86.5 + - - +
717D ALA* 1.3 58.9 + - - +
719D LEU* 3.5 6.9 + - - +
720D SER* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 717 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711D GLN* 4.4 18.6 - - + +
713D GLY 3.0 13.7 + - - +
714D VAL 3.2 7.6 + - - +
716D ASP* 1.3 75.5 - - - +
718D LEU* 1.3 59.7 + - - +
720D SER* 3.3 8.4 + - - -
721D LEU* 2.9 27.9 + - - +
726D LEU* 4.8 3.5 - - - +
729D PHE* 3.6 39.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 718 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714D VAL* 2.9 17.9 + - + +
715D ASP* 3.7 7.9 - - - +
717D ALA* 1.3 76.2 - - - +
719D LEU* 1.3 58.9 + - - +
721D LEU* 3.2 8.0 + - - +
722D LYS* 2.9 28.1 + - - +
729D PHE* 4.9 5.3 - - + -
739D MET* 5.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 719 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715D ASP 2.9 18.1 + - - +
716D ASP* 3.7 8.1 - - - +
718D LEU* 1.3 76.5 - - - +
720D SER* 1.3 58.0 + - - +
722D LYS* 3.4 7.5 + - - +
723D THR* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 720 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716D ASP 2.9 17.3 + - - -
717D ALA* 3.5 10.1 - - - -
719D LEU* 1.3 77.2 - - - +
721D LEU* 1.3 57.2 + - - +
723D THR* 4.3 5.2 - - - -
724D GLY 3.0 7.8 + - - -
725D LYS* 3.0 40.1 + - - -
726D LEU* 3.3 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 721 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D MET 5.3 8.1 - - - +
538D VAL 6.0 0.4 - - - -
539D SER* 4.3 22.0 - - - +
717D ALA 2.9 16.1 + - - +
718D LEU* 3.2 8.9 + - - +
720D SER* 1.3 76.1 - - - +
722D LYS* 1.3 62.0 + - - +
724D GLY* 3.9 6.6 + - - -
726D LEU* 3.5 26.0 - - + +
727D ASP 5.3 4.3 - - - +
728D ALA 5.5 3.8 - - - +
729D PHE* 5.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 722 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718D LEU 2.9 15.7 + - - +
719D LEU* 3.4 8.7 + - - +
721D LEU* 1.3 76.1 - - - +
723D THR* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 723 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719D LEU 2.9 17.7 + - - -
720D SER* 3.7 7.9 - - - -
721D LEU 3.3 0.2 - - - -
722D LYS* 1.3 80.9 - - - +
724D GLY* 1.3 57.8 + - - +
725D LYS* 3.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 724 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720D SER 3.0 4.4 + - - -
721D LEU 3.9 6.4 + - - -
722D LYS 3.6 1.4 - - - -
723D THR* 1.3 78.9 - - - +
725D LYS* 1.3 62.7 + - - +
726D LEU 3.3 7.0 + - - -
----------------------------------------------------------
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