Contacts of the helix formed by residues 733 - 742 (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 ALA 733 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D GLU 5.3 0.4 - - - +
532D THR* 3.1 19.0 + - - +
533D GLY 2.7 21.8 + - - +
535D SER* 3.3 29.2 - - - +
732D ASP* 1.3 69.6 - - - +
734D ALA* 1.3 61.5 + - - +
736D LEU* 3.3 2.4 + - - +
737D ASN* 2.8 41.8 + - - +
756D VAL* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 734 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D PHE* 3.6 27.2 - - + -
530D ILE* 4.2 17.9 - - + -
531D GLU 4.3 3.6 + - - +
532D THR* 3.3 9.2 + - - +
732D ASP* 3.0 10.1 + - - +
733D ALA* 1.3 78.4 - - - +
735D VAL* 1.3 58.4 + - - +
737D ASN* 3.2 8.7 + - - +
738D TYR* 2.9 30.8 + - - +
762D TYR* 4.4 1.3 - - + -
797D LEU* 5.5 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 735 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D GLU* 3.5 29.4 - - + +
414D ALA 4.4 7.9 - - - +
416D PHE* 4.2 13.7 - - + -
714D VAL* 4.6 10.5 - - + -
731D TYR* 3.7 26.9 - - + -
732D ASP* 3.1 11.8 + - + +
734D ALA* 1.3 74.7 - - - +
736D LEU* 1.3 59.3 + - + +
738D TYR* 3.5 6.6 + - + +
739D MET* 2.9 33.1 + - + +
762D TYR* 3.3 23.3 - - - +
907D GLU* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D SER* 3.3 32.3 - - - +
536D VAL 4.0 0.9 - - - +
537D MET* 3.6 38.7 - - + +
714D VAL* 5.0 3.8 - - + -
729D PHE* 3.8 18.6 - - + +
731D TYR* 3.6 34.1 - - + +
732D ASP 3.2 14.9 + - - +
733D ALA* 3.7 4.3 - - - +
735D VAL* 1.3 79.5 - - + +
737D ASN* 1.3 63.4 + - - +
739D MET* 3.8 7.4 - - + +
740D ALA* 2.9 31.9 + - - +
750D THR* 5.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D SER* 5.2 3.3 + - - -
733D ALA* 2.8 34.5 + - - +
734D ALA* 3.5 7.9 - - - +
736D LEU* 1.3 77.3 - - - +
738D TYR* 1.3 60.1 + - - +
740D ALA* 3.5 4.9 + - - +
741D GLY* 2.9 24.8 + - - -
750D THR* 4.2 18.2 - - - -
754D GLY* 5.5 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674C ASN* 5.8 3.5 - - - +
414D ALA* 4.7 9.0 - - + +
415D PRO* 3.5 46.0 - - + +
418D ILE* 5.7 2.3 - - - +
734D ALA 2.9 16.3 + - - +
735D VAL* 3.9 4.9 - - + +
737D ASN* 1.3 73.7 - - - +
739D MET* 1.3 70.8 + - - +
741D GLY* 3.1 2.5 + - - +
742D ARG* 2.7 47.8 + - + +
796D TRP 3.1 26.4 + - - -
797D LEU* 4.0 24.0 - - + +
798D THR 4.1 11.9 - - - -
799D GLY* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714D VAL* 5.8 10.3 - - + -
715D ASP* 5.2 13.7 - - + +
718D LEU* 5.0 20.0 - - + -
735D VAL* 2.9 23.5 + - + +
736D LEU* 3.8 10.5 - - + +
738D TYR* 1.3 88.5 - - - +
740D ALA* 1.3 61.0 + - - +
742D ARG 2.9 30.9 - - - +
743D ASP* 3.5 15.2 - - + +
748D LEU* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D MET* 5.6 2.0 - - + -
736D LEU 2.9 18.6 + - - +
737D ASN* 3.8 5.4 - - - +
739D MET* 1.3 76.4 - - - +
741D GLY* 1.3 64.2 + - - +
742D ARG 3.6 0.9 + - - -
743D ASP* 4.9 3.5 + - - +
745D GLY 5.3 0.7 - - - +
746D CYS* 5.8 0.7 - - - -
748D LEU* 3.7 33.0 - - + +
749D VAL* 4.2 12.6 - - - -
750D THR* 4.4 7.4 - - - +
801D CYS* 3.8 15.4 - - - +
802D HIS* 5.7 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D ASN 2.9 15.0 + - - -
738D TYR* 3.1 4.2 + - - -
740D ALA* 1.3 78.3 - - - +
742D ARG* 1.3 56.2 + - - +
743D ASP 4.1 0.2 - - - -
799D GLY* 3.7 14.1 - - - -
800D ILE* 2.7 28.2 + - - +
801D CYS* 2.8 21.7 + - - +
802D HIS* 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C PRO* 5.8 4.5 - - + -
738D TYR* 2.7 40.2 + - + +
739D MET* 2.9 27.3 - - - +
741D GLY* 1.3 74.2 - - - +
743D ASP* 1.3 56.7 + - - +
798D THR 4.7 7.9 - - - +
799D GLY* 4.8 0.4 - - - -
800D ILE* 4.2 10.1 - - + -
----------------------------------------------------------
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