Contacts of the helix formed by residues 730 - 739 (chain A) in PDB entry 4EJX
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 ARG 730 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A SER* 3.3 29.8 - - - +
729A GLN* 1.3 71.0 - - - +
731A GLU* 1.3 60.6 + - - +
732A TRP* 3.3 2.9 - - - -
733A GLU* 2.7 59.6 + - - +
734A LYS* 3.5 8.3 + - - +
746A ASN* 3.6 10.3 - - - +
749A LEU* 3.3 35.7 + - - +
750A ASP* 2.7 30.5 + - - +
758A SER* 5.3 5.8 + - - -
947A PHE* 6.4 0.2 - - - -
949A ASN* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A GLN* 3.2 16.7 - - + +
730A ARG* 1.3 74.7 - - - +
732A TRP* 1.3 63.7 + - - +
733A GLU 3.2 1.8 - - - -
734A LYS* 3.7 26.0 + - - +
735A GLU* 3.0 44.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.7 38.0 + - + +
729A GLN 4.6 3.9 + - - +
730A ARG 3.3 0.4 - - - -
731A GLU* 1.3 77.3 - - - +
733A GLU* 1.3 61.6 + - - +
735A GLU* 4.4 4.9 - - - -
736A LEU* 3.6 49.0 + - + +
947A PHE* 3.2 22.0 - - + +
948A GLY* 3.4 42.7 - - - +
1018A LEU* 3.9 23.1 - - + -
1032A GLU* 4.0 16.6 - - + -
1033A THR 5.1 0.4 - - - -
1034A THR* 4.1 30.7 + - + +
1108A NAG 6.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A ARG* 2.7 55.0 + - - +
731A GLU 3.2 0.6 - - - -
732A TRP* 1.3 78.7 - - - +
734A LYS* 1.3 63.3 + - - +
736A LEU* 3.7 3.9 + - - +
737A HIS* 3.3 45.0 + - + -
744A VAL 4.6 5.0 - - - +
746A ASN* 2.7 30.8 + - - +
749A LEU* 3.3 10.4 - - + +
947A PHE* 4.1 31.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A ARG 3.5 8.8 + - - +
731A GLU* 3.7 25.2 + - - +
732A TRP 3.5 0.2 - - - -
733A GLU* 1.3 76.6 - - - +
735A GLU* 1.3 56.7 + - + +
737A HIS* 3.4 4.8 + - - +
738A HIS* 2.7 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.9 27.0 - - + +
119A ASN* 5.5 2.6 - - - +
731A GLU* 3.0 42.0 + - - +
732A TRP* 4.6 2.8 - - - +
733A GLU 3.5 0.4 - - - -
734A LYS* 1.3 73.0 - - + +
736A LEU* 1.3 60.9 + - - +
738A HIS* 4.2 5.8 - - - -
739A LEU* 2.8 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE 4.5 4.7 - - - +
116A TYR* 3.9 17.0 - - + -
117A PRO* 3.8 25.0 - - + +
732A TRP* 3.6 33.6 + - + +
733A GLU 3.8 5.2 - - - +
734A LYS 3.3 0.4 - - - -
735A GLU* 1.3 77.5 - - - +
737A HIS* 1.3 67.0 + - + +
739A LEU* 3.2 6.4 + - - +
740A GLN* 3.1 45.6 + - + +
947A PHE* 4.5 12.8 - - + -
1018A LEU* 5.4 0.7 - - + -
1032A GLU* 3.4 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A GLU* 3.3 43.3 + - + +
734A LYS* 3.9 4.7 - - - +
736A LEU* 1.3 84.2 - - + +
738A HIS* 1.3 54.8 + - - +
740A GLN* 3.1 19.0 + - - +
741A GLU 2.9 6.9 + - - -
742A GLN* 2.6 53.4 + - + +
744A VAL* 3.8 38.2 + - + -
745A SER 5.5 1.3 + - - -
746A ASN* 4.2 10.9 + - - -
947A PHE* 4.7 10.4 - + - -
1028A HIS* 5.9 5.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 5.2 0.5 + - - -
734A LYS* 2.7 34.6 + - + +
735A GLU* 3.8 5.4 - - - +
737A HIS* 1.3 74.7 - - - +
739A LEU* 1.3 75.3 + - + +
741A GLU* 2.9 24.9 + - - +
742A GLN 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.7 34.5 - - + +
116A TYR* 4.4 2.2 - - - +
117A PRO* 4.2 15.3 - - + -
125A ARG* 3.5 36.1 - - - +
129A LYS* 3.4 23.9 + - - +
164A ILE* 4.4 1.7 - - - +
735A GLU* 2.8 35.8 + - + +
736A LEU* 3.6 5.4 - - - +
738A HIS* 1.3 91.6 - - + +
740A GLN* 1.3 59.4 - - - +
741A GLU 3.4 0.7 - - - -
----------------------------------------------------------
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