Contacts of the helix formed by residues 738 - 746 (chain A) in PDB entry 5I4E
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 PHE 738 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A LEU* 1.3 73.4 - - - +
739A GLN* 1.3 68.7 + - - +
741A PHE* 3.3 1.1 + - - -
742A ARG* 3.2 21.2 + - - +
760A GLY* 3.7 17.7 - - - -
761A LYS* 3.5 37.5 - - + -
764A CYS* 3.3 35.0 - - + -
780A VAL* 5.2 4.0 - - + -
781A GLY 3.3 25.8 - - - -
782A GLN 3.5 13.7 - - - -
783A SER* 3.4 28.9 + - - -
784A LYS* 3.7 18.6 - - - -
785A ILE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A LEU* 3.9 32.8 - - + +
738A PHE* 1.3 84.1 + - - +
740A GLU* 1.3 59.8 + - + +
742A ARG* 3.9 7.0 - - - +
743A GLN* 3.1 30.0 + - - +
760A GLY* 5.3 1.9 - - - -
783A SER 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 3.5 27.0 - - + +
737A LEU* 3.2 22.7 + - + +
739A GLN* 1.3 79.4 - - + +
741A PHE* 1.3 61.0 + - - +
743A GLN* 4.0 7.0 - - + +
744A ARG* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 3.6 28.0 - - + +
737A LEU 3.1 16.6 + - - +
738A PHE 3.7 3.8 - - - +
740A GLU* 1.3 74.3 - - - +
742A ARG* 1.3 58.7 + - - +
744A ARG 3.1 1.2 + - - -
745A TYR* 2.8 63.5 + + + +
764A CYS* 4.1 9.9 - - - -
767A MET* 3.9 31.9 - - + -
768A ILE* 4.3 13.2 - - + -
771A LEU* 4.1 21.8 - - + -
773A LEU* 5.0 0.2 - - + -
785A ILE* 3.5 20.2 - - + -
787A PHE* 3.4 26.2 - + - -
795A LEU* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A PHE 3.2 14.3 + - - +
739A GLN* 3.9 6.7 - - - +
741A PHE* 1.3 77.9 - - - +
743A GLN* 1.3 63.3 + - - +
746A GLU* 3.3 53.4 + - - +
753A ILE* 3.7 45.0 - - + +
755A LYS 4.5 10.1 + - - -
757A PHE* 4.8 8.9 - - - +
758A MET* 5.1 3.0 - - - +
759A ASP 4.5 9.3 + - - +
760A GLY* 6.6 0.2 - - - -
763A ALA* 4.0 19.2 - - + +
764A CYS* 4.7 5.4 - - - -
767A MET* 3.6 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A GLN 3.1 17.8 + - - +
740A GLU* 4.0 7.2 - - + +
742A ARG* 1.3 85.9 - - - +
744A ARG* 1.3 70.3 + - + +
746A GLU* 4.3 10.9 + - - +
799A ARG* 5.5 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 5.1 0.9 - - + -
740A GLU* 2.9 33.3 + - + +
743A GLN* 1.3 86.9 - - + +
745A TYR* 1.3 90.0 + - + +
746A GLU 3.8 0.5 + - - -
747A ILE* 4.9 1.6 + - - +
796A GLU* 2.7 34.4 + - - +
799A ARG* 2.8 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 3.9 12.3 - - + +
741A PHE* 2.8 57.3 + + + +
744A ARG* 1.3 88.2 - - + +
746A GLU* 1.4 57.4 + - - +
747A ILE 3.2 2.9 - - - +
748A LEU* 3.0 43.6 + - + +
749A THR* 3.7 2.4 + - - +
767A MET* 3.5 17.5 - - + +
771A LEU* 5.4 3.1 - - + -
792A LEU* 3.7 21.6 + - + +
795A LEU* 3.7 37.5 - - + -
796A GLU* 2.8 33.5 + - - +
799A ARG* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ARG* 3.3 52.0 + - - +
743A GLN* 4.3 8.7 + - - +
744A ARG 3.6 2.4 - - - -
745A TYR* 1.4 74.9 - - - +
747A ILE* 1.4 58.8 + - - +
748A LEU 3.4 0.5 + - - -
749A THR* 3.5 26.8 + - - +
750A PRO* 3.7 6.9 - - - +
753A ILE* 4.2 17.6 - - + +
767A MET* 4.1 5.6 - - + -
----------------------------------------------------------
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