Contacts of the helix formed by residues 733 - 749 (chain A) in PDB entry 5MQF
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 THR 733 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A LEU* 2.8 12.0 + - - -
732A PRO* 1.3 69.4 - - - +
734A PRO* 1.3 64.6 - - - +
736A GLU* 4.1 7.4 - - - +
737A ASN* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A MET* 6.1 5.6 - - + -
732A PRO* 3.4 7.4 - - + +
733A THR* 1.3 95.3 - - - +
735A ILE* 1.3 57.8 + - + +
737A ASN* 3.4 5.4 + - + +
738A MET* 2.9 28.6 + - - +
462D GLU* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ILE* 6.2 4.3 - - + -
696A MET* 5.0 16.1 - - + +
732A PRO* 2.7 28.3 + - + +
734A PRO* 1.3 75.3 - - + +
736A GLU* 1.3 59.1 + - - +
738A MET* 3.9 5.2 - - - +
739A ILE* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A LEU* 4.5 15.3 - - + -
732A PRO* 2.7 22.9 + - + +
733A THR* 4.1 6.5 - - - +
735A ILE* 1.3 72.4 - - - +
737A ASN* 1.3 57.5 + - - +
739A ILE* 3.9 4.6 - - - +
740A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A THR 2.9 20.6 + - - +
734A PRO* 3.8 5.6 - - + +
735A ILE 3.2 0.2 - - - -
736A GLU* 1.3 76.4 - - - +
738A MET* 1.3 59.5 + - - +
740A LEU* 3.7 5.5 - - - +
741A ARG* 2.9 27.5 + - - +
461D ASP* 4.4 3.2 - - + +
462D GLU* 3.9 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ASP* 6.5 1.1 - - + -
734A PRO 2.9 16.7 + - - +
735A ILE* 3.9 5.6 - - - +
737A ASN* 1.3 74.8 - - - +
739A ILE* 1.3 61.1 + - - +
741A ARG* 3.1 8.0 + - - +
742A TYR* 2.9 30.4 + - - +
462D GLU* 4.4 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A HIS* 4.1 28.0 - - + +
716A ALA* 4.9 1.9 - - - +
735A ILE 2.9 19.0 + - - +
736A GLU* 4.3 4.5 - - - +
738A MET* 1.3 75.9 - - - +
740A LEU* 1.3 57.1 + - - +
742A TYR* 4.5 5.1 - - - +
743A VAL* 2.7 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A GLU 2.9 22.2 + - - +
737A ASN* 3.7 7.9 - - - +
738A MET 3.1 0.2 - - - -
739A ILE* 1.3 75.0 - - - +
741A ARG* 1.3 60.9 + - - +
743A VAL* 3.5 6.0 - - - +
744A LYS* 2.9 28.8 + - - +
461D ASP* 5.0 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A ASN 2.9 15.3 + - - +
738A MET* 3.4 10.8 - - - +
740A LEU* 1.3 74.4 - - - +
742A TYR* 1.3 59.0 + - - +
744A LYS* 2.9 23.1 + - - +
745A ALA* 2.9 12.1 + - - +
461D ASP* 4.0 21.5 - - + +
462D GLU* 4.3 7.0 - - + +
463D SER* 4.6 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A MET 2.9 17.9 + - - +
739A ILE* 4.5 4.5 - - - +
741A ARG* 1.3 73.4 - - - +
743A VAL* 1.3 57.1 + - - +
745A ALA* 3.3 12.1 + - + +
746A LYS* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ALA* 3.7 28.7 - - + +
719A CYS* 6.4 0.4 - - + -
720A TRP* 5.1 8.8 - - + +
739A ILE 2.7 24.0 + - - +
740A LEU* 3.5 9.0 - - - +
741A ARG 3.1 0.2 - - - -
742A TYR* 1.3 76.5 - - - +
744A LYS* 1.3 57.2 + - - +
746A LYS* 3.1 10.8 + - - +
747A ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A LEU 2.9 12.4 + - - +
741A ARG* 2.9 11.1 + - - +
743A VAL* 1.3 72.8 - - - +
745A ALA* 1.3 61.2 + - - +
747A ALA* 3.2 9.9 + - - +
748A ASP* 2.9 26.3 + - - +
459D SER* 6.3 2.9 - - - -
461D ASP* 6.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A ARG 2.9 10.9 + - - +
742A TYR* 3.4 14.6 - - + +
743A VAL 3.2 0.2 - - - -
744A LYS* 1.3 77.7 - - - +
746A LYS* 1.3 56.5 + - - +
748A ASP* 3.1 10.1 + - - +
749A TRP* 2.9 25.3 + - - +
206D TRP* 5.8 6.5 - - + -
224D ALA* 5.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A TYR 2.9 13.7 + - - +
743A VAL* 3.1 12.3 + - - +
745A ALA* 1.3 72.7 - - - +
747A ALA* 1.3 66.4 + - - +
749A TRP* 3.1 18.4 + - - +
750A TRP* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TRP* 4.4 19.5 - - + +
743A VAL 2.9 12.2 + - - +
744A LYS* 3.2 13.4 + - - +
746A LYS* 1.3 75.8 - - - +
748A ASP* 1.3 57.1 + - - +
750A TRP* 3.1 9.5 + - - +
751A THR* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A LYS 2.9 13.1 + - - +
745A ALA* 3.4 13.0 - - - +
747A ALA* 1.3 73.6 - - - +
749A TRP* 1.3 64.7 + - - +
751A THR* 3.1 17.5 + - - -
752A ASN* 3.2 19.6 + - - +
204D LEU 5.1 10.1 - - - +
205D GLY* 6.0 3.1 - - - -
214R THR* 4.9 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE* 6.3 2.9 - - + -
745A ALA 2.9 13.3 + - - +
746A LYS* 3.1 14.3 + - - +
748A ASP* 1.3 75.1 - - - +
750A TRP* 1.3 57.5 + - - +
753A THR* 3.2 25.2 - - - +
224D ALA 5.9 3.8 - - - +
----------------------------------------------------------
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