Contacts of the helix formed by residues 723 - 738 (chain B) in PDB entry 2XWU
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 MET 723 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B VAL* 4.2 14.4 - - + +
681B LEU* 3.5 48.0 - - + +
682B GLN* 3.8 12.8 - - - +
685B PHE* 4.2 8.5 - - + -
709B PHE* 4.5 11.7 - - + -
720B PHE* 2.8 40.6 + - + +
722B PRO* 1.3 82.0 - - + +
724B VAL* 1.3 64.3 + - - +
725B PRO 3.3 0.2 - - - -
726B GLN* 3.0 32.1 + - + +
727B LEU* 2.8 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B PHE* 3.6 11.6 + - + +
721B ALA* 3.2 15.7 + - + +
723B MET* 1.3 75.5 - - - +
725B PRO* 1.3 76.7 - - + +
727B LEU* 3.0 2.9 + - - +
728B CYS* 2.8 34.7 + - - -
750B LEU* 4.9 3.4 - - + -
754B PHE* 3.4 38.8 - - + -
760B HIS* 4.2 15.5 - - + +
763B PRO* 4.3 2.2 - - + -
764B ILE* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B ALA 3.6 5.6 - - - +
722B PRO 3.5 14.8 - - - +
724B VAL* 1.3 100.0 - - + +
726B GLN* 1.3 65.2 + - + +
728B CYS* 3.6 2.6 + - - +
729B GLU* 3.4 19.8 + - - +
760B HIS* 5.3 2.7 - - + +
763B PRO* 4.1 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B GLN* 4.9 6.5 - - - +
685B PHE* 2.7 58.2 - - + +
722B PRO 4.9 5.8 + - - +
723B MET* 3.0 28.5 + - + +
725B PRO* 1.3 79.9 - - + +
727B LEU* 1.3 63.3 + - - +
729B GLU* 3.4 7.4 + - - +
730B MET* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B PHE* 4.6 3.5 - - - -
709B PHE* 3.3 48.2 - - + -
713B VAL* 4.5 2.7 - - + -
720B PHE* 3.4 33.2 - - + -
723B MET* 2.8 21.2 + - + +
724B VAL* 3.5 3.4 - - - +
726B GLN* 1.3 71.9 - - - +
728B CYS* 1.3 60.0 + - - +
730B MET* 3.1 4.3 + - + +
731B LEU* 2.7 51.3 + - + +
734B MET* 5.0 3.6 - - + -
746B LEU* 4.4 7.2 - - + -
750B LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B VAL* 2.8 42.0 + - - +
725B PRO 4.1 3.8 - - - +
727B LEU* 1.3 72.4 - - - +
729B GLU* 1.3 58.2 + - - +
731B LEU* 3.8 0.9 - - - +
732B GLY* 2.9 28.2 + - - -
750B LEU* 4.4 6.7 - - - -
763B PRO* 3.9 16.8 - - + +
764B ILE* 3.9 23.1 - - - -
767B LEU* 3.9 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B PHE* 6.3 1.1 - - + -
689B GLN* 6.1 2.7 - - - +
725B PRO 3.4 10.9 + - - +
726B GLN* 3.6 9.9 - - - +
727B LEU 3.2 0.4 - - - -
728B CYS* 1.3 79.2 - - - +
730B MET* 1.3 63.9 + - + +
732B GLY* 3.7 1.3 + - - -
733B ARG* 3.5 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B PHE* 3.4 29.8 - - + -
688B ILE* 4.7 4.7 - - + -
689B GLN* 4.5 13.5 - - + +
692B LEU* 3.3 31.1 - - + +
705B VAL* 3.4 20.4 - - + -
709B PHE* 3.3 29.2 - - + -
726B GLN 3.1 13.3 + - - +
727B LEU* 3.1 5.7 + - - +
729B GLU* 1.3 80.6 - - + +
731B LEU* 1.3 59.3 + - - +
733B ARG* 3.5 6.3 + - - +
734B MET* 3.0 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B CYS* 4.9 4.7 - - - -
727B LEU* 2.7 31.1 + - + +
728B CYS 3.8 3.4 - - - +
730B MET* 1.3 72.7 - - - +
732B GLY* 1.3 59.8 + - - +
734B MET* 3.1 23.4 + - + +
735B TYR* 2.7 33.7 + - + +
743B ALA* 3.7 34.1 - - + +
746B LEU* 3.8 36.3 - - + -
747B THR* 4.3 6.1 - - - +
750B LEU* 4.5 2.9 - - + -
767B LEU* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B CYS 2.9 16.0 + - - -
729B GLU 4.2 1.6 - - - -
730B MET 3.4 0.4 - - - -
731B LEU* 1.3 76.4 - - - +
733B ARG* 1.3 56.5 + - - +
735B TYR* 3.6 3.3 + - - +
736B SER* 3.0 32.1 + - - -
767B LEU* 3.8 8.6 - - - +
770B LEU* 3.2 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 5.9 1.8 - - + -
696B LEU* 3.8 15.7 - - + +
729B GLU* 3.5 17.2 + - - +
730B MET* 3.5 9.1 + - - +
731B LEU 3.2 0.6 - - - -
732B GLY* 1.3 72.6 - - - +
734B MET* 1.3 67.1 + - - +
736B SER* 3.8 4.6 - - - -
737B THR* 2.9 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 3.9 16.2 - - + -
696B LEU* 4.0 13.5 - - + -
702B VAL* 4.1 24.2 - - + +
705B VAL* 4.4 9.9 - - + -
706B CYS* 4.9 7.6 - - - -
709B PHE* 5.1 2.5 - - + -
727B LEU* 5.0 4.3 - - + -
730B MET* 3.0 57.2 + - + +
731B LEU* 3.1 41.0 + - + +
733B ARG* 1.3 78.7 - - - +
735B TYR* 1.3 57.8 + - - +
737B THR* 3.8 0.5 - - - -
738B ILE* 2.9 39.1 + - + +
743B ALA* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B LEU* 2.7 21.0 + - + +
732B GLY* 4.0 5.8 - - - +
734B MET* 1.3 75.1 - - - +
736B SER* 1.3 62.2 + - - +
738B ILE 3.9 2.2 - - - -
739B PRO* 3.1 41.9 - - + +
740B GLN 3.4 31.4 - - - -
743B ALA* 3.7 20.6 - - + +
744B LEU* 3.7 18.6 - - + +
770B LEU* 5.2 1.3 - - + -
771B VAL* 3.2 44.4 - - + -
774B VAL* 3.7 20.6 - - + +
775B THR* 2.3 38.2 + - - +
778B LEU* 5.4 0.3 - - - +
789B ILE* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B GLY 3.0 19.4 + - - -
733B ARG* 3.8 6.7 - - - -
734B MET 3.3 0.2 - - - -
735B TYR* 1.3 77.5 - - - +
737B THR* 1.3 65.6 + - - +
739B PRO* 4.2 4.5 - - - +
770B LEU* 3.8 19.4 - - - +
774B VAL* 4.0 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LEU* 3.0 46.8 - - + +
697B ASN* 3.3 30.1 + - - +
733B ARG 2.9 17.6 + - - -
734B MET 3.8 1.6 - - - -
736B SER* 1.3 80.7 - - - +
738B ILE* 1.3 60.7 + - + +
739B PRO* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LEU 3.7 13.9 - - - +
697B ASN* 4.5 7.0 - - - +
698B ASP 4.0 2.9 - - - -
699B ALA* 3.3 42.0 - - + +
702B VAL* 3.7 24.5 - - + -
734B MET* 2.9 17.9 + - + +
735B TYR* 3.4 5.0 - - - +
737B THR* 1.3 80.7 - - + +
739B PRO* 1.3 66.5 - - + +
740B GLN* 3.5 20.7 + - + +
----------------------------------------------------------
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