Contacts of the helix formed by residues 738 - 755 (chain A) in PDB entry 2VUW
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 PRO 738 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A GLU* 3.6 17.7 - - - +
646A GLU* 4.2 10.5 - - + -
736A TYR* 3.5 44.9 - - + +
737A HIS* 1.3 82.7 - - - +
739A TYR* 1.3 65.5 + - - +
740A SER 3.0 0.9 - - - -
741A ASN* 3.0 22.2 + - - +
742A VAL 3.7 2.4 + - - -
785A SER 3.8 11.9 - - - +
786A SER* 3.7 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A GLU* 3.8 38.8 - - + +
737A HIS 2.9 0.6 + - - -
738A PRO* 1.3 79.2 - - - +
740A SER* 1.3 63.2 + - - +
742A VAL* 2.9 16.6 + - + +
743A LEU* 2.9 49.2 + - + +
782A LEU* 2.9 41.2 + - + +
784A PHE 3.2 28.3 - - - -
785A SER* 3.4 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A GLU* 2.6 39.1 + - - +
648A ARG* 4.3 2.1 + - - +
725A MSE 3.8 31.4 - - - -
728A GLU* 5.1 3.4 - - - +
737A HIS* 3.0 9.1 + - - +
738A PRO 3.0 0.6 - - - -
739A TYR* 1.3 79.1 - - - +
741A ASN* 1.3 63.0 + - - +
743A LEU* 3.3 12.6 + - - +
744A TRP* 3.1 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LEU* 4.0 30.0 + - + +
640A GLU* 2.9 29.4 + - - +
645A PHE 3.0 24.9 + - - -
646A GLU* 3.5 4.3 - - - +
647A HIS* 3.2 27.5 + - - +
648A ARG 4.8 0.7 + - - -
738A PRO* 3.0 13.9 + - - +
740A SER* 1.3 76.6 + - - +
742A VAL* 1.3 60.5 + - - +
744A TRP* 3.4 6.6 + - - +
745A LEU* 2.9 36.1 + - - +
787A ALA* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A PRO 4.2 0.7 - - - +
739A TYR* 2.9 21.4 + - + +
741A ASN* 1.3 74.1 - - - +
743A LEU* 1.3 65.9 + - - +
745A LEU* 3.2 9.2 + - - +
746A HIS* 2.8 22.4 + - - +
781A MSE 3.3 32.8 - - + +
782A LEU* 4.1 5.6 - - + -
784A PHE 3.7 11.7 - - - +
785A SER 4.0 1.8 - - - -
786A SER* 3.4 47.8 - - - +
787A ALA 3.9 0.7 - - - +
790A LEU* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A TYR* 5.1 2.0 - - - +
721A ILE* 3.7 19.9 - - + +
724A LEU* 3.9 44.6 - - + +
725A MSE 4.0 25.1 - - + +
728A GLU* 5.1 1.6 - - + -
739A TYR* 2.9 43.9 + - + +
740A SER* 3.5 9.9 - - - +
741A ASN 3.3 0.2 - - - -
742A VAL* 1.3 76.5 - - - +
744A TRP* 1.4 57.5 + - - +
746A HIS* 3.1 7.7 + - - +
747A TYR* 2.9 27.5 + - - +
782A LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LEU* 5.8 0.7 - - + -
647A HIS* 5.5 1.1 - - + -
648A ARG* 3.3 44.3 + - - +
649A ASP* 3.7 3.6 - - - -
650A LEU* 3.4 49.1 - - + -
651A HIS* 3.7 15.3 - - - -
718A GLN* 4.0 18.6 - - + -
721A ILE* 3.4 28.4 - - + +
722A TYR* 3.7 26.9 - + - -
725A MSE 3.6 10.7 - - + -
740A SER 3.1 29.6 + - - +
741A ASN* 3.9 6.5 - - - +
742A VAL 3.3 0.4 - - - -
743A LEU* 1.4 75.6 - - - +
745A LEU* 1.3 57.4 + - - +
747A TYR* 3.2 29.0 + + - +
748A LEU* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.6 6.9 - - + +
632A LEU* 3.8 32.8 - - + -
633A THR* 3.7 27.1 - - - +
636A LEU* 3.9 21.1 - - + -
741A ASN 2.9 21.9 + - - +
742A VAL 3.2 2.4 + - - +
744A TRP* 1.3 76.2 - - - +
746A HIS* 1.3 56.8 + - - +
748A LEU* 3.3 9.8 + - + +
749A THR* 2.9 32.4 + - - -
777A PHE* 5.5 0.9 - - + -
781A MSE 3.4 15.7 - - + -
787A ALA* 4.1 15.0 - - + -
790A LEU* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A TYR* 2.7 37.2 + + - +
742A VAL 2.8 13.1 + - - +
743A LEU 3.1 9.4 + - - +
745A LEU* 1.3 73.7 - - - +
747A TYR* 1.3 59.6 + - - +
749A THR* 3.2 2.1 + - - -
750A ASP* 2.9 31.0 + - - +
778A HIS* 3.1 52.3 + + - -
781A MSE 3.4 24.0 - - + +
782A LEU* 3.7 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LEU 3.6 3.6 - - - -
651A HIS* 3.5 28.1 - - + +
652A TRP* 2.9 34.5 + - - -
716A ASP* 3.6 20.8 + - - -
717A TYR* 3.6 23.7 - + + -
718A GLN* 3.6 30.6 + - + -
721A ILE* 3.9 10.8 - - + -
743A LEU 2.9 12.3 + - - +
744A TRP* 3.5 23.3 - + + +
746A HIS* 1.3 77.7 - - - +
748A LEU* 1.3 73.6 + - + +
750A ASP* 3.4 3.8 - - - +
751A LYS* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 4.1 19.4 - - + +
629A LEU* 4.5 9.9 - - + -
632A LEU* 3.8 24.2 - - + -
650A LEU* 3.8 35.0 - - + +
652A TRP* 4.2 7.9 - - + -
655A VAL* 4.0 15.9 - - + -
744A TRP 2.9 22.3 + - - +
745A LEU* 3.7 10.5 - - + +
746A HIS 3.2 0.2 - - - -
747A TYR* 1.3 94.3 - - + +
749A THR* 1.3 60.5 + - - +
751A LYS* 3.2 6.9 + - + +
752A MSE 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.6 9.6 - - + +
745A LEU 2.9 17.6 + - - -
746A HIS 3.2 4.0 + - - -
748A LEU* 1.3 75.4 - - - +
750A ASP* 1.3 62.5 + - - +
752A MSE 3.1 10.6 + - - +
753A LEU* 3.1 22.5 + - + +
774A ILE* 4.0 18.6 - - + +
777A PHE* 3.4 35.7 - - + -
778A HIS* 3.8 28.7 - - + -
781A MSE 3.6 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A TYR* 4.1 25.6 - - + +
746A HIS* 2.9 17.5 + - - +
747A TYR* 3.4 9.5 - - - +
749A THR* 1.3 77.1 - - - +
751A LYS* 1.3 63.7 + - - +
753A LEU* 3.2 2.3 + - - -
754A LYS* 2.7 75.2 + - - +
755A GLN* 5.2 1.9 - - - +
778A HIS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 5.4 2.7 - - + -
652A TRP* 3.7 46.9 - - + -
716A ASP* 2.9 33.4 + - - -
717A TYR* 4.7 3.8 - - - +
747A TYR* 3.0 45.6 + - + +
748A LEU* 3.2 11.6 + - + +
750A ASP* 1.3 84.7 + - - +
752A MSE 1.3 63.2 + - + +
755A GLN* 2.9 59.8 + - + +
756A MSE 2.9 13.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 4.0 22.4 - - + -
619A LEU* 5.2 0.7 - - - -
622A LEU* 4.1 5.3 - - + +
625A ALA* 3.9 31.9 - - + +
628A ILE* 3.3 46.9 - - + -
629A LEU* 4.3 17.3 - - + -
632A LEU* 5.4 1.1 - - + -
748A LEU* 3.0 22.0 + - + +
749A THR* 3.1 11.4 + - - +
751A LYS* 1.3 76.6 - - - +
753A LEU* 1.3 64.1 + - + +
756A MSE 3.5 36.4 - - - +
758A PHE* 3.7 17.3 - - - -
774A ILE* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 4.6 17.3 - - + -
749A THR 3.1 18.0 + - - +
750A ASP* 4.0 3.4 - - - +
752A MSE 1.3 81.8 - - - +
754A LYS* 1.3 66.6 + - + +
756A MSE 5.1 2.0 - - - +
771A LYS* 4.8 6.9 - - + +
774A ILE* 3.9 32.5 - - + +
775A GLN* 4.0 27.8 - - + +
778A HIS* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ASP* 2.7 46.7 + - - +
753A LEU* 1.3 90.6 - - + +
755A GLN* 1.3 68.5 + - + +
756A MSE 4.6 2.4 - - - +
778A HIS* 4.3 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ARG* 2.8 37.5 + - - +
652A TRP* 3.7 34.0 - - + -
716A ASP* 4.9 4.7 + - - +
750A ASP* 5.2 2.9 - - - +
751A LYS* 2.9 41.9 + - + +
754A LYS* 1.3 88.8 - - + +
756A MSE 1.3 63.9 + - - +
757A THR* 4.5 0.3 - - - -
----------------------------------------------------------
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