Contacts of the helix formed by residues 705 - 723 (chain A) in PDB entry 3JWR
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 SER 705 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A GLY 3.8 2.2 + - - -
704A LEU* 1.3 73.6 - - - +
706A ILE* 1.3 68.1 + - - +
707A GLU* 3.8 7.3 + - - +
708A GLU* 2.9 42.4 + - - +
709A TYR* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU 4.6 1.6 - - - +
705A SER* 1.3 77.9 - - - +
707A GLU* 1.3 58.2 + - - +
709A TYR* 3.8 3.3 - - + +
710A LYS* 2.9 32.2 + - + +
902A IBM 3.9 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A SER* 3.1 7.0 + - - +
706A ILE* 1.3 76.7 - - - +
708A GLU* 1.3 71.6 + - + +
710A LYS* 2.7 46.5 + - - +
711A THR* 3.1 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PHE* 4.3 16.8 - - - -
641A LEU* 4.1 22.0 - - + +
703A GLY 4.6 0.9 - - - +
704A LEU* 3.5 21.0 - - + +
705A SER* 2.9 40.8 + - - +
707A GLU* 1.3 76.7 - - + +
709A TYR* 1.3 68.7 + - - +
711A THR* 2.9 15.7 + - - -
712A THR* 2.9 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 5.6 1.2 - - - +
693A LEU* 6.0 2.0 - - + -
694A ASN* 3.5 24.2 + - - -
701A LEU* 4.0 19.1 - - + -
704A LEU* 3.6 14.5 - - + +
705A SER 2.9 17.7 + - - +
706A ILE* 3.8 6.1 - - + +
708A GLU* 1.3 74.0 - - - +
710A LYS* 1.3 68.7 + - + +
712A THR* 3.2 2.0 + - - -
713A LEU* 3.0 57.6 + - + +
902A IBM 3.4 81.5 + + + +
903A IBM 5.8 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ILE* 2.9 20.4 + - + +
707A GLU* 2.7 38.6 + - - +
708A GLU 3.0 0.2 + - - -
709A TYR* 1.3 83.6 - - + +
711A THR* 1.3 64.4 + - + +
713A LEU* 3.8 6.5 + - - +
714A LYS* 3.5 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 3.5 16.2 - - - +
707A GLU* 3.1 30.5 + - - +
708A GLU* 2.9 15.2 + - - -
710A LYS* 1.3 78.2 - - + +
712A THR* 1.3 67.2 + - - +
713A LEU 3.2 1.3 - - - -
714A LYS* 3.1 20.2 + - + +
715A ILE* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 3.5 18.3 - - - +
644A LEU* 4.0 22.7 - - + -
645A ALA* 4.2 9.4 - - + -
701A LEU* 4.2 10.1 - - + -
704A LEU* 3.4 17.3 - - - +
708A GLU 2.9 12.6 + - - -
709A TYR* 3.4 7.9 - - - -
711A THR* 1.3 77.0 + - - +
713A LEU* 1.3 58.4 + - - +
715A ILE* 3.1 14.0 + - - +
716A ILE* 2.9 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 4.2 17.8 - - + -
689A CYS* 6.3 0.4 - - - -
690A LEU* 5.0 13.9 - - + -
693A LEU* 4.6 15.7 - - + -
701A LEU* 5.1 2.7 - - + -
709A TYR* 3.0 60.5 + - + +
710A LYS* 3.9 6.5 - - - +
712A THR* 1.3 79.2 - - - +
714A LYS* 1.3 62.6 + - - +
716A ILE* 3.3 18.2 + - + +
717A LYS* 3.0 24.4 + - - +
903A IBM 4.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS 3.5 11.9 + - - +
711A THR* 3.1 23.8 + - + +
712A THR 3.1 0.4 - - - -
713A LEU* 1.3 80.2 - - - +
715A ILE* 1.3 68.2 + - - +
717A LYS* 3.2 8.4 + - + +
718A GLN* 2.7 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 4.4 19.5 - - + +
642A GLU* 4.0 25.4 - - + +
645A ALA* 3.7 17.3 - - + -
646A LEU* 5.5 3.6 - - + +
711A THR* 3.2 20.4 - - - +
712A THR* 3.4 6.7 - - - +
714A LYS* 1.3 80.0 - - + +
716A ILE* 1.3 59.9 + - - +
718A GLN* 3.2 18.6 + - - +
719A ALA* 2.8 30.1 + - + +
756A LEU* 4.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ALA* 3.8 21.1 - - + +
648A ILE* 4.1 28.0 - - + -
649A ALA* 4.2 15.0 - - + -
686A PHE* 4.4 7.2 - - + -
689A CYS* 4.2 20.4 - - - -
693A LEU* 4.8 5.6 - - + -
701A LEU* 5.0 1.1 - - + -
712A THR* 2.9 38.1 + - + +
713A LEU* 3.7 20.0 - - + +
714A LYS 3.3 0.2 - - - -
715A ILE* 1.3 72.7 - - - +
717A LYS* 1.3 65.0 + - - +
719A ALA* 3.2 5.8 + - - +
720A ILE* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A HIS* 4.6 17.7 + - - -
686A PHE* 3.7 42.9 - - + +
713A LEU 3.0 12.9 + - - +
714A LYS* 3.2 12.5 + - + +
716A ILE* 1.3 78.3 - - - +
718A GLN* 1.3 63.3 + - + +
720A ILE* 3.9 1.2 - - - +
721A LEU* 3.0 51.0 + - + +
903A IBM 5.5 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A LYS* 2.7 46.0 + - + +
715A ILE* 3.5 23.1 - - - +
717A LYS* 1.3 76.9 - - + +
719A ALA* 1.3 61.9 + - - +
721A LEU* 3.6 7.4 + - - +
722A ALA* 3.1 24.3 + - - +
753A GLU* 3.8 33.1 - - + +
756A LEU* 5.9 2.8 - - - +
757A ALA* 5.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ALA 4.9 1.1 - - - +
646A LEU* 5.2 7.4 - - + -
649A ALA* 3.5 23.3 - - + -
715A ILE* 2.8 23.7 + - + +
716A ILE* 3.2 5.4 + - - +
718A GLN* 1.3 70.5 - - - +
720A ILE* 1.3 67.3 + - - +
722A ALA* 3.1 19.3 + - - +
723A THR* 3.5 5.0 + - - +
756A LEU* 5.6 2.5 - - + -
757A ALA* 5.9 0.4 - - - +
760A MET* 3.6 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ALA* 4.2 15.3 - - + +
652A SER* 4.1 19.1 - - - +
653A HIS* 4.0 16.2 - - - +
682A GLU* 3.4 27.6 - - - +
685A HIS* 4.0 13.7 - - + -
686A PHE* 3.9 30.3 - - + +
689A CYS* 4.2 13.7 - - + -
716A ILE* 3.0 20.5 + - + +
717A LYS 4.0 2.7 - - - +
719A ALA* 1.3 75.9 - - - +
721A LEU* 1.3 61.5 + - - +
723A THR* 2.6 31.9 + - - -
760A MET* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A SER* 3.7 17.0 - - - -
682A GLU* 4.1 12.3 - - + +
683A HIS* 3.6 41.5 - - + +
686A PHE* 6.1 1.8 - - + -
717A LYS* 3.0 48.6 + - + +
718A GLN* 3.9 6.3 - - - +
720A ILE* 1.3 77.0 - - + +
722A ALA* 1.3 56.5 + - - +
724A ASP* 2.9 32.1 + - - +
727A LEU* 3.3 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A GLN 3.1 15.7 + - - +
719A ALA* 3.1 13.7 + - - +
721A LEU* 1.3 75.0 - - - +
723A THR* 1.3 55.9 + - - +
724A ASP 3.1 13.1 + - - +
727A LEU* 4.4 9.6 - - - +
728A TYR* 4.5 5.0 + - - +
757A ALA* 3.6 41.8 - - + +
760A MET* 4.3 2.7 - - + -
761A THR* 3.5 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A HIS* 4.0 21.4 + - + -
682A GLU* 3.6 4.4 - - - +
719A ALA 3.7 5.4 - - - +
720A ILE 2.6 17.6 + - - +
721A LEU 3.0 0.6 + - - -
722A ALA* 1.3 74.1 - - - +
724A ASP* 1.3 61.7 + - - +
725A LEU* 3.3 17.9 + - - +
760A MET* 3.6 38.1 - - + -
761A THR* 4.8 5.6 - - - +
764A ASP* 3.6 26.1 - - + +
900A MG 3.4 21.5 - - - -
----------------------------------------------------------
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