Contacts of the helix formed by residues 708 - 729 (chain A) in PDB entry 4H1V
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 708 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLY* 1.3 72.3 - - - -
709A GLY* 1.3 61.9 + - - +
710A SER 3.3 0.2 - - - -
711A LYS* 3.6 6.4 - - - +
712A GLU* 3.1 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 3.6 28.5 + - - -
707A GLY* 4.3 0.2 - - - -
708A SER* 1.3 78.7 - - - +
710A SER* 1.3 62.1 + - - +
712A GLU* 3.5 13.2 + - - +
713A ALA* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.2 16.3 - - - +
322A TYR* 3.6 31.4 - - - +
323A GLY 4.8 0.9 + - - -
324A GLU 4.4 6.1 + - - -
706A SER* 4.1 16.6 + - - -
707A GLY* 3.9 18.7 - - - -
708A SER 3.3 0.2 - - - -
709A GLY* 1.3 77.5 - - - +
711A LYS* 1.3 57.4 + - - +
713A ALA* 3.6 2.6 + - - +
714A ALA* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLY 3.2 20.5 + - - +
708A SER* 3.6 8.3 - - - +
709A GLY 3.3 0.2 - - - -
710A SER* 1.3 76.8 - - - +
712A GLU* 1.3 64.4 + - - +
714A ALA* 3.5 6.6 + - + +
715A ASP* 2.6 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.0 1.4 - - - +
315A TYR* 5.4 1.6 - - + -
708A SER* 3.1 21.8 + - - +
709A GLY* 3.6 13.8 - - - +
710A SER 3.4 0.2 - - - -
711A LYS* 1.3 76.4 - - - +
713A ALA* 1.3 57.9 + - - +
715A ASP* 3.2 6.4 + - - +
716A MET* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 3.9 32.4 - - + +
318A LEU* 5.5 1.8 - - + -
319A LEU* 4.0 19.3 - - + -
322A TYR* 4.3 12.6 - - + -
709A GLY 3.3 13.3 + - - +
710A SER 3.9 4.5 - - - +
712A GLU* 1.3 78.7 - - - +
714A ALA* 1.3 58.3 + - - +
716A MET* 3.7 1.0 - - - +
717A LEU* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.2 16.1 - - + +
710A SER 3.1 18.0 + - - +
711A LYS* 3.9 8.7 - - + +
712A GLU 3.2 0.2 - - - -
713A ALA* 1.3 75.6 - - - +
715A ASP* 1.3 62.5 + - - +
717A LEU* 3.4 5.6 + - - +
718A LYS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.6 21.4 - - + +
711A LYS* 2.6 54.6 + - - +
712A GLU* 3.7 6.2 - - - +
714A ALA* 1.3 77.6 - - - +
716A MET* 1.3 62.6 + - - +
718A LYS* 3.4 7.6 + - - +
719A ALA* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.1 7.2 - - + -
18A VAL* 3.6 34.0 - - + +
19A GLY 3.7 10.8 - - - +
22A ILE* 3.7 20.4 - - + -
23A ILE* 3.7 30.3 - - + -
311A LEU* 5.0 0.4 - - + -
315A TYR* 3.5 39.9 - - + +
712A GLU 2.8 18.3 + - - +
713A ALA 3.7 4.9 - - - +
715A ASP* 1.3 73.7 - - - +
717A LEU* 1.3 58.5 - - - +
719A ALA* 3.2 3.7 + - - +
720A LEU* 2.9 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 3.3 38.6 - - + +
315A TYR* 3.9 13.0 - - + -
316A GLN* 3.4 39.7 - - + +
319A LEU* 3.7 26.7 - - + -
713A ALA 2.9 15.6 + - - +
714A ALA* 3.7 6.1 - - - +
715A ASP 3.4 0.2 - - - -
716A MET* 1.3 77.1 - - - +
718A LYS* 1.3 56.9 + - - +
720A LEU* 3.4 6.1 + - + +
721A GLN* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ALA 3.0 15.9 + - - +
715A ASP* 3.6 8.5 - - - +
716A MET 3.2 0.2 - - - -
717A LEU* 1.3 76.5 - - - +
719A ALA* 1.3 61.4 + - - +
721A GLN* 3.3 41.7 + - - +
722A GLY* 3.1 17.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
14A VAL* 3.3 26.3 - - - +
15A PHE* 3.8 23.8 - - + -
18A VAL* 3.9 14.6 - - + -
715A ASP 3.1 13.7 + - - +
716A MET 3.2 7.8 + - - +
718A LYS* 1.3 75.8 - - - +
720A LEU* 1.3 58.6 + - - +
722A GLY* 3.2 2.5 + - - +
723A ALA* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.8 22.9 - - + -
23A ILE* 3.9 15.0 - - + -
308A ILE* 3.8 27.2 - - + +
311A LEU* 4.0 11.4 - - + -
312A ALA* 3.8 33.4 - - + +
315A TYR* 4.2 7.2 - - + -
716A MET* 2.9 38.8 + - + +
717A LEU* 3.7 10.3 - - + +
719A ALA* 1.3 76.0 - - - +
721A GLN* 1.3 57.1 + - - +
723A ALA* 3.2 4.9 + - - +
724A SER* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU 3.0 13.4 + - - +
718A LYS* 3.3 46.0 + - - +
720A LEU* 1.3 76.1 - - - +
722A GLY* 1.3 61.0 + - - +
724A SER* 3.0 20.6 + - - +
725A GLN* 3.1 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.7 8.7 - - - -
718A LYS* 3.1 10.8 + - - +
719A ALA* 3.2 4.0 + - - -
721A GLN* 1.3 79.8 - - - +
723A ALA* 1.3 56.8 + - - +
725A GLN* 3.6 7.0 - - - +
726A ILE* 3.1 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 14.1 - - + +
14A VAL* 4.3 2.4 - - + +
15A PHE* 3.5 35.0 - - + -
308A ILE* 3.6 20.2 - - + -
719A ALA 2.9 6.1 + - - +
720A LEU* 3.4 8.7 - - - +
721A GLN 3.2 0.2 - - - -
722A GLY* 1.3 75.3 - - - +
724A SER* 1.3 60.9 + - - +
726A ILE* 3.2 4.7 + - - +
727A ILE* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 4.3 14.1 - - - +
309A ASN* 4.5 12.1 - - - -
720A LEU 3.0 13.4 + - - -
721A GLN* 3.0 17.8 + - - +
723A ALA* 1.3 75.8 - - - +
725A GLN* 1.3 57.2 + - - +
727A ILE* 3.3 10.1 + - - +
728A ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A GLN* 3.1 19.7 + - + +
722A GLY* 3.6 9.4 - - - +
724A SER* 1.3 78.4 + - - +
726A ILE* 1.3 63.7 + - + +
728A ALA* 3.3 7.8 + - - +
729A GLU* 2.6 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 28.0 - - + +
10A LYS* 3.8 47.3 - - + +
11A LEU* 4.1 13.2 - - + -
14A VAL* 3.7 25.6 - - + -
722A GLY 3.1 16.8 + - - +
723A ALA 3.2 6.9 + - - +
725A GLN* 1.3 78.2 - - + +
727A ILE* 1.3 61.0 + - - +
729A GLU* 3.4 22.8 + - - +
730A ILE* 3.9 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.8 6.1 - - + -
11A LEU* 4.5 13.5 - - + -
301A LEU* 4.6 13.7 - - + -
304A LEU* 4.3 13.5 - - + -
305A LYS* 3.6 49.1 - - + +
308A ILE* 3.7 29.8 - - + -
723A ALA 3.0 15.4 + - - +
724A SER* 3.7 8.1 - - - +
726A ILE* 1.3 76.5 - - - +
728A ALA* 1.3 64.9 + - - +
730A ILE* 3.3 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A SER 2.8 18.3 + - - +
725A GLN* 3.3 11.2 + - - +
727A ILE* 1.3 78.1 - - - +
729A GLU* 1.3 57.2 + - + +
730A ILE 3.0 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 3.9 8.5 - - - +
10A LYS* 5.4 4.0 + - - -
725A GLN* 2.6 47.6 + - - +
726A ILE* 3.6 18.1 - - - +
727A ILE 3.2 0.8 - - - -
728A ALA* 1.3 74.9 - - + +
730A ILE* 1.3 60.4 + - - +
731A ARG* 4.0 1.7 + - - +
----------------------------------------------------------
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