Contacts of the helix formed by residues 705 - 730 (chain A) in PDB entry 3BRV
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
----------------------------------------------------------
706A GLU* 1.3 65.0 + - - +
707A GLU* 3.6 12.8 + - - +
708A LEU* 3.4 28.0 + - - +
709A VAL* 3.2 26.4 + - - +
57B GLU* 3.0 30.9 + - - +
61B LEU* 3.6 21.4 - - - +
62D ARG* 4.1 14.1 - - - +
66D ARG* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A SER* 1.3 73.5 + - - +
707A GLU* 1.3 57.5 + - + +
709A VAL* 3.5 9.4 + - - +
710A ALA* 3.0 28.7 + - - +
----------------------------------------------------------
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* 3.3 6.8 + - - +
706A GLU* 1.3 75.2 - - + +
708A LEU* 1.3 67.2 + - - +
709A VAL 3.1 1.6 - - - -
710A ALA* 3.7 7.1 - - + +
711A GLU* 2.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A SER* 3.4 20.5 + - - +
707A GLU* 1.3 79.7 - - - +
709A VAL* 1.3 57.8 + - + +
711A GLU* 3.6 9.3 + - - +
712A ALA 3.1 11.6 + - - -
61B LEU* 5.5 1.6 - - + -
62D ARG* 3.4 48.9 - - + +
65D ILE* 3.4 16.8 - - + +
66D ARG* 3.7 50.5 - - + +
69D ASN* 3.1 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A SER 3.2 13.9 + - - +
706A GLU* 3.6 12.6 - - - +
707A GLU 3.1 0.6 - - - -
708A LEU* 1.3 79.6 - - + +
710A ALA* 1.3 63.7 + - - +
712A ALA* 3.4 6.9 + - - +
713A HIS* 3.2 22.0 + - - +
60B GLU* 4.5 11.4 - - + +
61B LEU* 4.3 18.4 - - + -
64B ALA* 3.7 30.7 - - + +
65D ILE* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLU 3.0 18.2 + - - +
707A GLU* 3.3 9.8 + - + +
709A VAL* 1.3 73.6 - - - +
711A GLU* 1.3 66.3 + - - +
713A HIS* 3.4 8.3 + - - +
714A ASN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLU 2.8 16.2 + - - +
708A LEU* 3.7 15.1 - - - +
710A ALA* 1.3 77.1 - - - +
712A ALA* 1.3 58.8 + - - +
714A ASN* 3.2 8.5 + - + +
715A LEU* 2.9 40.9 + - + +
69D ASN* 3.1 24.4 - - - +
73D ARG* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A LEU 3.1 12.5 + - - +
709A VAL* 3.4 6.7 + - - +
710A ALA 3.2 0.6 - - - -
711A GLU* 1.3 78.9 - - - +
713A HIS* 1.3 56.1 + - - +
715A LEU* 3.2 3.2 + - - +
716A CYS* 2.9 40.3 + - - -
64B ALA* 5.7 5.8 - - + -
68B SER* 5.6 6.7 - - - -
65D ILE* 4.0 11.0 - - + -
69D ASN* 3.1 27.1 - - - +
72D LEU* 4.4 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A VAL 3.2 11.0 + - - +
710A ALA* 3.6 10.1 - - - +
712A ALA* 1.3 78.3 - - - +
714A ASN* 1.3 72.4 + - - +
716A CYS* 3.5 6.9 + - - +
717A THR* 2.9 43.4 + - - -
67B GLN* 5.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ALA* 3.0 17.9 + - - +
711A GLU* 3.2 12.7 + - + +
713A HIS* 1.3 90.6 - - - +
715A LEU* 1.3 56.8 + - + +
717A THR* 3.4 7.4 + - - -
718A LEU* 3.2 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A GLU* 2.9 27.6 + - + +
712A ALA 3.8 3.6 - - - +
714A ASN* 1.3 71.0 - - + +
716A CYS* 1.3 55.5 + - - +
718A LEU* 3.5 19.8 + - + +
719A LEU* 2.7 34.5 + - - +
69D ASN* 3.3 44.6 - - + +
72D LEU* 3.8 19.2 - - + +
73D ARG* 3.9 45.3 - - + +
76D CYS* 4.0 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ALA* 2.9 22.4 + - - +
713A HIS* 3.8 8.5 - - - +
715A LEU* 1.3 73.8 - - - +
717A THR* 1.3 61.3 + - - +
719A LEU* 3.9 6.8 - - - +
720A GLU* 2.8 35.3 + - - +
68B SER* 3.8 29.2 - - - -
71B ILE* 3.5 37.0 - - + +
72B LEU* 6.3 0.4 - - - -
72D LEU* 3.9 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A HIS* 2.9 35.7 + - - -
714A ASN* 3.6 7.9 + - - -
715A LEU 3.3 0.2 - - - -
716A CYS* 1.3 75.4 - - - +
718A LEU* 1.4 53.7 - - + +
720A GLU* 3.1 14.2 + - + +
721A ASN* 2.8 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ASN* 3.2 17.2 + - + +
715A LEU* 3.7 22.0 - - + +
717A THR* 1.4 73.8 - - + +
719A LEU* 1.3 65.4 + - - +
721A ASN* 3.2 13.7 + - + +
722A ALA* 2.9 26.2 + - - +
76D CYS* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU 2.7 21.5 + - - +
716A CYS* 3.9 4.9 - - - +
718A LEU* 1.3 70.8 - - - +
720A GLU* 1.3 64.5 + - - +
722A ALA* 3.8 2.3 - - - +
723A ILE* 3.0 37.6 + - + +
71B ILE* 4.8 10.8 - - + -
72B LEU* 5.1 5.4 - - + -
75B ARG* 4.0 19.7 - - + -
719C LEU* 3.8 33.2 - - + -
723C ILE* 5.0 0.2 - - + -
72D LEU* 3.8 16.4 - - + -
75D ARG* 4.3 13.2 - - + -
76D CYS* 3.5 12.4 - - - -
79D LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A CYS 2.8 23.2 + - - +
717A THR* 3.2 14.3 + - + +
719A LEU* 1.3 75.1 - - - +
721A ASN* 1.3 60.5 + - - +
723A ILE* 3.3 3.3 + - - +
724A GLN* 3.0 28.6 + - - +
71B ILE* 3.9 25.8 - - + +
74B GLU* 5.3 0.7 - - - +
75B ARG* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A THR* 2.8 38.1 + - - +
718A LEU* 3.2 15.6 + - + +
720A GLU* 1.3 74.2 - - - +
722A ALA* 1.3 57.8 + - - +
724A GLN* 3.2 7.1 + - - +
725A ASP* 2.9 42.0 + - - +
----------------------------------------------------------
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 LEU 2.9 17.7 + - - +
719A LEU* 3.8 2.5 - - - +
721A ASN* 1.3 76.6 - - - +
723A ILE* 1.3 63.5 + - - +
725A ASP* 4.6 2.7 - - - -
726A THR* 3.1 21.9 + - - -
76D CYS* 4.8 7.6 - - + +
79D LEU* 3.8 30.3 - - + -
80D LEU* 4.8 11.2 - - + -
83D GLN* 3.2 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A LEU* 3.0 28.5 + - + +
720A GLU 3.8 3.6 - - - +
722A ALA* 1.3 76.3 - - - +
724A GLN* 1.3 57.3 + - - +
726A THR* 3.4 6.3 + - - -
727A VAL* 3.0 31.3 + - + +
75B ARG* 3.9 25.8 - - + +
78B GLU* 3.8 38.4 - - + +
79B LEU* 3.7 41.1 - - + -
719C LEU* 4.8 0.7 - - + -
79D LEU* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A GLU 3.0 17.2 + - - +
721A ASN* 3.2 8.9 + - - +
723A ILE* 1.3 76.0 - - - +
725A ASP* 1.3 64.5 + - - +
727A VAL* 3.3 25.9 - - - +
728A ARG* 3.4 6.8 - - - +
78B GLU* 5.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ASN* 2.9 24.3 + - - +
722A ALA* 3.6 7.1 - - - +
724A GLN* 1.3 75.5 - - - +
726A THR* 1.3 63.8 + - - +
728A ARG* 3.3 5.8 + - - +
729A GLU* 3.0 25.5 + - - +
83D GLN* 3.9 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ALA 3.1 12.8 + - - -
723A ILE* 3.5 11.3 - - - -
724A GLN 3.3 0.6 - - - -
725A ASP* 1.3 78.4 - - - +
727A VAL* 1.3 59.4 + - + +
728A ARG 3.0 6.6 + - - -
729A GLU* 3.5 2.7 + - - +
730A GLN* 3.1 19.8 + - - +
79B LEU* 5.7 5.2 - - + -
82B PHE* 3.7 17.7 - - + -
79D LEU* 4.4 10.8 + - + +
82D PHE* 3.7 33.0 - - + -
83D GLN* 3.2 23.5 + - + +
86D GLN* 3.6 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A ILE* 3.0 31.0 + - + +
724A GLN* 3.3 6.0 - - - +
726A THR* 1.3 72.6 - - + +
728A ARG* 1.3 58.9 + - - +
730A GLN* 4.6 3.4 - - - +
731A ASP* 3.9 19.6 - - - +
78B GLU* 3.7 29.6 - - + +
79B LEU* 5.9 0.9 - - + -
82B PHE* 4.1 31.4 - - + -
85B SER* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A GLN 3.4 13.7 - - - +
725A ASP* 3.5 7.2 - - - +
726A THR 3.0 1.6 + - - -
727A VAL* 1.3 77.3 - - - +
729A GLU* 1.3 69.7 + - - +
730A GLN 3.3 1.4 - - - +
731A ASP* 3.2 22.2 + - - +
732A GLN* 3.4 14.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
725A ASP 3.0 17.0 + - - +
726A THR* 3.8 5.4 - - - +
728A ARG* 1.3 76.7 - - - +
730A GLN* 1.3 56.5 + - - +
732A GLN* 2.9 19.5 + - - +
83D GLN* 6.1 2.7 - - + -
86D GLN* 4.3 10.5 - - + +
90D LYS* 2.8 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A THR 3.1 7.4 + - - +
727A VAL* 5.1 2.0 - - - +
729A GLU* 1.3 74.4 - - - +
731A ASP* 1.3 70.0 + - - +
732A GLN 3.3 7.9 + - - +
733A SER* 4.6 6.1 + - - -
82B PHE* 3.5 29.0 - - + -
85B SER* 2.5 48.8 + - - +
86B GLN* 3.3 13.1 - - + -
89B GLU* 3.7 19.4 - - + +
86D GLN* 3.0 33.2 - - - +
90D LYS* 4.1 5.2 + - - +
----------------------------------------------------------
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