Contacts of the helix formed by residues 681 - 689 (chain A) in PDB entry 3BDP
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 ILE 681 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLN* 4.1 24.0 - - + -
659A LEU* 4.2 13.2 - - + -
671A LEU* 3.8 27.6 - - + -
674A ALA* 3.9 22.7 - - + -
675A PHE* 3.8 28.3 - - + -
679A LEU 3.0 7.4 + - - +
680A ASP* 1.3 72.1 + - - +
682A HIS* 1.3 80.7 + - + +
684A LYS* 4.3 7.4 - - + -
685A THR* 2.7 44.6 + - - +
709A ASN* 4.2 2.5 - - - +
743A PHE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLN* 3.7 24.3 + - - -
680A ASP* 3.0 5.2 + - - +
681A ILE* 1.3 84.5 - - + +
683A THR* 1.3 61.8 + - - +
686A ALA* 3.0 23.6 + - - +
702A ARG* 3.5 36.0 + - + +
705A ALA* 3.3 11.4 - - - +
706A LYS* 3.6 47.0 + - + +
709A ASN* 2.9 40.0 + - - +
710A PHE 5.5 0.4 + - - -
910A SO4 3.8 10.7 + - - -
915A SO4 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A ASP* 3.0 23.9 + - + +
682A HIS* 1.3 75.6 - - - +
684A LYS* 1.3 59.6 + - - +
686A ALA* 3.2 5.6 + - - +
687A MET* 2.8 37.4 + - - +
694A GLU* 4.0 32.1 - - + +
697A VAL* 4.0 18.9 - - + +
702A ARG* 3.5 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ASN* 3.0 28.0 + - - +
674A ALA* 4.1 26.0 - - + +
677A ARG* 6.0 1.8 - - - +
679A LEU* 4.1 22.7 - - + +
680A ASP 2.9 18.8 + - - +
681A ILE* 3.8 11.4 - - + +
683A THR* 1.3 78.2 - - - +
685A THR* 1.3 57.3 + - - +
687A MET* 3.4 23.7 + - + +
688A ASP* 3.0 52.4 + - - +
743A PHE* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A LEU* 5.9 0.2 - - - +
681A ILE* 2.7 28.6 + - - +
682A HIS 3.9 3.4 - - - -
683A THR 3.3 0.2 - - - -
684A LYS* 1.3 73.2 - - - +
686A ALA* 1.3 61.6 + - - +
688A ASP* 3.2 5.1 + - - -
689A ILE* 2.9 38.7 + - + +
705A ALA* 3.9 16.4 - - + +
708A VAL* 5.2 1.6 - - + -
709A ASN* 3.2 29.8 + - - +
739A TYR* 4.0 23.5 - - + -
743A PHE* 4.4 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A HIS 3.0 17.7 + - - +
683A THR 3.5 4.5 - - - +
685A THR* 1.3 73.3 - - - +
687A MET* 1.3 65.9 + - - +
690A PHE* 2.9 41.8 + - + +
697A VAL* 4.1 17.7 - - + -
701A MET* 3.8 19.5 - - - +
702A ARG* 4.2 0.7 - - - -
705A ALA* 3.3 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LEU* 6.3 0.7 - - + -
683A THR* 2.8 23.6 + - - +
684A LYS* 3.5 30.3 - - + +
685A THR 3.3 0.2 - - - -
686A ALA* 1.3 75.0 - - - +
688A ASP* 1.3 61.9 + - - +
691A GLN* 3.0 23.2 + - - -
692A VAL* 3.1 31.5 + - - +
693A SER* 4.7 1.8 - - - -
694A GLU* 3.5 34.3 - - + +
697A VAL* 3.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ASN* 2.7 31.5 + - - -
684A LYS* 3.0 38.5 + - - +
685A THR* 3.7 5.4 - - - +
686A ALA 3.1 0.4 - - - -
687A MET* 1.3 80.2 - - - +
689A ILE* 1.3 61.9 + - + +
691A GLN* 3.5 9.1 + - - +
738A ARG* 3.1 16.8 + - - -
742A SER* 3.4 24.8 + - - +
743A PHE* 3.7 7.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A THR* 2.9 36.9 + - + +
688A ASP* 1.3 72.0 - - + +
690A PHE* 1.3 96.9 + - + +
704A GLN 5.3 0.4 - - - +
705A ALA* 4.4 16.8 - - + -
708A VAL* 4.6 15.0 - - + -
735A PHE* 4.7 12.1 - - + +
738A ARG* 2.5 48.3 + - + +
739A TYR* 3.8 33.0 - - + +
742A SER* 4.6 2.2 - - - +
743A PHE* 5.4 0.4 - - + -
----------------------------------------------------------
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