Contacts of the helix formed by residues 678 - 686 (chain B) in PDB entry 2P0C
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 ASP 678 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ANP 3.7 28.4 + - - +
676B TYR 4.4 1.6 - - - +
677B GLY* 1.3 74.8 - - - -
679B LEU* 1.3 61.5 + - - +
680B HIS* 3.2 16.8 + - - +
681B THR* 2.7 42.8 + - - -
682B TYR* 3.4 18.1 + - - +
727B ARG* 3.3 30.8 - - - +
729B CYS 3.3 7.6 - - - +
730B MET* 3.7 7.2 - - + -
731B LEU* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ASP* 1.3 69.4 - - - +
680B HIS* 1.3 59.9 + - - +
682B TYR* 3.1 11.5 + - + +
683B LEU* 2.9 46.5 + - + +
703B PHE* 3.9 42.6 - - + -
707B ILE* 4.0 16.4 - - + -
726B ALA* 3.5 12.6 - - + +
729B CYS* 2.8 20.5 + - + +
731B LEU* 4.2 18.5 - - + +
737B VAL* 4.3 6.7 - - + -
793B ILE* 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ANP 5.3 4.6 + - - -
678B ASP* 3.2 10.7 + - - +
679B LEU* 1.3 77.1 - - - +
681B THR* 1.3 64.0 + - - +
683B LEU* 3.4 6.5 + - + +
684B LEU* 3.2 48.3 + - + +
726B ALA* 3.2 13.7 + - + -
727B ARG* 3.7 24.0 - - + +
792B GLU* 3.2 27.4 + - - -
797B GLY* 3.3 29.4 + - - -
798B MET 4.9 2.0 + - - -
799B THR* 5.3 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A PRO* 4.5 2.2 - - + -
803A GLY* 3.9 23.1 + - - +
2B ANP 5.3 3.5 + - - -
678B ASP* 2.7 31.5 + - - -
680B HIS* 1.3 79.7 + - - +
682B TYR* 1.3 56.7 + - - +
684B LEU* 3.5 9.6 + - + +
685B TYR* 2.9 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B TYR 5.1 6.1 - - - +
678B ASP 3.4 7.1 + - - +
679B LEU* 3.1 18.3 + - + +
681B THR* 1.3 76.7 - - - +
683B LEU* 1.3 68.2 + - - +
685B TYR* 3.3 9.8 + + - +
686B SER* 3.0 21.3 + - - -
692B PRO* 3.5 36.9 - - + +
695B ILE* 3.7 27.8 - - + +
703B PHE* 4.0 16.1 - + - -
731B LEU* 3.5 31.0 - - + -
735B MET* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 2.9 46.3 + - + +
680B HIS* 3.4 9.8 + - - +
682B TYR* 1.3 74.1 - - - +
684B LEU* 1.3 60.2 + - - +
686B SER* 2.6 25.7 + - - -
687B ARG* 3.8 4.7 - - - +
695B ILE* 4.1 11.7 - - + -
700B LEU* 3.8 29.2 - - + -
703B PHE* 4.5 1.6 - - + -
726B ALA* 4.5 4.7 - - + -
792B GLU 3.9 9.2 - - - +
793B ILE* 3.8 36.8 - - + +
796B ARG* 3.7 25.3 - - - +
797B GLY* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A MET* 3.8 24.1 - - + +
799A THR 6.3 0.2 - - - +
802A PRO* 3.9 28.3 - - + -
680B HIS* 3.2 40.6 + - + +
681B THR* 3.7 7.9 - - - +
683B LEU* 1.3 75.3 - - - +
685B TYR* 1.3 66.3 + - - +
687B ARG* 3.0 34.3 + - - +
688B LEU* 3.9 3.3 + - - +
796B ARG 3.7 17.0 - - - +
797B GLY* 3.7 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A PRO* 3.4 36.7 + - + -
803A GLY* 3.9 7.1 + - - -
804A VAL* 5.9 0.3 - - - +
820A LYS* 3.7 26.6 + - + -
681B THR* 2.9 44.5 + - + +
682B TYR* 3.3 9.6 + + - +
684B LEU* 1.3 75.4 - - - +
686B SER* 1.3 56.9 + - - +
687B ARG 3.0 0.4 - - - -
688B LEU* 2.9 35.9 + - + +
691B GLY* 3.8 10.9 - - - -
692B PRO* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A GLU* 3.0 19.9 - - - +
682B TYR 3.0 9.5 + - - -
683B LEU 2.6 20.7 + - - -
685B TYR* 1.3 75.3 - - - +
687B ARG* 1.3 60.0 + - - +
688B LEU 3.3 1.3 - - - -
692B PRO* 3.4 17.7 - - - +
693B LYS 3.5 17.5 - - - +
694B HIS* 4.1 4.7 + - - -
695B ILE* 3.4 32.3 + - - +
796B ARG* 4.3 7.8 + - - -
----------------------------------------------------------
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