Contacts of the helix formed by residues 693 - 699 (chain A) in PDB entry 2C3U
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 ASN 693 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A CYS* 1.3 80.7 - - - +
694A GLN* 1.3 62.5 + - - +
695A CYS* 3.3 3.4 - - - -
696A ALA* 3.7 4.3 + - - +
697A PHE* 3.4 18.2 + - - +
706A PRO* 3.7 13.3 - - - +
736A PHE* 3.4 31.3 - - - -
738A ILE* 3.8 5.3 - - - +
796A LEU* 4.2 2.5 - - - +
797A LYS* 3.2 31.2 - - - +
800A GLN* 3.4 28.9 - - + +
801A PHE* 3.6 18.7 - - - -
2233A SF4 3.1 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A CYS* 3.5 22.5 - - + +
693A ASN* 1.3 76.8 - - - +
695A CYS* 1.3 67.6 + - - +
697A PHE* 3.2 8.6 + - - +
698A VAL* 3.1 26.2 + - - +
754A ILE* 4.5 15.9 - - + +
756A PRO* 3.8 23.7 - - + +
796A LEU* 4.4 18.0 - - + +
1046A LYS* 2.8 39.3 + - + +
2233A SF4 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ASN 4.8 0.4 - - - -
694A GLN* 1.3 80.0 - - - +
696A ALA* 1.3 67.5 + - - +
698A VAL* 3.3 3.3 + - - +
699A CYS* 3.2 17.8 + - - +
704A ILE* 3.5 38.2 - - + +
738A ILE* 4.0 10.8 - - - -
751A CYS* 3.7 16.7 - - + +
754A ILE* 4.9 0.9 - - - +
762A LEU* 3.5 17.3 - - + -
2233A SF4 2.3 50.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ASN 3.7 2.8 + - - +
694A GLN 3.3 0.4 - - - -
695A CYS* 1.3 83.2 - - - +
697A PHE* 1.3 62.4 + - - +
698A VAL 3.4 0.2 + - - -
699A CYS* 3.5 10.5 + - - +
704A ILE* 3.6 29.6 - - + +
706A PRO* 3.6 30.1 - - + -
800A GLN* 3.2 17.7 - - + +
822A ARG* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ASN 3.4 11.9 + - - +
694A GLN* 3.2 13.4 + - - +
696A ALA* 1.3 79.1 - - - +
698A VAL* 1.3 58.6 + - - +
699A CYS 3.8 0.7 + - - +
796A LEU* 4.1 12.6 - - + -
799A SER* 3.5 17.9 - - - -
800A GLN* 3.3 29.0 + - - +
819A PRO* 4.4 4.7 - - - +
822A ARG* 4.3 3.8 + - - +
823A VAL* 4.1 21.1 - - + +
1042A MET* 3.9 32.8 - - + +
1046A LYS* 3.5 42.0 - - + -
1049A PHE* 4.0 12.8 - + - -
1050A LEU* 3.9 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLN 3.1 12.4 + - - +
695A CYS 3.3 3.1 + - - +
696A ALA 3.2 0.2 - - - -
697A PHE* 1.3 78.5 - - - +
699A CYS* 1.3 63.6 + - - +
700A PRO* 3.4 7.6 - - - +
750A ASN* 3.5 32.0 - - + +
751A CYS* 4.1 11.0 - - - +
754A ILE* 4.0 8.5 - - + -
819A PRO* 3.6 13.5 - - - +
1042A MET* 4.3 6.7 - - - -
1046A LYS* 3.6 23.6 - - - -
1084A GLN* 3.3 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A CYS 3.2 12.4 + - - +
696A ALA* 3.5 11.2 + - - +
697A PHE 4.8 0.5 - - - +
698A VAL* 1.3 74.5 - - - +
700A PRO* 1.3 62.2 - - - +
701A HIS 3.0 17.4 + - - -
702A SER* 3.4 8.9 + - - +
703A ALA* 3.3 34.5 - - - +
704A ILE* 4.7 5.6 - - + +
819A PRO* 4.1 10.9 - - - +
822A ARG* 4.1 10.6 - - - -
2234A SF4 2.3 40.6 - - - -
----------------------------------------------------------
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