Contacts of the helix formed by residues 896 - 900 (chain A) in PDB entry 3SQD
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 896 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A LEU* 4.2 8.5 - - - -
894A ALA* 3.1 9.7 - - - +
895A GLU* 1.3 82.7 - - - +
897A ALA* 1.3 66.5 + - - +
898A GLN* 3.4 19.1 + - - +
899A LYS* 3.0 27.0 + - - +
900A CYS 3.3 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A LEU* 3.7 20.2 - - + +
896A SER* 1.3 73.2 - - - +
898A GLN* 1.3 60.7 + - + +
900A CYS* 3.0 20.6 + - - +
916A THR* 3.3 38.8 - - - +
917A ALA* 3.9 10.5 - - - +
920A VAL* 3.0 17.3 - - - +
997A CYS* 4.2 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A SER* 3.1 11.2 + - - +
897A ALA* 1.3 76.6 - - + +
899A LYS* 1.3 62.9 + - + +
900A CYS 5.1 0.9 - - - +
920A VAL* 4.1 18.7 - - + +
996A GLU* 5.0 12.3 + - - +
997A CYS* 4.0 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PHE* 3.4 26.0 - - + +
894A ALA* 4.3 1.6 - - - -
895A GLU* 3.3 36.5 + - + +
896A SER* 3.0 24.3 + - - +
898A GLN* 1.3 83.8 - - + +
900A CYS* 1.3 57.9 + - - +
901A THR* 3.8 2.1 + - - +
955B LEU* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PHE 3.3 9.0 - - - -
869A VAL 4.2 0.2 - - - -
870A LEU* 3.6 28.0 - - + -
894A ALA* 3.9 6.3 - - + -
896A SER 3.3 8.4 + - - +
897A ALA 3.0 16.0 + - - +
898A GLN 3.4 0.9 - - - +
899A LYS* 1.3 78.7 - - - +
901A THR* 1.3 60.9 + - - +
902A HIS 3.0 35.7 - - - -
903A LEU* 4.5 0.7 - - - -
920A VAL* 4.1 5.5 - - - +
921A VAL* 3.6 30.6 - - + +
922A LYS* 5.6 0.2 - - - +
----------------------------------------------------------
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