Contacts of the strand formed by residues 801 - 806 (chain A) in PDB entry 3I8C
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 VAL 801 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU* 5.5 2.9 - - + -
756A ALA* 3.5 46.7 - - + +
759A GLN 5.4 1.8 - - - +
760A ALA* 4.0 14.6 - - + +
761A LEU* 3.1 21.3 + - - +
792A LEU* 4.1 20.4 - - + -
793A ILE 3.6 4.0 - - - +
794A ILE* 4.6 9.5 - - + +
799A PHE 4.1 1.8 + - - +
800A GLU* 1.3 69.1 - - - +
802A LEU* 1.3 67.6 + - - +
803A HIS 3.5 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A CYS* 4.8 4.3 - - + -
761A LEU* 3.3 22.8 + - + +
762A SER* 3.2 25.3 + - - -
793A ILE* 2.5 28.1 + - + +
794A ILE 4.5 0.2 - - - -
795A ASP* 3.9 38.1 - - + +
800A GLU* 2.8 14.3 + - + +
801A VAL* 1.3 76.8 - - - +
803A HIS* 1.3 58.8 + - - +
853A TYR* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A SER* 3.0 22.2 + - - +
763A SER* 3.0 33.2 + - - -
764A SER* 2.5 32.6 + - - -
791A LEU 4.4 1.1 - - - -
792A LEU* 3.4 3.1 - - - -
793A ILE* 2.7 36.5 + - + +
801A VAL* 3.5 7.9 - - - +
802A LEU* 1.3 78.7 - - - +
804A ALA* 1.3 66.4 + - - +
853A TYR* 4.2 20.4 - + + +
856A GLY 5.0 4.8 + - - +
857A LYS* 6.4 0.2 - - - -
858A LEU* 3.1 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A SER* 3.8 14.4 - - - +
760A ALA* 3.7 22.2 - - + -
762A SER 3.3 5.8 + - - +
763A SER* 3.3 6.1 - - - -
764A SER 2.8 27.2 + - - +
790A ASN* 4.5 6.1 - - - +
791A LEU 3.4 4.5 - - - -
792A LEU* 4.0 18.2 - - + -
803A HIS* 1.3 81.5 - - - +
805A HIS* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A SER* 2.9 22.5 + - - -
765A VAL 3.2 25.1 - - - -
766A SER* 3.4 24.0 + - - -
790A ASN* 3.1 8.3 - - - -
791A LEU* 3.0 38.7 + - + +
803A HIS* 4.4 0.6 - - - -
804A ALA* 1.3 73.2 - - - +
806A GLN* 1.3 68.0 + - - +
807A PHE* 4.1 12.4 - + - -
851A PHE* 3.8 21.2 - + + -
858A LEU* 3.7 27.9 + - + +
860A THR* 4.3 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ARG* 3.4 22.9 + - - +
741A GLU* 5.8 0.6 + - - -
764A SER 3.1 16.5 + - - +
765A VAL* 3.5 14.8 - - + +
766A SER* 2.7 33.3 + - - -
788A VAL* 3.5 28.6 - - + +
789A HIS 3.7 0.4 - - - -
790A ASN* 3.3 13.7 + - - +
804A ALA 4.1 0.4 - - - -
805A HIS* 1.3 78.0 - - - +
807A PHE* 1.3 71.3 + - - +
----------------------------------------------------------
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