Contacts of the helix formed by residues 805 - 814 (chain A) in PDB entry 1JZ3
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 ALA 805 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ASP 3.7 13.5 - - - +
793A ILE 3.7 18.6 - - - +
794A GLY* 5.1 2.2 - - - -
796A SER* 4.6 0.7 - - - -
802A ASP* 3.1 27.3 + - - +
804A ASN* 1.3 82.2 - - - +
806A TRP* 1.3 67.5 + - - +
807A VAL* 4.4 1.8 - - + +
808A GLU* 3.0 19.3 + - + +
809A ARG* 3.0 10.6 + - - +
1001A PRO* 4.5 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A ASN 5.0 6.9 + - - -
792A ASP* 3.4 16.2 + - - +
804A ASN 3.6 1.4 + - - -
805A ALA* 1.3 71.2 - - - +
807A VAL* 1.4 58.8 + - - +
809A ARG* 3.0 18.5 + - - +
810A TRP* 2.9 69.7 + + + -
877A PRO* 4.2 7.9 - - + -
878A HIS* 3.4 42.2 - - + -
991A MET* 3.2 27.2 - - + +
1001A PRO* 3.8 30.7 - - + +
1002A SER 5.0 0.2 - - - -
1003A VAL* 4.4 13.2 + - + +
1008A GLN* 3.7 33.9 - - + -
8407A DMS 5.1 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A PRO* 3.6 32.8 - - + -
792A ASP* 2.8 27.8 + - + +
793A ILE* 3.7 20.6 - - + +
796A SER* 4.5 2.2 - - - -
805A ALA* 4.5 0.9 - - + -
806A TRP* 1.4 74.0 - - - +
808A GLU* 1.3 79.7 + - + +
810A TRP* 3.7 10.8 - - - +
811A LYS* 2.9 41.7 + - + +
816A TYR* 4.2 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A SER* 2.7 34.5 + - - +
801A ILE* 3.2 22.1 - - + +
802A ASP 3.1 32.5 - - - +
803A PRO* 4.0 8.5 - - + -
805A ALA* 3.0 6.3 + - + +
807A VAL* 1.3 82.4 - - + +
809A ARG* 1.3 61.7 + - - +
811A LYS* 2.9 38.9 + - - +
812A ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A PRO* 2.4 37.1 + - - +
804A ASN* 2.3 46.0 + - - +
805A ALA 3.0 10.3 + - - +
806A TRP* 3.0 24.2 + - + +
808A GLU* 1.3 77.2 - - - +
810A TRP* 1.3 63.6 + - - +
812A ALA* 3.9 4.6 - - - +
813A ALA* 3.0 25.5 + - - +
877A PRO* 3.5 23.7 - - + +
1001A PRO* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A THR* 5.6 2.0 - - + -
786A ARG* 4.1 4.9 - - + -
788A PRO* 5.0 0.9 - - + -
792A ASP* 3.6 42.4 - - + -
806A TRP* 2.9 35.3 + + + +
807A VAL* 3.7 9.4 - - - +
809A ARG* 1.3 78.5 - - - +
811A LYS* 1.3 64.5 + - - +
813A ALA* 3.3 2.4 + - - +
814A GLY 3.1 3.1 + - - -
815A HIS* 3.0 58.5 + + + +
816A TYR* 3.7 35.0 - + + -
877A PRO* 4.1 8.1 - - + -
878A HIS 2.8 21.5 + - - -
879A PRO* 3.9 1.8 - - - +
880A ALA* 3.6 29.8 - - + -
991A MET* 3.5 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 811 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ALA* 6.0 0.6 - - - +
801A ILE* 4.0 10.7 - - - +
807A VAL* 2.9 36.3 + - + +
808A GLU* 2.9 37.1 + - - +
810A TRP* 1.3 78.2 - - - +
812A ALA* 1.3 60.0 + - - +
814A GLY* 2.7 22.2 + - - -
815A HIS 5.1 0.4 - - - +
816A TYR* 4.0 23.5 - - + +
817A GLN* 4.5 8.9 - - - +
844A HIS* 5.4 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A GLU 2.9 18.5 + - - +
809A ARG* 3.9 4.5 - - - +
811A LYS* 1.3 79.1 - - - +
813A ALA* 1.3 61.9 + - - +
814A GLY* 3.1 0.9 + - - -
844A HIS* 4.6 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A ARG 3.0 17.7 + - - +
810A TRP 3.9 0.2 - - - +
811A LYS 3.1 0.4 - - - -
812A ALA* 1.3 78.1 - - - +
814A GLY* 1.3 60.8 + - - +
815A HIS* 3.7 15.0 - - + -
844A HIS* 3.6 13.9 + - - +
849A LEU* 3.6 17.9 - - + +
876A THR* 3.9 5.2 - - - +
877A PRO* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LYS 2.7 16.3 + - - -
812A ALA 3.1 1.2 + - - -
813A ALA* 1.3 80.2 - - - +
815A HIS* 1.3 66.5 + - - +
816A TYR 3.2 2.9 - - - -
817A GLN* 2.9 17.6 + - - +
818A ALA* 2.9 16.1 + - - +
844A HIS* 3.6 24.5 - - - -
849A LEU* 4.2 3.8 - - - -
----------------------------------------------------------
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