Contacts of the helix formed by residues 89 - 94 (chain B) 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 ASN 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B SER* 1.3 74.2 - - - +
90B TRP* 1.3 61.1 + - - +
91B GLN* 3.7 10.1 - - - +
92B MET* 2.8 34.2 + - + +
93B HIS* 3.8 2.9 + - - -
147B ASN* 4.6 3.4 - - - +
205B MET* 3.7 23.6 - - - +
206B SER* 3.1 29.0 + - - +
209B PHE* 3.6 23.1 - - - +
363B HIS 4.0 2.0 + - - +
365B GLN* 3.0 38.7 + - - +
366B VAL* 4.0 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.5 36.3 - + + -
62B TRP* 3.5 15.8 - + - +
88B SER* 4.1 2.1 + - - -
89B ASN* 1.3 72.3 - - - +
91B GLN* 1.3 65.6 + - - +
93B HIS* 3.2 16.1 + - + +
95B TYR* 3.2 25.6 + - + -
96B ASP* 3.0 37.1 + - - -
119B PRO* 3.7 28.3 - - + -
120B THR 4.3 0.4 - - - -
121B GLY* 3.4 27.4 - - - -
123B TYR* 3.5 20.5 + - - +
188B VAL* 3.5 32.1 - - + -
190B ARG* 4.2 4.3 - - + -
206B SER* 3.0 35.9 + - - -
207B GLY* 3.7 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN* 3.0 1.9 - - - +
90B TRP* 1.3 85.2 - - - +
92B MET* 1.3 71.4 + - + +
93B HIS 3.1 0.7 - - - -
94B GLY* 3.2 16.5 + - - -
96B ASP* 3.0 39.1 + - - +
97B ALA 3.6 0.9 - - - +
98B PRO* 3.4 40.0 - - + +
190B ARG* 3.4 13.1 - - - -
205B MET* 3.3 12.5 - - + +
206B SER* 2.8 50.6 + - - +
592B PHE* 6.0 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B SER* 6.1 0.4 - - - -
89B ASN* 2.8 22.3 + - + +
91B GLN* 1.3 94.1 - - + +
93B HIS* 1.4 67.7 + - + +
94B GLY 3.3 1.6 - - - -
98B PRO* 4.0 13.0 - - + -
205B MET* 3.6 20.4 - - + -
361B PRO 5.3 0.7 - - - +
362B LEU 4.0 18.1 - - - +
363B HIS* 3.9 8.5 - - + +
364B GLY* 3.7 37.2 - - - +
575B LEU* 4.0 18.2 - - + -
592B PHE* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 6.1 0.4 - - - -
84B VAL* 3.8 13.4 - - + +
85B VAL* 3.5 12.9 - - - +
88B SER* 3.4 35.1 + - - -
89B ASN 4.5 5.7 + - - -
90B TRP* 3.2 6.4 + - - +
91B GLN 3.1 1.0 - - - -
92B MET* 1.4 85.4 - - + +
94B GLY* 1.3 60.3 + - - +
95B TYR* 3.4 24.7 - - + -
363B HIS* 6.4 0.8 - - - -
8414B DMS 3.2 43.4 - - + +
8421B DMS 3.5 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN 3.2 13.8 + - - -
92B MET 3.3 1.2 - - - -
93B HIS* 1.3 80.1 - - - +
95B TYR* 1.3 64.2 + - - +
96B ASP* 3.3 5.9 + - - -
8421B DMS 3.9 17.5 + - - +
----------------------------------------------------------
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