Contacts of the helix formed by residues 145 - 154 (chain A) in PDB entry 2JIF
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 LEU 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.1 26.8 + - + +
144A THR* 1.3 91.0 + - - +
146A ILE* 1.3 61.2 + - - +
147A ASN 3.7 0.2 - - - -
148A THR* 4.1 0.2 - - - -
149A LEU* 3.1 38.3 + - - +
174A PHE* 3.7 45.8 - - + -
289A SER* 3.6 37.4 - - - +
290A LEU* 4.2 9.2 - - + +
293A GLY* 4.1 3.1 - - - -
414A GLU* 3.9 23.3 - - - +
1433A FAD 5.7 1.8 - - - +
1434A COS 5.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 2.9 22.6 + - + +
142A GLN* 3.6 9.6 - - - +
145A LEU* 1.3 70.5 - - - +
147A ASN* 1.3 65.4 + - - +
148A THR 3.3 0.2 + - - -
149A LEU* 3.7 2.4 - - - +
150A ILE* 3.3 23.6 + - + +
166A LEU* 3.8 34.8 - - + -
172A GLY* 3.8 24.2 - - - +
173A SER 3.6 32.3 - - - +
174A PHE* 3.7 13.7 - - + +
218A LEU* 3.8 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A MET 2.8 31.1 + - - +
104A GLY* 3.7 10.5 - - - -
107A VAL* 3.8 19.8 - - + +
142A GLN* 2.8 28.5 + - - +
143A ASN* 3.5 14.9 + - - +
146A ILE* 1.3 73.7 - - - +
148A THR* 1.3 57.2 + - - +
150A ILE* 3.5 1.3 + - - +
151A ARG* 2.8 38.9 + - - +
163A LEU* 4.2 6.9 - - - +
166A LEU* 3.5 30.3 + - - +
167A THR* 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 4.8 3.3 + - - -
143A ASN 3.2 14.6 + - - -
144A THR* 3.4 23.0 + - - +
145A LEU 3.7 0.2 + - - -
146A ILE 3.2 0.6 - - - -
147A ASN* 1.3 75.9 - - - +
149A LEU* 1.3 60.8 + - - +
151A ARG* 3.7 19.0 + - - +
152A LYS* 2.8 60.4 + - + +
153A HIS* 6.0 0.7 - - - +
289A SER* 4.9 10.3 - - - -
292A GLU* 3.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 3.1 25.5 + - - +
146A ILE 3.4 4.2 + - - +
148A THR* 1.3 76.5 - - - +
150A ILE* 1.3 57.0 + - - +
153A HIS* 2.9 43.9 + - + +
174A PHE* 3.6 31.0 - - + -
218A LEU* 3.4 23.6 - - + -
220A MET* 5.5 3.1 - - + -
234A SER* 5.3 3.1 - - - +
276A LEU* 3.8 19.4 - - + +
285A TYR* 3.4 45.8 - - + +
286A ALA* 4.4 1.3 - - - +
289A SER* 3.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.3 17.5 + - + +
147A ASN 4.1 1.8 - - - +
148A THR 3.3 0.4 - - - -
149A LEU* 1.3 74.0 - - - +
151A ARG* 1.3 67.2 + - - +
154A GLY* 3.0 23.9 + - - -
158A GLN* 4.3 10.3 - - + +
159A LYS* 3.6 21.5 - - + +
162A TYR* 4.2 8.1 - - + -
163A LEU* 4.1 22.0 - - + -
166A LEU* 3.5 28.7 - - + -
216A LEU* 3.9 18.4 - - + -
218A LEU* 4.5 2.9 - - + -
236A LEU* 4.2 13.9 - - + -
276A LEU* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.6 47.3 + - - +
107A VAL* 3.8 23.1 - - - +
143A ASN 5.4 0.8 + - - -
147A ASN* 2.8 29.0 + - - +
148A THR* 3.7 18.0 + - - +
150A ILE* 1.3 74.9 - - - +
152A LYS* 1.3 97.9 + - + +
159A LYS* 3.6 21.4 + - - -
163A LEU* 4.0 15.9 - - + -
1436A CL 3.6 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 5.3 1.2 + - - -
148A THR* 2.8 40.8 + - + +
151A ARG* 1.3 117.6 - - + +
153A HIS* 1.3 82.9 + - + +
154A GLY 3.8 1.5 - - - +
292A GLU* 4.3 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 6.0 1.0 - - - +
149A LEU* 2.9 33.3 + - + +
152A LYS* 1.3 97.5 + - + +
154A GLY* 1.3 64.1 + - - +
155A THR* 4.0 0.9 + - - +
276A LEU* 3.8 12.1 - - + -
277A GLY* 3.2 31.6 + - - -
285A TYR* 3.3 56.1 + + + +
288A GLY* 6.2 1.2 - - - -
289A SER 6.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.0 21.2 + - - -
151A ARG 4.6 0.2 - - - -
152A LYS 3.8 1.3 - - - +
153A HIS* 1.3 81.0 - - - +
155A THR* 1.3 68.1 + - - +
156A GLU* 4.8 0.7 - - - +
158A GLN* 3.4 14.8 - - - -
159A LYS* 3.5 14.0 + - - -
276A LEU* 3.6 8.4 - - - +
----------------------------------------------------------
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