Contacts of the helix formed by residues 142 - 153 (chain V) in PDB entry 1JJ2
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 ASP 142 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V GLU 5.6 0.7 - - - -
132V VAL* 5.9 1.8 - - - +
141V HIS* 1.3 77.7 - - - +
143V THR* 1.3 57.0 + - - +
144V GLU* 3.7 10.6 - - + +
145V GLY* 3.3 18.4 - - - +
146V ILE* 2.6 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V GLU* 2.9 39.4 + - + +
57V PRO 4.0 1.3 - - - -
58V SER* 3.7 25.4 - - - +
141V HIS 4.0 0.4 + - - -
142V ASP* 1.3 74.4 + - - +
144V GLU* 1.3 60.1 + - - +
146V ILE* 4.1 0.4 - - - +
147V ASP* 2.8 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142V ASP* 3.0 11.5 - - + +
143V THR* 1.3 82.2 - - - +
145V GLY* 1.3 55.1 + - - +
147V ASP* 3.7 6.7 - - - +
148V ASP* 2.7 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137V GLN* 4.9 2.1 + - - -
141V HIS* 3.9 16.3 + - - -
142V ASP* 2.9 21.1 + - - +
144V GLU* 1.3 79.2 - - - +
146V ILE* 1.3 64.5 + - - +
148V ASP* 3.4 9.8 + - - +
149V LEU* 3.4 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V ALA* 4.2 8.1 - - + +
5V VAL* 5.4 1.8 - - + -
53V ALA 4.5 4.5 - - - +
54V PHE* 3.7 22.7 - - - +
55V GLY* 3.4 32.8 - - - +
56V GLU 4.6 0.4 - - - +
57V PRO* 3.7 16.2 - - + -
141V HIS* 3.7 14.2 - - + +
142V ASP 2.6 16.7 + - - +
143V THR 4.1 0.9 - - - +
145V GLY* 1.3 68.6 - - - -
147V ASP* 1.3 71.8 - - - +
149V LEU* 3.0 15.0 + - + +
150V LEU* 2.8 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V PRO* 3.3 9.0 - - - +
58V SER* 2.5 45.0 + - - -
61V THR* 2.8 26.0 + - - +
143V THR* 2.8 25.5 + - - +
144V GLU* 3.7 8.0 - - - +
146V ILE* 1.3 75.8 - - - +
148V ASP* 1.3 58.1 + - - +
150V LEU* 3.8 0.3 - - - +
151V GLU* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144V GLU* 2.7 32.9 + - - +
145V GLY* 3.7 8.8 - - - +
146V ILE 3.2 0.2 - - - -
147V ASP* 1.3 77.8 - - - +
149V LEU* 1.3 64.6 + - - +
151V GLU* 3.3 8.2 + - - +
152V ALA* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V VAL* 4.8 4.9 - - + -
7V LEU* 4.1 9.4 - - + -
53V ALA* 3.5 31.9 - - + -
121V PRO* 4.4 7.4 - - + -
125V HIS* 4.2 15.7 - - + -
137V GLN* 4.0 29.6 - - + +
141V HIS* 4.4 2.5 - - + +
145V GLY 3.4 8.8 + - - +
146V ILE* 3.0 16.0 + - + +
148V ASP* 1.3 79.1 - - - +
150V LEU* 1.3 64.2 + - + +
152V ALA* 3.1 6.3 + - + +
153V MET* 3.0 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V ALA* 4.0 10.8 - - + -
5V VAL* 4.0 16.2 - - + -
32V CYS* 4.4 10.1 - - - -
57V PRO* 3.8 11.7 - - + -
61V THR* 3.6 24.5 - - + -
62V LEU* 5.8 3.4 - - + +
65V VAL* 3.8 22.6 - - + +
118V LEU* 3.9 25.2 - - + +
146V ILE* 2.8 47.4 + - + +
149V LEU* 1.3 73.8 - - + +
151V GLU* 1.3 56.2 + - - +
153V MET* 3.2 8.0 + - + +
154V ARG* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60V GLU* 5.7 0.9 - - - +
61V THR* 2.6 39.3 + - + -
64V THR* 5.1 14.1 - - + +
65V VAL* 5.3 0.9 - - + -
147V ASP* 2.8 24.3 + - - +
148V ASP* 3.8 7.0 - - - +
150V LEU* 1.3 73.5 - - - +
152V ALA* 1.3 60.9 + - - +
153V MET 3.1 4.9 - - - -
154V ARG* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121V PRO* 4.2 9.2 - - + -
122V ARG* 2.7 70.5 + - + +
124V GLY 6.0 0.4 - - - +
148V ASP 2.9 18.1 + - - +
149V LEU* 3.1 6.0 + - + +
151V GLU* 1.3 76.7 - - - +
153V MET* 1.3 52.5 + - - +
154V ARG* 3.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V VAL* 3.7 26.2 - - + -
7V LEU* 4.6 4.5 - - + -
30V ASN* 4.2 13.5 - - - +
118V LEU* 3.6 28.9 - - + +
119V HIS 3.0 39.6 + - - +
121V PRO* 3.5 29.2 - - + -
122V ARG* 3.7 4.7 - - - +
149V LEU* 3.0 54.4 + - + +
150V LEU 3.4 5.8 - - - +
151V GLU 3.1 0.4 - - - -
152V ALA* 1.3 78.4 - - - +
154V ARG* 1.3 62.2 + - - +
----------------------------------------------------------
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