Contacts of the helix formed by residues 145 - 154 (chain M) in PDB entry 3J0S
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 145 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M TYR* 3.6 17.8 + - - -
141M GLU* 3.0 28.5 + - - +
142M GLU* 3.7 10.0 + - - +
143M VAL 3.4 1.0 - - - -
144M LYS* 1.3 86.0 - - - +
146M ARG* 1.3 65.9 + - - +
147M CYS* 3.4 10.4 + - + +
148M THR* 3.5 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M ASP* 5.0 13.7 + - - +
68M TYR* 3.6 33.8 + - - +
69M ALA* 5.5 0.6 - - - +
144M LYS 3.5 12.4 + - - -
145M ASP* 1.3 71.2 - - - +
147M CYS* 1.3 63.7 + - - +
149M LEU 3.3 2.4 + - - -
150M ALA* 3.1 9.0 + - - +
161M LEU* 3.1 54.9 - - + +
162M GLU* 5.5 3.4 - - - +
165M PRO* 3.1 43.5 - - + +
166M LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS* 6.3 0.7 - - - -
145M ASP* 3.2 7.9 - - + +
146M ARG* 1.3 80.4 - - - +
148M THR* 1.3 57.7 + - - +
150M ALA* 3.1 9.4 + - - +
151M GLU* 2.8 32.8 + - - +
166M LEU* 5.1 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS* 5.6 3.6 + - - -
68M TYR* 5.0 3.1 - - - +
135M LEU* 3.3 32.6 - - + +
136M GLN 5.6 7.0 - - - +
142M GLU* 3.2 37.4 + - + +
145M ASP* 3.5 9.9 + - - +
146M ARG 3.3 0.8 - - - -
147M CYS* 1.3 77.6 - - - +
149M LEU* 1.3 63.1 + - - +
151M GLU* 3.4 26.5 + - - +
152M LYS 3.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M TYR* 3.7 43.4 + - + +
85M TYR* 4.1 17.7 - - + +
87M ALA* 4.6 20.0 - - + +
89M TYR* 5.4 2.5 - - + -
100M VAL* 6.0 0.9 - - + -
135M LEU* 3.9 15.9 - - + +
145M ASP 4.1 1.0 + - - -
146M ARG 3.3 3.0 + - - +
148M THR* 1.3 78.2 - - - +
150M ALA* 1.3 60.2 + - - +
152M LYS* 3.3 38.2 - - + +
153M LEU* 3.7 10.8 - - + +
161M LEU* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M ARG 3.1 12.5 + - - +
147M CYS* 3.1 13.2 + - - +
149M LEU* 1.3 76.0 - - - +
151M GLU* 1.3 62.8 + - - +
153M LEU* 3.0 35.5 - - + +
154M GLY 3.2 4.9 + - - -
155M GLY* 3.4 16.0 + - - -
158M VAL* 5.4 1.8 - - + -
161M LEU* 4.0 2.0 - - + +
166M LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 3.4 30.5 - - + +
292A ASP* 3.4 21.6 - - - +
326A LYS* 5.8 1.9 + - - -
135M LEU* 5.6 2.5 - - + +
147M CYS* 2.8 20.9 + - - +
148M THR* 3.4 21.9 - - - +
149M LEU 3.3 0.6 - - - -
150M ALA* 1.3 72.8 - - - +
152M LYS* 1.3 63.0 + - - +
154M GLY* 3.3 17.0 + - - +
155M GLY* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M ALA* 4.9 3.4 - - + -
98M ASP* 4.1 21.3 - - + +
100M VAL* 3.1 36.1 - - + -
133M HIS* 4.1 31.6 + - + -
134M GLU 5.7 0.2 - - - +
135M LEU* 3.2 39.4 - - + +
148M THR 3.9 2.5 + - - +
149M LEU* 3.3 25.6 + - + +
151M GLU* 1.3 78.7 - - - +
153M LEU* 1.3 69.9 + - + +
154M GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M TYR* 3.2 55.6 - - + +
98M ASP* 4.3 1.8 - - - +
149M LEU* 3.7 12.6 - - + +
150M ALA* 3.0 28.3 - - + +
152M LYS* 1.3 96.8 - - + +
154M GLY* 1.3 55.9 + - - +
155M GLY 3.7 0.4 - - - -
158M VAL* 3.5 40.2 - - + -
161M LEU* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M ALA 3.2 4.0 + - - -
151M GLU* 3.3 11.9 + - - +
152M LYS 3.3 3.2 - - - -
153M LEU* 1.3 79.1 - - - +
155M GLY* 1.3 59.4 + - - +
156M SER* 3.4 7.0 + - - -
----------------------------------------------------------
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