Contacts of the helix formed by residues 64 - 70 (chain M) 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 SER 64 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259 G 5.8 6.5 - - - -
269 C 5.6 3.1 - - - -
1219 C 5.9 2.4 - - - -
42M HIS* 3.6 18.8 - - - -
62M HIS* 2.8 34.7 + - - +
63M SER* 1.3 74.7 + - - +
65M ASP* 1.3 63.6 + - - +
66M LEU 2.6 17.1 + - - -
67M ALA* 3.1 18.5 + - - +
75M THR* 4.7 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209 A 6.0 0.7 - - - -
1219 C 5.3 11.9 - - - +
62M HIS* 2.5 44.7 + - - +
64M SER* 1.3 76.7 + - - +
66M LEU* 1.3 60.1 + - - +
67M ALA 3.4 0.7 - - - -
68M GLU* 3.4 34.3 - - - +
69M TYR* 3.5 11.6 - - - -
87M LEU* 3.8 4.4 - - - +
91M ARG* 3.0 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M HIS 3.8 1.5 + - - +
63M SER* 2.9 21.8 - - - +
64M SER 2.6 6.9 + - - -
65M ASP* 1.3 72.9 - - - +
67M ALA* 1.3 57.8 + - - +
68M GLU 3.0 1.8 - - - -
69M TYR* 2.8 30.4 + - + +
71M TRP* 3.6 30.1 + - + +
80M SER* 4.0 18.8 - - - +
83M LEU* 3.9 44.0 - - + +
84M THR* 4.1 8.3 - - - +
87M LEU* 4.0 21.8 - - + -
175M LEU* 4.0 15.7 - - + +
179M LEU* 5.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M SER 4.5 0.2 + - - -
64M SER 3.1 11.8 + - - +
66M LEU* 1.3 73.8 - - - +
68M GLU* 1.3 52.7 + - - +
69M TYR 2.7 16.7 + - - -
70M GLY* 2.7 13.7 + - - -
71M TRP* 3.2 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219 C 5.6 1.6 + - - -
64M SER 4.5 0.2 + - - -
65M ASP* 3.4 37.8 + - - +
66M LEU 3.0 0.2 - - - -
67M ALA* 1.3 77.7 - - - +
69M TYR* 1.3 74.7 + - + +
70M GLY 3.6 0.2 - - - -
91M ARG* 4.7 0.2 + - - -
185M GLU* 2.6 38.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M ASP 3.5 23.1 - - - -
66M LEU* 2.8 11.0 + - + +
67M ALA 2.7 5.7 + - - -
68M GLU* 1.3 91.5 - - + +
70M GLY* 1.3 55.3 + - - +
71M TRP 3.8 0.4 - - - -
87M LEU* 4.1 17.0 - - + +
91M ARG* 3.3 25.7 + - - -
175M LEU* 3.5 24.9 - - + +
178M THR* 4.5 16.0 + - + +
179M LEU* 4.1 14.6 - - + -
183M ASP* 3.0 34.5 - - + -
184M ILE* 3.0 20.6 + - + -
185M GLU* 3.3 13.7 + - - +
186M LEU* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M ALA 2.7 15.5 + - - -
69M TYR* 1.3 75.4 - - - +
71M TRP* 1.3 58.9 - - - +
72M GLU* 3.5 1.9 + - - +
171M HIS* 2.8 23.9 + - - -
175M LEU* 4.6 5.3 - - - +
----------------------------------------------------------
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