Contacts of the helix formed by residues 149 - 154 (chain G) in PDB entry 2EHO
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 THR 149 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E GLN* 4.7 1.8 - - - +
87G MSE 4.4 13.5 - - + -
89G SER 4.5 0.9 - - - +
90G PRO* 3.5 33.0 - - + +
91G TYR* 5.8 0.2 - - - -
92G TYR* 4.4 9.5 - - + -
93G MSE 6.0 0.9 - - - +
94G GLU* 5.6 1.8 + - - -
124G ARG* 4.4 3.1 - - - +
147G ASN 4.3 6.3 - - - +
148G LEU* 1.3 80.8 - - - +
150G LEU* 1.3 70.3 + - - +
151G MSE 4.3 4.7 + - - +
152G GLU* 2.9 45.2 + - - +
153G ILE* 3.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E MSE 5.2 10.5 - - + -
39E PHE* 5.9 3.4 - - + -
174E ARG* 5.5 7.4 - - - +
203E GLN* 5.0 13.0 - - - +
1G MSE 3.5 31.0 - - + -
6G VAL* 3.5 13.2 - - + -
9G LEU* 3.9 20.6 - - + -
90G PRO 4.6 3.2 + - - +
91G TYR* 3.9 24.2 - - + +
94G GLU* 5.3 0.2 - - - +
149G THR* 1.3 68.9 - - - +
151G MSE 1.3 68.7 + - - +
152G GLU 2.6 2.4 + - - -
153G ILE* 2.7 19.8 + - + -
154G ASN* 2.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ALA* 4.1 32.1 - - + +
6G VAL* 3.7 10.2 - - + +
93G MSE 4.9 4.7 - - + -
94G GLU* 3.1 39.8 + - + +
121G TRP* 4.2 12.6 - - + -
149G THR* 3.6 5.9 + - - +
150G LEU* 1.3 76.5 - - - +
152G GLU* 1.3 60.6 + - + +
154G ASN* 4.6 3.6 - - - -
155G THR* 2.8 41.0 + - + +
186H PHE* 3.2 42.2 - - + -
189H TRP* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G PHE* 5.6 1.3 - - - -
92G TYR* 3.0 26.5 + - + -
93G MSE 6.3 0.4 - - + -
121G TRP* 3.9 20.1 - - + -
124G ARG* 2.5 46.2 + - - +
125G ILE* 6.2 3.6 - - + -
128G LEU* 3.9 17.5 - - + +
148G LEU* 3.8 10.9 - - + +
149G THR* 3.0 35.9 + - - +
150G LEU 2.6 4.2 + - - -
151G MSE 1.3 73.5 - - + +
153G ILE* 1.3 63.1 + - + +
155G THR* 3.1 19.3 + - - -
156G SER 3.9 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 5.7 2.0 - - + -
172E PHE* 3.5 50.3 - - + -
203E GLN* 5.5 13.0 - - + +
0G MSE 4.5 0.3 - - - +
128G LEU* 5.1 5.4 - - - -
145G LEU* 4.9 5.8 - - + -
148G LEU* 3.7 36.8 - - + -
149G THR 3.1 18.2 - - - +
150G LEU* 2.7 19.7 + - + +
152G GLU* 1.3 71.7 - - - +
154G ASN* 1.3 67.1 + - + +
155G THR 3.4 0.4 - - - -
157G GLY* 3.0 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 3.7 25.1 - - - -
0G MSE 3.9 13.3 - - - +
1G MSE 2.5 64.5 + - - +
2G ASP 5.0 0.7 - - - -
3G ALA* 5.9 0.3 + - - -
6G VAL* 4.6 7.4 - - + +
150G LEU* 2.6 27.3 + - - +
151G MSE 4.3 3.8 - - - +
153G ILE* 1.3 78.6 - - + +
155G THR* 1.3 63.0 + - - +
156G SER 3.6 0.4 - - - -
157G GLY* 4.2 4.0 - - - +
158G THR 5.5 1.5 + - - -
185H ASP* 5.2 4.0 - - - +
----------------------------------------------------------
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