Contacts of the helix formed by residues 193 - 198 (chain B) in PDB entry 2G5W
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 ILE 193 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B HIS 4.8 0.8 + - - -
168B TYR* 3.7 20.9 - - + +
185B ILE* 3.5 25.8 - - + -
186B HIS 3.5 20.8 + - - +
187B GLY* 3.7 17.5 - - - -
191B TYR 2.9 2.4 + - - -
192B LEU* 1.3 75.4 - - - +
194B ASP* 1.3 55.4 + - - +
196B PHE* 2.8 26.9 + - - +
197B LEU* 3.0 25.1 + - + +
218B PHE* 3.6 27.8 - - + -
219B LEU* 4.0 26.0 - - + +
222B VAL* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLY 4.0 3.9 - - - +
188B ALA* 4.0 16.6 - - - -
189B HIS 3.7 2.8 + - - -
190B GLY* 3.1 30.8 + - - +
191B TYR 2.7 15.3 + - - +
193B ILE* 1.3 76.2 - - - +
195B GLN* 1.3 55.8 + - - +
196B PHE 3.1 0.9 - - - -
197B LEU* 3.6 22.0 - - - +
198B LYS* 2.7 75.9 + - - +
201B ILE* 4.6 1.4 - - - +
240B SER* 4.1 4.0 + - - +
248B ALA* 3.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL 2.9 23.0 - - - +
111B GLY* 3.7 1.6 - - - -
112B ARG* 3.2 32.1 + - + +
113B ALA 3.9 0.5 + - - -
127B SER* 2.6 32.9 + - - +
128B SER* 2.6 31.9 + - - +
190B GLY 2.9 24.5 - - - +
191B TYR 3.3 0.8 - - - +
192B LEU* 3.0 23.5 + - - +
194B ASP* 1.3 76.3 - - - +
196B PHE* 1.3 55.1 + - - +
198B LYS 4.7 0.4 - - - -
201B ILE* 3.4 31.2 - - + +
202B ASN* 3.7 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER 4.4 3.6 - - - -
128B SER* 3.6 32.1 - - - -
156B LEU* 4.5 5.4 - - + -
161B ILE* 4.1 23.8 - - + -
192B LEU* 3.4 36.4 + - + -
193B ILE* 2.8 8.5 + - + +
195B GLN* 1.3 78.5 - - - +
197B LEU* 1.3 65.5 + - + +
202B ASN* 2.7 35.3 + - - +
204B ARG* 3.8 20.4 - - - -
208B TYR* 4.1 15.0 - + + -
214B ASN 5.8 0.4 - - - -
215B ARG* 3.3 18.1 - - - +
218B PHE* 3.6 37.9 - + + -
219B LEU 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLY 3.9 15.7 - - - +
193B ILE* 3.0 26.2 + - + +
194B ASP* 3.3 24.0 + - - +
196B PHE* 1.3 80.1 - - - +
198B LYS* 1.3 63.9 + - - +
215B ARG* 3.3 40.7 + - - +
216B CYS* 4.0 27.4 - - - -
219B LEU* 4.1 22.2 - - + -
239B VAL* 4.3 10.1 - - + -
250B ASP* 3.7 1.2 - - - +
256B LEU* 3.7 19.0 - - + +
260B VAL* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 2.7 53.8 + - - +
195B GLN 4.3 0.9 - - - +
197B LEU* 1.3 72.7 - - - +
199B ASP* 1.3 59.3 + - - +
200B GLY 3.3 0.9 - - - +
201B ILE* 3.5 8.0 + - + +
202B ASN* 3.1 25.5 + - - +
240B SER* 3.0 20.3 + - - -
241B PRO* 3.5 17.5 - - - -
243B ILE 2.8 28.7 + - - -
248B ALA* 2.8 26.5 + - + +
249B THR 3.8 11.4 - - - +
250B ASP* 3.6 23.8 - - + +
256B LEU* 4.0 4.9 - - + -
----------------------------------------------------------
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