Contacts of the helix formed by residues 192 - 205 (chain B) in PDB entry 6TXC
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 192 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLN 3.5 3.4 + - - -
191B ILE* 1.3 73.8 - - - +
193B GLU* 1.3 59.4 + - - +
194B ARG* 3.0 15.0 - - - +
195B ASP* 2.9 46.2 + - - +
196B VAL* 3.1 14.0 + - - +
294B LYS* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 1.3 72.6 - - - +
194B ARG* 1.3 56.7 + - - +
195B ASP 3.4 0.2 - - - -
196B VAL* 3.7 13.6 - - + +
197B LEU* 3.1 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 3.5 13.9 - - - +
193B GLU* 1.3 76.7 - - - +
195B ASP* 1.3 64.5 + - - +
197B LEU* 3.5 2.9 + - - +
198B CYS* 3.1 28.5 + - - -
257B TYR 5.8 1.6 - - - +
258B GLY 3.5 24.2 - - - +
259B LEU* 4.1 14.1 - - + -
260B ILE* 3.4 28.1 - - - +
263B GLU* 2.8 27.3 + - - +
264B ASP* 2.9 41.4 + - - +
290B ARG* 4.0 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 5.2 0.4 - - - -
191B ILE* 3.6 11.0 - - + -
192B SER* 2.9 34.0 + - - +
194B ARG* 1.3 78.4 + - - +
196B VAL* 1.3 62.5 + - - +
198B CYS* 3.3 3.0 + - - +
199B VAL* 3.0 29.1 + - - +
290B ARG* 3.0 36.2 + - - +
294B LYS* 3.0 27.7 + - - -
297B LEU* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY* 4.8 5.6 - - - +
179B VAL* 4.0 28.3 - - + -
180B HIS* 4.9 20.2 - - + +
191B ILE* 4.0 14.1 - - + -
192B SER 3.1 13.6 + - - +
193B GLU* 3.7 15.5 - - + +
194B ARG 3.2 0.2 - - - -
195B ASP* 1.3 77.0 - - - +
197B LEU* 1.3 64.2 + - + +
199B VAL* 3.2 3.3 + - - +
200B GLN* 2.9 41.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
129B HIS* 3.7 52.3 - - + +
131B LEU* 4.3 9.2 - - + -
132B LEU* 4.3 13.0 - - + -
193B GLU* 3.1 22.7 + - + +
194B ARG* 3.8 4.3 - - - +
195B ASP 3.4 0.2 - - - -
196B VAL* 1.3 75.6 - - + +
198B CYS* 1.3 57.5 + - - +
200B GLN* 3.3 18.4 + - - +
201B ILE* 2.8 39.5 + - + +
257B TYR* 4.3 9.0 - - + +
259B LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG 3.1 21.8 + - - +
195B ASP 3.6 1.3 - - - +
197B LEU* 1.3 76.2 - - - +
199B VAL* 1.3 62.0 + - - +
201B ILE* 3.5 1.2 + - - -
202B ALA* 3.1 18.7 + - - +
259B LEU* 3.7 12.1 - - - -
264B ASP* 3.5 44.0 - - - -
267B PHE* 3.5 25.1 - - + -
268B ILE* 3.6 17.5 - - + +
271B GLN* 3.4 8.7 - - - +
290B ARG* 3.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 3.7 31.5 - - + +
179B VAL* 4.1 11.0 - - + -
195B ASP 3.0 20.4 + - - +
196B VAL 3.2 3.8 + - - +
198B CYS* 1.3 72.3 - - - +
200B GLN* 1.3 65.5 + - - +
202B ALA* 3.3 2.8 + - - +
203B GLY 3.0 18.2 + - - -
267B PHE* 4.1 14.4 - - + -
271B GLN* 3.5 22.9 - - - +
297B LEU* 4.2 23.1 - - + +
300B ILE* 3.8 16.2 - - + -
301B VAL* 3.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU 4.9 8.3 + - - -
129B HIS* 5.1 2.9 - - - +
132B LEU* 3.8 29.2 - - + +
172B GLY* 3.7 20.7 + - - +
173B TYR* 5.2 4.6 + - - +
175B ALA* 4.4 1.1 - - - -
176B GLY* 3.7 26.0 - - - -
196B VAL* 2.9 33.0 + - - +
197B LEU* 3.6 23.4 - - - +
199B VAL* 1.3 77.1 - - - +
201B ILE* 1.3 57.5 + - - +
203B GLY* 3.3 2.3 + - - -
204B LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.7 29.8 - - + -
132B LEU* 3.4 18.8 - - + -
135B ILE* 3.8 22.9 - - + -
197B LEU 2.8 25.7 + - - +
198B CYS 3.8 4.3 - - - +
200B GLN* 1.3 72.2 - - - +
202B ALA* 1.3 63.2 + - - +
204B LEU* 3.3 5.9 + - - +
205B CYS* 3.0 26.6 + - - +
241B PHE* 3.9 22.0 - - + -
254B MET* 4.7 3.6 - - + -
259B LEU* 4.2 14.6 - - + -
268B ILE* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B CYS 3.1 9.1 + - - +
199B VAL 3.6 2.7 - - - +
201B ILE* 1.3 75.7 - - - +
203B GLY* 1.3 60.0 + - - +
205B CYS 3.3 1.7 + - - -
206B HIS* 2.9 31.7 + - - +
268B ILE* 4.0 19.5 - - + +
271B GLN* 3.3 47.1 - - + +
272B ILE* 4.1 7.2 - - + +
301B VAL* 4.0 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER 3.8 0.9 - - - +
171B VAL* 3.4 17.9 - - - +
172B GLY* 3.7 11.0 - - - -
175B ALA* 4.5 0.4 - - - -
199B VAL 3.0 11.8 + - - -
200B GLN 3.6 3.4 - - - -
202B ALA* 1.3 77.1 - - - +
204B LEU* 1.3 57.0 + - - +
206B HIS* 2.9 26.9 + - - -
301B VAL* 3.6 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 5.2 4.7 - - + -
132B LEU* 3.9 43.7 - - + +
135B ILE* 4.8 9.4 - - + -
136B ILE* 4.0 13.5 - - + -
141B PHE* 3.2 32.1 - - + -
144B LEU* 5.2 0.2 - - - +
168B SER* 3.3 24.2 + - - +
169B LEU* 3.7 46.4 - - + +
172B GLY* 3.6 5.3 - - - -
200B GLN 2.8 14.9 + - - +
201B ILE* 3.5 6.3 - - + +
203B GLY* 1.3 75.4 - - - +
205B CYS* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.8 27.4 - - - -
141B PHE* 4.7 2.9 - - - -
201B ILE* 3.0 22.7 + - + +
202B ALA* 3.5 2.2 - - - +
204B LEU* 1.3 80.6 - - - +
206B HIS* 1.3 61.8 + - - +
207B ASP 3.2 4.4 + - - -
208B LEU* 3.3 40.0 + - + +
237B SER* 3.8 6.8 - - - +
241B PHE* 3.8 30.7 - - + -
272B ILE* 4.0 10.1 - - + +
----------------------------------------------------------
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