Contacts of the helix formed by residues 204 - 219 (chain B) in PDB entry 4IRX
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 LYS 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP* 3.1 16.9 + - - -
48B SER* 2.8 31.9 + - - -
49B GLN* 4.4 9.3 - - - +
77B ASN* 6.0 3.4 - - - +
201B ALA 2.9 10.3 + - - +
202B ASN* 3.3 14.8 - - + +
203B SER* 1.3 86.6 + - - +
205B ARG* 1.3 60.0 + - - +
206B ASP* 3.3 17.9 - - - +
207B GLN* 3.8 22.7 - - + +
208B ALA* 2.9 27.5 + - - +
233B ASP* 4.6 0.7 - - - -
234B MSE 3.8 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO* 5.1 4.0 - - - +
204B LYS* 1.3 72.2 - - - +
206B ASP* 1.3 58.7 + - - +
208B ALA* 3.2 6.0 + - - +
209B LEU* 3.0 27.8 + - + +
233B ASP* 2.8 63.1 + - - +
236B MSE 3.5 26.1 - - - +
237B GLY* 3.8 12.5 - - - +
240B GLU* 4.8 14.5 + - - +
260B ILE* 4.8 5.1 - - - +
262B GLU* 3.1 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 3.3 22.2 - - - +
205B ARG* 1.3 74.5 + - - +
207B GLN* 1.3 73.9 + - - +
209B LEU* 3.4 15.4 + - - +
210B THR* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR 5.1 0.5 - - - +
201B ALA* 3.6 23.5 - - + +
202B ASN* 2.8 33.2 + - - +
204B LYS* 3.3 23.2 + - + +
206B ASP* 1.3 86.6 + - - +
208B ALA* 1.3 59.0 + - - +
210B THR* 3.3 6.7 + - - +
211B VAL* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.9 3.6 - - + -
201B ALA* 3.5 10.7 - - + +
204B LYS 2.9 10.6 + - - +
205B ARG 3.2 8.3 + - - +
207B GLN* 1.3 77.0 - - - +
209B LEU* 1.3 61.9 + - - +
211B VAL* 4.6 0.9 - - - -
212B THR* 2.7 34.0 + - - +
229B CYS* 6.2 0.2 - - - -
234B MSE 3.2 48.0 - - + +
237B GLY* 4.2 2.6 - - - -
238B ALA 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 3.0 11.8 + - + +
206B ASP* 3.7 11.9 - - - +
207B GLN 3.2 0.6 - - - -
208B ALA* 1.3 76.3 - - - +
210B THR* 1.3 62.7 + - + +
213B GLN* 2.9 51.2 + - - +
237B GLY* 3.6 14.3 - - - +
240B GLU* 3.9 19.1 - - + +
241B ALA* 3.5 33.1 - - - +
244B ALA* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 3.4 11.7 + - - +
207B GLN* 3.3 11.3 + - - +
209B LEU* 1.3 78.6 - - + +
211B VAL* 1.3 69.6 + - - +
213B GLN* 3.3 16.3 + - - +
214B ASN* 3.0 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.0 13.5 - - + -
199B GLN* 3.6 29.7 - - + +
200B THR 4.0 18.6 - - - +
201B ALA* 4.5 2.5 - - + -
207B GLN* 2.9 29.7 + - + +
208B ALA* 4.2 3.8 - - - +
210B THR* 1.3 77.8 + - - +
212B THR* 1.3 63.0 + - - +
214B ASN* 3.3 7.1 + - - +
215B ILE* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 6.0 0.7 - - + -
166B ILE* 4.1 17.4 - - + +
208B ALA* 2.7 25.7 + - - +
211B VAL* 1.3 75.0 - - - +
213B GLN* 1.3 64.3 + - - +
215B ILE* 3.2 10.7 + - + +
216B LEU* 2.9 29.2 + - + +
227B ILE* 3.8 31.2 - - + -
238B ALA* 3.9 17.4 - - - +
241B ALA* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 2.9 43.2 + - - +
210B THR* 3.6 18.3 - - - +
212B THR* 1.3 78.2 - - - +
214B ASN* 1.3 60.8 + - - +
216B LEU* 3.3 7.2 + - - +
217B THR* 3.0 32.0 + - - +
241B ALA* 3.7 19.5 - - + +
244B ALA* 3.7 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR* 3.0 25.2 + - - +
211B VAL* 3.8 6.1 - - - +
213B GLN* 1.3 76.6 - - - +
215B ILE* 1.3 65.6 + - + +
217B THR* 3.3 9.1 + - - +
218B SER* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 3.8 19.1 - - + -
166B ILE* 3.7 28.9 - - + -
197B THR* 3.6 31.4 - - + -
199B GLN* 3.6 32.1 - - + +
211B VAL* 3.0 21.4 + - + +
212B THR* 3.2 9.4 + - + +
214B ASN* 1.3 77.7 - - + +
216B LEU* 1.3 65.8 + - + +
218B SER* 2.8 24.2 + - - +
219B MSE 3.2 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 2.9 26.3 + - + +
213B GLN* 3.7 6.5 - - - +
215B ILE* 1.3 78.5 - - + +
217B THR* 1.3 63.1 + - - +
219B MSE 3.1 6.1 + - - -
220B ARG* 3.0 25.9 + - - +
223B PRO* 5.1 2.1 - - + +
224B PRO* 3.5 35.2 - - + -
227B ILE* 4.7 8.3 - - + -
241B ALA* 3.7 36.6 - - + +
242B VAL* 4.0 12.6 - - + +
245B ALA* 4.2 15.5 - - + -
247B LEU* 4.7 13.5 - - + -
252B VAL* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 3.0 16.0 + - - +
214B ASN* 3.6 13.6 + - - +
215B ILE 3.2 0.2 - - - -
216B LEU* 1.3 76.0 - - - +
218B SER* 1.3 63.5 + - - +
219B MSE 3.2 0.9 + - - -
220B ARG* 3.4 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 5.9 0.2 - - - +
214B ASN 3.0 12.6 + - - -
215B ILE* 2.8 21.9 + - - +
217B THR* 1.3 77.5 - - - +
219B MSE 1.3 70.8 + - - +
220B ARG 3.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 3.8 16.2 - - - +
164B VAL* 4.0 1.6 - - - -
196B VAL* 3.7 38.8 - - + +
197B THR* 4.2 8.1 - - + -
215B ILE* 3.3 36.6 - - + +
216B LEU 3.1 5.2 + - - +
218B SER* 1.3 92.6 - - - +
220B ARG* 1.3 57.8 + - - +
221B ASP 3.2 3.4 - - - -
222B THR* 2.9 37.3 + - - +
223B PRO* 3.2 3.0 - - + +
224B PRO* 3.8 30.1 - - + -
----------------------------------------------------------
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