Contacts of the helix formed by residues 204 - 221 (chain B) in PDB entry 1U5Q
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 GLY 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B HIS* 3.2 45.3 + - - -
147B MET 5.0 0.2 - - - -
148B ILE* 3.8 14.1 - - - +
177B ALA* 4.9 2.2 - - - +
203B ASP* 1.3 79.9 - - - +
205B LYS* 1.3 60.6 + - - +
206B VAL* 3.1 0.7 - - - -
207B ASP* 3.0 13.6 + - - +
208B VAL* 3.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B GLU* 4.6 2.7 - - - +
203B ASP* 2.9 25.7 + - - +
204B GLY* 1.3 73.7 - - - +
206B VAL* 1.3 65.3 + - - +
208B VAL* 2.9 20.4 + - - +
209B TRP 3.1 4.5 + - - -
266B PRO* 3.0 36.9 + - + +
267B GLN* 4.1 9.9 + - - +
269B ARG* 2.9 45.3 + - + +
270B PRO 3.9 12.1 - - - +
271B THR* 3.9 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.6 20.9 - - + -
150B ARG* 4.8 7.4 - - + -
190B ALA* 3.8 18.4 - - + +
192B GLU* 3.5 18.2 - - - +
193B VAL* 3.6 27.6 - - + -
202B TYR* 3.6 22.2 - - + -
203B ASP 3.4 18.8 - - - +
205B LYS* 1.3 76.8 - - - +
207B ASP* 1.3 63.0 + - - +
209B TRP* 3.4 3.8 + - - +
210B SER* 2.9 30.2 + - - -
269B ARG* 3.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.6 18.9 - - + +
143B HIS* 2.8 27.2 + - + +
148B ILE* 3.4 8.4 - - - +
149B HIS* 2.8 31.1 + - - +
150B ARG* 2.7 29.8 + - - -
152B VAL* 3.7 9.8 - - + +
204B GLY 3.0 9.0 + - - +
206B VAL* 1.3 78.5 - - - +
208B VAL* 1.3 61.0 + - - +
210B SER* 3.7 3.3 + - - +
211B LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 5.8 1.1 - - + -
139B LEU* 5.3 2.2 - - + -
143B HIS* 4.7 1.6 - - + -
204B GLY 4.4 3.6 - - - +
205B LYS* 2.9 19.4 + - - +
207B ASP* 1.3 78.4 - - - +
209B TRP* 1.3 61.7 + - - +
211B LEU* 3.3 8.3 + - - +
212B GLY 3.0 17.2 + - - -
261B CYS* 3.3 22.1 - - - +
269B ARG* 3.9 6.7 - - + -
270B PRO* 3.7 19.1 - - + +
271B THR 3.9 0.7 - - - -
272B SER* 3.6 36.3 - - - +
275B LEU* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR 5.3 0.6 + - - -
188B TRP 3.4 10.5 - - - -
189B MET 3.3 13.3 + - - -
190B ALA* 3.3 25.4 - - + -
191B PRO* 3.7 20.6 - - + -
205B LYS 3.1 5.1 + - - -
206B VAL 3.5 7.6 - - - +
207B ASP 3.2 0.2 - - - -
208B VAL* 1.3 75.1 - - - +
210B SER* 1.3 68.6 + - - +
212B GLY 2.9 11.4 + - - -
213B ILE* 3.0 25.5 + - + +
237B ILE* 4.3 15.2 - - + +
242B SER* 3.5 24.0 - - - -
243B PRO* 4.3 11.0 - - + -
261B CYS 3.6 9.2 - - - -
262B LEU* 3.1 50.5 - - + +
263B GLN 3.7 14.4 - - - -
264B LYS* 3.8 17.9 - - + -
269B ARG* 3.7 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG* 5.4 4.7 - - - -
151B ASP* 5.6 0.2 - - - -
152B VAL* 3.5 35.4 + - - +
188B TRP* 2.8 27.4 + - - +
189B MET* 4.6 2.6 - - - -
190B ALA 4.7 0.5 + - - -
206B VAL* 2.9 18.0 + - - +
207B ASP* 3.8 5.1 + - - -
209B TRP* 1.3 76.0 - - - +
211B LEU* 1.3 57.6 + - - +
213B ILE* 3.3 4.8 + - - +
214B THR* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 3.9 33.4 - - + +
135B ALA* 4.4 18.4 - - + -
136B LEU* 4.2 21.1 - - + -
139B LEU* 4.0 14.1 - - + -
152B VAL* 3.7 12.0 - - + +
157B ILE* 4.7 4.3 - - + -
207B ASP 2.8 19.0 + - - +
208B VAL* 3.4 7.0 - - - +
209B TRP 3.1 0.2 - - - -
210B SER* 1.3 74.8 - - - +
212B GLY* 1.3 59.7 + - - +
214B THR* 3.2 10.6 + - + -
215B CYS* 2.8 29.7 + - - -
218B LEU* 6.5 0.4 - - + -
257B PHE* 4.0 19.7 - - + -
261B CYS* 4.6 4.5 - - - -
275B LEU* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL 3.0 7.1 + - - -
209B TRP 2.9 9.0 + - - -
211B LEU* 1.3 76.6 - - - +
213B ILE* 1.3 61.1 + - - +
215B CYS* 3.1 18.2 + - - +
216B ILE* 3.2 15.4 + - - +
258B VAL* 4.3 4.5 - - - +
261B CYS* 3.6 24.6 - - - +
262B LEU* 4.0 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR 3.5 24.5 - - - +
188B TRP* 3.5 20.6 - - + -
209B TRP* 3.0 34.7 + - + +
210B SER 3.3 6.5 + - - +
212B GLY* 1.3 73.5 - - - +
214B THR* 1.3 58.9 + - - +
216B ILE* 3.1 8.5 + - - +
217B GLU* 2.9 24.8 + - - +
223B PRO* 3.7 17.3 - - + -
224B PRO* 3.9 12.5 - - + +
243B PRO* 3.8 28.9 - - + -
262B LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 3.6 3.3 + - - +
153B LYS* 3.2 26.5 + - - -
154B ALA* 3.6 28.7 - - + +
157B ILE* 4.0 16.2 - - + -
188B TRP* 3.7 1.2 - - - +
210B SER 2.9 20.6 + - - -
211B LEU* 3.4 15.0 - - + -
213B ILE* 1.3 78.2 - - - +
215B CYS* 1.3 63.5 + - - +
217B GLU* 3.0 11.3 + - - +
218B LEU* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 4.9 0.2 - - - -
132B THR* 3.3 39.5 - - - -
211B LEU* 2.8 21.7 + - - -
212B GLY* 3.1 10.3 + - - +
214B THR* 1.3 74.0 - - - +
216B ILE* 1.3 62.1 + - - +
218B LEU* 3.3 10.9 + - - +
219B ALA* 3.1 22.5 + - - +
254B PHE* 3.8 16.8 - - + -
257B PHE* 3.9 19.5 - - - -
258B VAL* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 3.2 8.0 + - - +
213B ILE* 3.1 9.5 + - + +
215B CYS* 1.3 76.5 - - - +
217B GLU* 1.3 54.2 + - - +
219B ALA 3.0 0.7 + - - -
220B GLU* 2.7 64.9 + - + +
222B LYS 4.3 2.7 - - - +
224B PRO* 3.8 34.5 - - + -
243B PRO 4.3 0.2 - - - -
244B ALA 3.8 23.6 - - - +
245B LEU* 4.1 16.2 - - + -
258B VAL* 3.9 12.3 - - + -
262B LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 4.9 4.7 + - - -
116B LEU* 3.5 10.2 - - + +
154B ALA* 3.0 35.1 + - + +
155B GLY 4.6 2.9 + - - -
188B TRP* 2.9 41.0 + - - +
213B ILE 2.9 12.6 + - - +
214B THR* 3.0 9.4 + - - +
216B ILE* 1.3 78.4 - - - +
218B LEU* 1.3 54.6 + - - +
221B ARG* 2.7 47.4 + - - +
222B LYS* 3.5 21.5 + - - -
223B PRO* 4.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.6 28.7 - - + -
116B LEU* 3.7 12.6 - - + +
122B PRO* 3.3 6.4 - - - +
123B LEU* 3.1 40.1 + - + -
128B ILE* 3.7 32.8 - - + +
131B VAL* 3.9 26.0 - - + -
132B THR* 4.3 8.7 - - - +
154B ALA* 3.9 14.1 - - + -
157B ILE* 5.6 0.4 - - + -
211B LEU* 6.5 0.2 - - + -
214B THR* 2.9 29.1 + - + +
215B CYS* 3.8 6.3 - - - +
216B ILE 3.2 0.2 - - - -
217B GLU* 1.3 76.2 - - - +
219B ALA* 1.3 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 3.1 20.5 - - - +
128B ILE* 3.7 13.5 - - + -
215B CYS 3.1 15.1 + - - +
216B ILE 3.0 2.6 + - - +
218B LEU* 1.3 77.1 - - - +
220B GLU* 1.3 61.4 + - + +
245B LEU* 3.6 24.2 - - + -
250B TRP* 3.4 31.5 - - + -
254B PHE* 3.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 4.6 2.0 - - - -
216B ILE* 2.7 36.0 + - + +
219B ALA* 1.3 83.1 - - + +
221B ARG* 1.3 70.6 + - - +
222B LYS* 3.1 18.0 + - - +
224B PRO* 5.5 2.3 - - - +
244B ALA 5.1 0.5 - - - +
245B LEU* 3.6 11.1 - - + +
246B GLN* 2.8 63.3 + - + +
247B SER 4.4 0.9 + - - -
250B TRP* 5.1 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.0 26.8 + - + +
117B GLU* 5.7 0.6 - - - +
120B LYS* 3.2 53.3 + - - +
121B LYS* 3.7 34.9 - - - +
122B PRO* 3.9 6.3 - - + -
217B GLU* 2.7 28.4 + - - +
218B LEU 4.4 1.4 + - - -
219B ALA 3.9 0.6 - - - -
220B GLU* 1.3 75.1 - - - +
222B LYS* 1.3 69.6 + - + +
----------------------------------------------------------
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