Contacts of the helix formed by residues 236 - 253 (chain B) in PDB entry 1Q4L
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 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B HIS* 3.2 47.1 - - - +
176B GLY* 4.9 5.7 + - - -
177B ILE 4.0 4.0 + - - -
178B CYS* 3.6 26.4 - - - +
207B LEU* 3.9 7.1 - - - +
235B THR* 1.3 71.6 - - - +
237B SER* 1.3 57.3 + - - +
238B ILE 3.0 10.7 + - - -
239B ASP* 3.1 12.9 + - - +
240B VAL 4.0 0.2 + - - -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLU* 4.3 2.1 + - - -
235B THR* 2.9 18.0 + - - -
236B SER* 1.3 74.9 - - - +
238B ILE* 1.3 64.6 + - - +
239B ASP 3.2 0.4 - - - -
240B VAL* 3.3 15.8 + - - +
241B TRP 3.2 12.6 + - - -
325B PRO* 3.5 37.8 - - - +
328B ARG* 3.1 23.6 + - - -
329B LEU 5.9 0.7 - - - -
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B CYS* 3.6 28.0 - - - -
180B ARG* 4.0 21.1 - - + -
217B ILE* 4.1 13.5 - - + -
218B CYS* 5.6 3.1 - - + -
222B TYR 4.8 0.2 - - - +
224B ALA* 4.2 20.2 - - + +
226B GLU* 3.7 17.7 - - - +
227B LEU* 4.2 14.8 - - + -
234B TYR* 3.9 31.6 - - + -
235B THR 3.3 12.5 + - - +
236B SER 3.0 1.4 - - - -
237B SER* 1.3 78.8 + - - +
239B ASP* 1.3 65.5 + - - +
241B TRP* 3.3 4.3 + - - +
242B SER* 3.1 25.4 + - - -
328B ARG* 4.2 0.4 - - - +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 3.9 16.5 - - + +
173B HIS* 2.8 29.7 + - + +
178B CYS* 3.4 10.6 - - - -
179B HIS* 2.9 23.7 + - - +
180B ARG* 3.0 24.8 + - - -
181B ASP 4.4 0.2 + - - -
182B ILE* 3.7 17.3 + - + +
236B SER 3.1 9.4 + - - +
238B ILE* 1.3 79.6 - - - +
240B VAL* 1.3 59.1 + - - +
242B SER* 3.3 8.3 + - - -
243B ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 5.0 3.1 - - + -
169B LEU* 4.8 3.4 - - + -
173B HIS* 4.8 2.5 - - + -
236B SER 4.7 2.5 - - - +
237B SER* 3.3 19.5 + - - +
238B ILE 3.2 0.6 - - - -
239B ASP* 1.3 76.6 - - - +
241B TRP* 1.3 60.4 + - - +
243B ALA* 3.1 7.2 + - - +
244B GLY* 2.8 26.9 + - - -
320B LEU* 3.5 31.1 - - + +
328B ARG* 4.1 14.4 - - + -
329B LEU 3.6 24.2 - - - +
330B THR* 4.8 0.7 - - - -
331B PRO* 4.1 28.7 - - + -
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Residues in contact with TRP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR 5.0 0.4 + - - -
222B TYR 3.5 14.6 - - - -
223B ARG 3.2 12.3 + - - -
224B ALA* 3.4 24.5 - - + -
225B PRO* 3.5 35.4 - - + -
237B SER 3.2 6.3 + - - -
238B ILE 3.3 8.3 + - - +
240B VAL* 1.3 77.6 - - - +
242B SER* 1.3 61.8 + - - +
244B GLY* 3.0 3.1 + - - -
245B CYS* 2.9 31.7 + - - -
257B PHE* 3.6 30.2 - + - -
269B ILE* 3.9 13.9 - - + -
273B LEU* 4.0 16.8 - - + -
320B LEU 4.5 4.9 - - - -
321B LEU* 3.4 45.3 - - + +
322B GLU 3.6 18.6 - - - -
328B ARG* 3.8 12.1 - - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 3.3 39.7 + - - +
218B CYS* 3.8 12.6 - - - -
222B TYR* 2.9 27.1 + - - -
238B ILE 3.1 13.2 + - - -
239B ASP* 3.5 6.8 + - - -
241B TRP* 1.3 77.3 - - - +
243B ALA* 1.3 63.8 + - - +
245B CYS* 3.0 13.8 + - - +
246B VAL* 3.0 15.6 + - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B MET* 3.4 10.3 - - + +
165B LEU* 4.0 21.3 - - + -
166B PHE* 3.7 29.4 - - + -
169B LEU* 4.3 6.5 - - + -
182B ILE* 4.1 8.0 - - + +
239B ASP 2.9 16.8 + - - +
240B VAL 3.6 5.4 - - - +
242B SER* 1.3 75.4 - - - +
244B GLY* 1.3 63.9 + - - +
246B VAL* 3.0 3.8 + - - +
247B LEU 2.9 19.1 + - - -
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL 2.8 14.9 + - - -
241B TRP 3.0 4.7 + - - -
243B ALA* 1.3 77.9 - - - +
245B CYS* 1.3 55.4 + - - +
247B LEU* 3.4 2.7 + - - +
248B ALA* 3.1 29.3 + - - +
317B CYS* 4.6 2.0 - - - -
320B LEU* 3.9 24.8 - - - +
321B LEU* 3.8 19.0 - - - +
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Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B TYR 3.5 18.2 - - - +
222B TYR* 3.5 20.6 - - + -
241B TRP* 2.9 43.2 + - - -
242B SER 3.0 8.5 + - - +
244B GLY* 1.3 74.5 - - - +
246B VAL* 1.3 60.2 + - - +
248B ALA* 3.9 1.2 - - - +
249B GLU* 3.0 30.7 + - - +
256B ILE* 4.4 14.9 + - + +
257B PHE* 4.1 13.5 - - - -
321B LEU* 4.1 6.7 - - - -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 4.9 3.4 - - + -
162B MET* 3.9 17.0 - - + -
165B LEU* 4.9 0.9 - - + -
182B ILE* 4.6 4.5 - - + -
183B LYS* 4.4 8.5 - - - -
184B PRO* 4.1 33.4 - - + -
187B LEU* 4.1 22.0 - - + -
222B TYR* 4.3 6.1 - - + -
242B SER 3.0 15.6 + - - +
243B ALA* 3.0 13.2 + - - +
245B CYS* 1.3 75.6 - - - +
247B LEU* 1.3 65.9 + - - +
249B GLU* 3.3 5.9 + - - +
250B LEU* 3.0 34.4 + - + +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.7 18.6 - - + -
162B MET* 3.5 41.9 - - + +
243B ALA 2.9 6.9 + - - +
244B GLY* 3.7 7.0 - - - +
246B VAL* 1.3 73.5 - - - +
248B ALA* 1.3 67.7 + - - +
250B LEU* 3.0 14.9 + - - +
251B LEU* 3.0 21.5 + - + +
313B ALA 4.0 7.9 - - - +
316B LEU* 3.7 26.0 - - + -
317B CYS* 3.4 25.1 - - - +
320B LEU* 4.1 12.1 - - + -
339B PHE* 4.1 13.9 - - + -
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLY 3.1 14.7 + - - +
245B CYS 3.9 0.2 - - - +
247B LEU* 1.3 79.7 - - - +
249B GLU* 1.3 57.2 + - - +
251B LEU* 3.3 1.3 + - - -
252B LEU* 2.8 36.0 + - - +
256B ILE* 3.8 38.8 - - + -
305B PHE* 3.8 12.8 - - + -
317B CYS* 4.1 14.3 - - - -
321B LEU* 4.6 3.1 - - + -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 5.9 2.3 - - - -
143B ALA* 5.6 7.1 - - + +
184B PRO* 4.1 12.8 - - - +
222B TYR* 2.6 38.9 + - - -
245B CYS 3.0 17.1 + - - +
246B VAL* 3.5 5.6 - - + +
247B LEU 3.1 0.2 - - - -
248B ALA* 1.3 77.1 - - - +
250B LEU* 1.3 60.0 + - + +
253B GLY* 2.7 33.2 + - - -
254B GLN* 3.5 27.3 - - - +
255B PRO* 3.7 25.4 - - + +
256B ILE* 5.0 1.1 - - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.1 20.2 - - + -
143B ALA* 3.8 28.5 - - + -
152B THR* 5.4 3.8 - - - +
153B LEU* 4.1 35.2 + - + +
158B VAL* 4.2 31.1 - - + +
161B TYR* 4.8 9.4 - - + -
162B MET* 4.4 14.6 - - + -
184B PRO* 6.4 0.7 - - + -
246B VAL* 3.0 31.8 + - + +
247B LEU 3.0 6.5 + - - +
249B GLU* 1.3 81.3 - - + +
251B LEU* 1.3 61.7 + - - +
253B GLY* 4.2 4.3 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B THR* 4.6 13.2 - - - +
155B VAL* 4.3 19.3 - - + -
158B VAL* 4.2 20.2 - - + -
247B LEU* 3.0 23.8 + - + +
248B ALA 3.8 3.8 - - - +
250B LEU* 1.3 77.2 - - - +
252B LEU* 1.3 63.0 + - - +
305B PHE* 3.9 28.2 - - + -
306B ARG* 5.0 5.9 + - - +
309B THR* 4.6 23.3 - - + +
310B PRO* 5.2 0.9 - - + -
313B ALA* 3.6 35.7 - - + -
314B ILE* 4.8 1.6 - - + +
317B CYS* 4.3 15.5 - - - -
339B PHE* 5.1 0.7 - - + -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 5.1 5.4 - - - +
248B ALA 2.8 14.0 + - - +
251B LEU* 1.3 78.8 - - - +
253B GLY* 1.3 59.3 + - - +
254B GLN* 3.4 23.5 + - + +
255B PRO 4.6 1.6 - - - +
256B ILE* 3.8 40.6 - - + -
304B VAL* 3.3 29.6 - - + +
305B PHE* 3.5 30.3 - - + -
306B ARG 5.2 1.1 - - - +
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 2.8 28.4 + - - -
151B GLN 6.0 1.3 - - - -
152B THR* 5.5 6.5 - - - -
249B GLU* 2.7 16.7 + - - -
250B LEU 4.2 4.2 + - - -
251B LEU 3.6 1.8 - - - -
252B LEU* 1.3 73.8 - - - +
254B GLN* 1.3 63.3 + - - +
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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) + - + + + + + -
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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