Contacts of the helix formed by residues 241 - 259 (chain F) in PDB entry 3A2C
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 ASP 241 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ALA* 3.6 18.8 - - + +
185F ARG* 3.0 47.3 + - - +
212F LYS* 4.8 12.4 - - + +
214F THR* 4.9 9.8 - - + +
239F LYS* 3.4 15.1 + - - +
240F TYR* 1.3 71.7 + - - +
242F LYS* 1.3 65.1 + - - +
243F SER 3.1 3.2 + - - -
244F CYS* 3.3 22.4 + - - +
245F ASP* 3.7 3.3 + - - -
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Residues in contact with LYS 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ARG* 4.7 8.9 + - - +
281D MET* 5.4 3.8 - - - -
178F HIS* 3.1 79.4 + - + +
181F ASN* 2.8 28.6 - - - +
183F ALA* 4.2 1.8 - - + -
214F THR* 3.5 32.9 + - + +
239F LYS 5.1 0.2 + - - -
240F TYR* 3.4 2.1 - - - +
241F ASP* 1.3 78.5 - - - +
243F SER* 1.3 61.5 + - - +
245F ASP* 3.4 8.8 - - - +
246F MET* 3.5 7.0 + - - +
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Residues in contact with SER 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E GLU* 4.5 0.3 + - - -
240F TYR* 3.0 31.8 + - - +
242F LYS* 1.3 79.9 - - - +
244F CYS* 1.3 57.1 + - - +
245F ASP 3.4 0.2 - - - -
246F MET* 3.3 10.6 - - - +
247F TRP 3.1 14.6 + - - -
310F PRO* 3.5 27.8 - - - +
313F ARG* 2.8 30.0 + - - -
314F MET 5.7 0.7 - - - -
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Residues in contact with CYS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ALA* 3.8 14.6 - - + -
233E GLU* 3.6 18.8 - - + +
185F ARG* 4.3 29.2 - - - -
240F TYR 4.9 2.9 - - - +
241F ASP* 3.3 16.3 + - - +
242F LYS 3.3 0.8 - - - -
243F SER* 1.3 78.8 + - - +
245F ASP* 1.3 60.5 + - - +
246F MET 3.0 0.9 - - - -
247F TRP* 3.4 3.8 - - - +
248F SER* 2.7 38.9 + - - -
313F ARG* 3.9 3.8 - - - +
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Residues in contact with ASP 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ILE* 4.0 15.7 - - + +
177F LEU* 5.4 0.3 - - - +
178F HIS* 2.9 28.7 + - + +
183F ALA* 3.5 1.6 - - - -
184F HIS* 2.9 29.4 + - - +
185F ARG* 2.7 28.6 + - - -
187F VAL* 4.2 6.2 + - - +
241F ASP 3.7 6.3 + - - -
242F LYS 3.4 10.7 + - - +
244F CYS* 1.3 77.7 - - - +
246F MET* 1.3 57.3 + - - +
248F SER* 3.3 7.5 + - - -
249F LEU* 3.0 33.4 + - - +
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Residues in contact with MET 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ILE* 4.7 0.9 - - - -
178F HIS* 4.3 8.3 - - + -
242F LYS 3.5 12.3 - - - +
243F SER* 3.3 14.1 + - - +
244F CYS 3.0 0.6 - - - -
245F ASP* 1.3 78.0 - - - +
247F TRP* 1.3 65.9 + - - +
248F SER 3.3 0.2 + - - -
249F LEU* 3.4 18.6 + - + +
250F GLY 3.1 16.5 + - - -
305F LEU* 3.7 32.0 - - + +
313F ARG* 4.3 5.6 - - - -
314F MET 3.4 20.2 - - - +
315F THR* 3.6 9.4 - - - +
316F ILE* 3.6 47.3 - - - +
319F PHE* 3.8 16.4 - - + -
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Residues in contact with TRP 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E TYR* 4.3 4.0 - - - +
230E VAL 3.4 23.6 + - - +
231E ALA* 3.6 18.2 - - + -
232E PRO* 3.4 40.2 - - + -
243F SER 3.1 6.9 + - - -
244F CYS* 3.4 8.5 - - - +
246F MET* 1.3 74.0 - - - +
248F SER* 1.3 69.9 + - - +
250F GLY* 3.1 5.0 + - - -
251F VAL* 3.0 36.3 + - + +
263F PHE* 3.2 43.7 - + - -
279F ILE* 4.2 6.7 - - + -
282F GLY* 5.9 0.4 - - - -
305F LEU 3.7 11.2 - - - -
306F LEU* 3.0 46.0 - - + +
307F LYS 3.9 6.7 - - - -
308F THR* 5.4 0.7 - - - -
313F ARG* 3.8 18.2 - - - +
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Residues in contact with SER 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E TYR* 4.4 9.1 + - - -
185F ARG* 6.0 1.4 - - - -
187F VAL* 3.3 37.5 + - - +
244F CYS* 2.7 27.1 + - - -
245F ASP* 3.5 6.9 + - - -
247F TRP* 1.3 79.8 - - - +
249F LEU* 1.3 68.3 + - - +
251F VAL* 2.9 8.2 + - - +
252F ILE* 2.9 28.3 + - - +
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Residues in contact with LEU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F MET* 3.4 20.9 - - + +
170F ILE* 3.8 25.8 - - + -
171F GLY* 4.4 3.6 - - - -
174F ILE* 3.9 13.9 - - + -
187F VAL* 4.5 8.3 - - + -
245F ASP 3.0 16.6 + - - +
246F MET* 3.6 25.1 - - + +
248F SER* 1.3 74.1 - - - +
250F GLY* 1.3 53.7 + - - +
252F ILE* 3.2 3.9 + - + -
253F MET* 2.7 36.7 + - - +
305F LEU* 4.1 8.5 - - + -
316F ILE* 3.8 29.4 - - + -
319F PHE* 3.9 17.5 - - + -
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F MET 3.1 5.1 + - - -
247F TRP 3.1 8.9 + - - -
249F LEU* 1.3 78.4 - - - +
251F VAL* 1.3 56.3 + - - +
253F MET* 3.8 3.3 - - - +
254F TYR* 2.9 31.2 + - - +
302F ILE* 4.4 5.6 - - - +
305F LEU* 3.5 27.6 - - - +
306F LEU* 3.8 12.6 - - - +
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Residues in contact with VAL 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E TYR* 4.1 29.4 - - + +
189F PRO* 6.1 0.7 - - + -
247F TRP* 3.0 40.4 + - + +
248F SER* 2.9 13.4 + - - +
250F GLY* 1.3 72.1 - - - +
252F ILE* 1.3 59.5 + - + +
254F TYR* 3.3 6.9 + - - +
255F ILE* 2.9 44.6 + - + +
261F PRO* 4.8 4.0 - - + -
262F PRO* 4.2 19.5 - - + +
263F PHE* 5.3 1.8 - - + -
306F LEU* 4.2 10.5 - - + -
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Residues in contact with ILE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E TYR* 6.6 0.2 - - + -
146F LEU* 4.3 10.5 - - + -
147F PHE* 4.4 3.4 - - + -
167F MET* 3.8 17.9 - - + -
170F ILE* 4.0 13.5 - - + -
187F VAL* 3.6 39.7 - - + +
188F LYS* 4.4 2.2 - - - -
189F PRO* 4.6 19.5 - - + -
192F LEU* 4.0 14.4 - - + -
248F SER 2.9 22.8 + - - +
249F LEU* 3.8 6.3 - - + +
251F VAL* 1.3 73.7 - - + +
253F MET* 1.3 68.4 + - - +
255F ILE* 3.1 7.7 + - - +
256F LEU* 2.9 34.5 + - + +
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Residues in contact with MET 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ALA* 6.4 0.2 - - + -
167F MET* 3.7 26.4 - - + -
249F LEU 2.7 14.9 + - - +
250F GLY* 3.8 2.7 - - - +
252F ILE* 1.3 71.9 - - - +
254F TYR* 1.3 63.5 + - - +
256F LEU* 3.2 5.0 + - - +
257F LEU* 3.2 32.0 + - + +
298F VAL* 4.8 3.6 - - - -
301F LEU* 4.2 17.0 - - + -
302F ILE* 3.9 22.9 - - + -
305F LEU* 3.3 34.3 - - + -
319F PHE* 3.7 17.5 - - + -
324F TRP* 3.9 24.2 - - + -
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Residues in contact with TYR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F GLY 2.9 18.8 + - - +
251F VAL 3.4 5.2 - - - +
253F MET* 1.3 78.6 - - - +
255F ILE* 1.3 61.7 + - - +
256F LEU 3.3 0.2 + - - -
257F LEU 3.3 6.6 + - - -
258F CYS* 3.5 21.2 + - - -
260F TYR* 3.1 33.6 - + - -
261F PRO 3.5 2.7 - - - -
262F PRO* 3.2 47.0 + - + +
264F TYR* 5.8 0.5 - - - -
284F TYR* 4.2 4.3 - + - -
285F GLU 2.6 24.9 + - - -
286F PHE* 3.6 22.4 - + - -
287F PRO* 4.0 1.7 - - - +
291F TRP* 3.6 30.7 + + - -
302F ILE* 4.0 20.3 - - + +
306F LEU* 4.7 0.2 - - + -
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Residues in contact with ILE 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PDY 4.0 21.8 - - + -
147F PHE* 3.5 39.5 - - + -
189F PRO* 4.4 10.5 - - + -
251F VAL* 2.9 37.9 + - + +
252F ILE* 3.1 2.4 + - - +
254F TYR* 1.3 76.1 - - - +
256F LEU* 1.3 58.8 + - - +
259F GLY* 2.7 46.4 + - - +
260F TYR 3.6 7.2 - - - +
261F PRO* 3.7 26.0 - - + -
338F THR* 3.9 1.9 - - - +
342F LEU* 4.7 0.7 - - + -
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LEU* 4.5 4.3 - - + -
147F PHE* 3.7 15.5 - - + -
150F ILE* 3.4 32.5 - - + -
158F PHE* 3.5 26.5 - - + -
163F ALA* 4.2 12.3 - - + +
166F ILE* 3.7 23.8 - - + -
167F MET* 3.7 35.0 - - + -
252F ILE* 2.9 21.4 + - + +
253F MET* 3.2 5.4 + - + +
255F ILE* 1.3 77.6 - - - +
257F LEU* 1.3 54.1 + - - +
336F LEU* 4.3 0.3 - - - +
338F THR* 2.6 28.6 + - - +
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F GLU* 3.9 23.6 - - + -
163F ALA* 3.7 25.6 - - + -
253F MET* 3.2 18.2 + - + +
254F TYR 3.3 0.2 + - - -
255F ILE 3.3 0.4 - - - -
256F LEU* 1.3 78.2 - - - +
258F CYS* 1.3 57.6 + - - +
290F GLU 4.1 10.4 - - - +
291F TRP* 3.6 33.7 - - + -
294F VAL* 4.5 8.3 - - + +
298F VAL* 3.3 31.2 - - + -
302F ILE* 3.7 9.0 - - + -
324F TRP* 4.2 4.9 - - + -
336F LEU* 3.4 27.9 - - + +
337F HIS 4.7 0.9 + - - -
338F THR* 3.4 3.2 + - - -
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Residues in contact with CYS 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F TYR* 3.5 13.2 + - - -
255F ILE 3.4 0.4 + - - -
257F LEU* 1.3 80.3 - - - +
259F GLY* 1.3 59.8 + - - +
260F TYR* 3.1 53.1 - - + -
290F GLU* 4.0 13.2 - - + +
291F TRP* 3.3 31.2 - - + +
337F HIS* 3.9 1.9 - - - +
338F THR* 3.7 11.1 + - - +
341F VAL* 3.2 26.2 - - - +
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Residues in contact with GLY 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PDY 3.9 7.1 + - - +
255F ILE* 2.7 24.5 + - - -
258F CYS* 1.3 74.2 - - - +
260F TYR* 1.3 59.3 + - - +
338F THR* 3.9 19.1 - - - +
341F VAL* 3.9 13.7 - - - +
342F LEU* 3.0 28.9 - - - +
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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