Contacts of the helix formed by residues 243 - 260 (chain B) in PDB entry 2BAP
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 VAL 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B SER* 4.0 29.2 - - - +
205B GLN* 5.5 1.8 - - - +
206B HIS* 4.6 9.2 - - + -
240B ASP* 3.1 25.6 + - + +
242B ALA* 1.3 84.6 - - + +
244B PRO* 1.4 68.8 - - - +
245B ASN* 3.6 6.5 - - - +
246B MET* 2.9 41.1 + - + +
247B MET 3.3 3.3 + - - -
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Residues in contact with PRO 244 (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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240B ASP 4.2 4.5 - - - +
241B PRO 3.5 14.1 - - - +
242B ALA 3.5 6.1 - - - +
243B VAL* 1.4 84.9 - - - +
245B ASN* 1.3 62.5 + - - +
246B MET 2.8 12.5 + - - -
247B MET* 2.8 18.0 + - + +
248B ILE* 2.8 28.5 + - + +
298B SER* 4.5 15.7 - - - +
301B LEU* 4.6 11.7 - - + -
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Residues in contact with ASN 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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206B HIS* 3.1 33.2 + - - +
210B ARG* 4.7 7.7 - - - +
243B VAL* 4.6 6.1 - - - +
244B PRO* 1.3 85.1 - - - +
246B MET* 1.3 57.9 + - - +
248B ILE* 3.9 14.9 - - + +
249B ASP* 2.9 32.6 + - - +
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Residues in contact with MET 246 (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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186B LEU* 4.9 3.8 - - + -
190B HIS* 5.8 1.1 - - + +
202B SER 4.8 0.4 - - - +
205B GLN* 3.6 35.9 - - + +
206B HIS* 3.4 42.2 + - + +
209B ILE* 3.5 36.2 - - + +
238B ALA* 4.0 26.5 - - + +
240B ASP* 5.8 0.9 - - - -
243B VAL* 2.9 29.1 + - + +
244B PRO 2.8 4.4 + - - -
245B ASN* 1.3 72.2 - - - +
247B MET* 1.3 53.7 + - - +
249B ASP* 3.0 5.4 + - - +
250B ALA* 2.6 35.6 + - - +
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Residues in contact with MET 247 (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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238B ALA 4.3 1.0 + - - -
239B MET* 3.7 36.3 - - + +
240B ASP 3.4 42.4 - - - +
241B PRO* 3.7 9.9 - - - -
243B VAL 3.3 1.4 + - - -
244B PRO* 2.8 12.3 + - + +
246B MET* 1.3 75.4 - - - +
248B ILE* 1.3 54.9 + - - +
250B ALA* 2.9 8.1 + - - +
251B ALA* 2.7 36.0 + - + +
288B PRO* 3.9 23.3 - - - +
289B LEU* 4.1 0.7 - - - -
292B GLY* 4.5 2.5 - - - -
301B LEU* 3.9 16.2 - - + -
305B CYS* 3.7 30.3 - - - -
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Residues in contact with ILE 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 PRO* 2.8 34.1 + - + +
245B ASN* 3.9 11.9 - - + +
247B MET* 1.3 71.4 - - - +
249B ASP* 1.3 62.0 + - - +
251B ALA* 4.2 4.2 - - - +
252B LYS* 3.3 46.7 + - + +
298B SER* 3.7 23.3 - - - +
300B ALA* 3.8 21.5 - - + +
301B LEU* 3.8 29.4 - - + +
304B GLY* 5.2 7.1 - - - -
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Residues in contact with ASP 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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206B HIS* 3.6 14.7 - - + -
209B ILE* 3.7 18.2 - - + -
210B ARG* 4.5 13.5 + - - +
213B LYS* 4.3 20.1 - - - +
245B ASN* 2.9 19.7 + - - +
246B MET* 3.0 9.7 + - - +
248B ILE* 1.3 78.6 - - - +
250B ALA* 1.3 65.6 + - - +
252B LYS* 3.8 12.7 + - - +
253B LEU* 3.4 27.0 + - - +
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Residues in contact with ALA 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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209B ILE* 4.1 8.0 - - + +
235B LEU* 3.7 27.5 - - + +
238B ALA* 3.8 15.3 - - + -
239B MET* 3.8 11.7 - - + -
246B MET 2.6 18.8 + - - +
247B MET* 2.9 6.9 + - - +
249B ASP* 1.3 71.3 - - - +
251B ALA* 1.3 65.2 + - - +
253B LEU* 3.3 6.1 + - - +
254B LEU* 3.1 25.8 + - - +
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Residues in contact with ALA 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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239B MET* 4.2 25.4 - - + +
247B MET* 2.7 20.7 + - + +
248B ILE* 4.2 4.3 - - - +
250B ALA* 1.3 71.6 - - - +
252B LYS* 1.3 51.1 + - - +
254B LEU* 2.8 10.0 + - - +
255B SER* 2.6 38.5 + - - -
289B LEU* 5.7 0.2 - - + -
304B GLY* 3.4 29.6 - - - +
308B LEU* 3.9 6.1 - - + +
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Residues in contact with LYS 252 (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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248B ILE* 3.3 41.4 + - + +
249B ASP* 4.1 14.3 + - - +
250B ALA 3.5 0.2 - - - -
251B ALA* 1.3 78.7 - - + +
253B LEU* 1.3 56.6 + - + +
255B SER* 3.4 7.6 + - - -
256B ALA* 3.1 28.4 + - - +
304B GLY* 5.4 4.0 - - - -
307B GLN* 3.6 21.7 - - - +
1182D MET* 5.1 0.4 - - + -
1186D LEU* 3.5 34.7 - - + +
1189D LEU* 4.3 0.2 - - - +
1190D GLN* 4.7 16.4 - - - +
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Residues in contact with LEU 253 (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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209B ILE* 3.7 29.4 - - + +
212B LEU* 4.7 2.2 - - + -
213B LYS* 3.6 32.3 - - + +
216B MET* 4.0 16.0 - - - +
235B LEU* 3.8 27.4 - - + -
249B ASP 3.4 16.5 + - - +
250B ALA 3.3 6.9 + - - +
251B ALA 3.0 0.8 - - - -
252B LYS* 1.3 76.4 - - + +
254B LEU* 1.3 67.4 + - - +
256B ALA* 3.4 15.2 - - - +
257B LEU* 3.4 18.1 + - - +
1182D MET* 3.7 28.0 - - + +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.7 26.9 - - + +
235B LEU* 3.6 28.5 - - + -
236B VAL* 4.0 26.0 - - + +
239B MET* 3.5 30.7 - - - -
250B ALA 3.1 13.1 + - - +
251B ALA 2.8 8.3 + - - +
253B LEU* 1.3 74.3 - - - +
255B SER* 1.3 64.7 + - - +
257B LEU* 3.1 24.5 + - + +
258B CYS* 3.4 11.2 + - - -
270B VAL* 4.4 16.1 - - + +
274B MET* 5.6 1.3 - - + -
308B LEU* 3.6 13.2 - - + -
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Residues in contact with SER 255 (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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251B ALA* 2.6 30.5 + - - +
252B LYS* 3.4 9.7 + - - -
254B LEU* 1.3 73.5 - - - +
256B ALA* 1.3 60.0 + - - +
258B CYS* 3.3 17.6 + - - +
259B ILE* 3.5 12.5 - - - +
307B GLN* 4.1 8.0 - - - +
308B LEU* 3.5 25.3 + - - +
311B ALA* 3.7 24.3 - - - +
1189D LEU* 4.1 12.8 - - - +
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Residues in contact with ALA 256 (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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252B LYS 3.1 22.0 + - - +
253B LEU 3.4 7.2 - - - +
254B LEU 3.2 0.2 - - - -
255B SER* 1.3 77.0 - - - +
257B LEU* 1.3 60.4 + - + +
258B CYS 3.6 0.2 + - - -
259B ILE* 3.6 15.3 + - - +
260B LEU* 3.0 19.5 - - - +
1182D MET* 3.6 33.4 - - + -
1185D LEU* 4.0 7.7 - - + +
1186D LEU* 4.5 5.6 - - + -
1189D LEU* 4.0 9.1 - - + +
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Residues in contact with LEU 257 (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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216B MET* 5.4 11.2 - - - -
222B ILE* 4.1 11.9 - - + +
225B MET* 5.8 3.8 - - + -
226B LEU* 3.6 27.4 - - + -
232B ILE* 4.7 13.5 - - + -
235B LEU* 4.3 19.3 - - + -
253B LEU 3.4 16.6 - - - +
254B LEU* 3.1 20.7 + - + +
256B ALA* 1.3 78.0 - - + +
258B CYS* 1.3 64.8 + - - +
260B LEU* 3.1 42.3 + - + +
266B MET* 3.5 16.9 - - + +
270B VAL* 5.0 6.1 - - + -
1182D MET* 6.4 0.9 - - - -
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Residues in contact with CYS 258 (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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254B LEU 3.5 15.9 - - - -
255B SER* 3.3 15.5 + - - +
257B LEU* 1.3 77.3 - - - +
259B ILE* 1.3 60.4 + - - +
260B LEU 3.5 4.0 + - - +
266B MET* 4.7 2.8 + - - +
267B ASN* 3.9 32.7 + - + +
270B VAL* 3.9 14.4 - - - -
308B LEU* 5.1 1.1 - - - -
311B ALA* 3.0 33.7 - - + +
312B LEU* 4.5 7.4 - - - -
315B PRO* 3.4 20.0 - - - +
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Residues in contact with ILE 259 (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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255B SER 3.5 13.9 - - - +
256B ALA* 3.9 10.1 - - - +
257B LEU 3.2 0.4 - - - -
258B CYS* 1.3 73.8 - - - +
260B LEU* 1.3 65.8 + - - +
261B PRO* 3.2 10.2 - - + +
311B ALA* 4.9 5.2 - - + -
315B PRO* 4.7 7.0 - - + -
1185D LEU* 4.5 23.1 - - + +
1189D LEU* 3.6 40.6 - - + -
1194D ALA* 3.7 37.5 - - + +
1195D PHE* 5.7 1.8 - - + -
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Residues in contact with LEU 260 (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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222B ILE* 3.5 34.3 - - + -
226B LEU* 4.2 0.4 - - + -
256B ALA 3.0 28.0 - - - +
257B LEU* 3.1 31.0 + - + +
258B CYS 4.2 4.0 - - - +
259B ILE* 1.3 77.2 - - - +
261B PRO* 1.3 68.3 - - + +
262B GLN 3.3 6.8 + - - -
263B PRO* 3.7 39.3 - - + +
264B GLU* 5.7 1.0 - - - -
265B ASP 5.8 0.5 + - - -
266B MET* 4.8 2.6 + - + +
1185D LEU* 3.7 24.5 - - + -
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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
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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