Contacts of the helix formed by residues 264 - 281 (chain B) in PDB entry 2ABQ
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 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU* 3.7 1.8 - - - -
262B GLY 3.7 0.8 + - - -
263B LYS* 1.3 75.9 - - - +
265B LEU* 1.3 67.4 + - - +
266B GLU* 3.7 7.9 + - - +
267B ASP* 2.6 40.4 + - - +
268B ALA* 2.8 25.8 + - - +
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Residues in contact with LEU 265 (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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157B PHE* 4.3 5.4 - - + -
212B GLU* 3.0 47.1 - - + +
213B SER* 4.2 10.8 - - - +
225B PHE* 4.3 11.4 - - + -
227B SER* 4.8 8.1 - - - +
255B PHE* 3.3 40.5 - - + -
259B LEU* 3.7 25.9 - - + +
264B SER* 1.3 74.8 - - - +
266B GLU* 1.3 63.6 - - - +
268B ALA 3.2 6.2 + - - -
269B VAL* 3.6 2.4 - - - +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PHE* 4.1 8.2 - - + -
227B SER* 5.1 5.3 + - - +
229B GLU* 5.0 17.5 - - + +
230B GLY 5.5 2.6 - - - +
232B PHE* 3.4 44.6 - - + -
264B SER* 3.7 7.2 + - - +
265B LEU* 1.3 80.7 - - - +
267B ASP* 1.3 79.3 + - - +
268B ALA 3.3 0.7 + - - -
269B VAL* 3.4 14.6 + - - +
270B PRO* 3.6 3.3 - - - +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LYS* 4.6 17.0 + - + +
264B SER* 2.6 33.2 + - - +
266B GLU* 1.3 91.6 - - - +
268B ALA* 1.3 60.5 + - - +
269B VAL 3.3 0.2 - - - -
270B PRO* 3.4 15.8 - - - +
271B PHE 4.7 1.0 + - - -
295B GLN* 5.1 3.6 + - - -
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Residues in contact with ALA 268 (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 PHE* 3.9 16.3 - - + +
258B ALA* 3.5 29.5 - - + +
259B LEU* 4.0 13.5 - - + -
263B LYS* 4.8 3.1 - - + +
264B SER 2.8 14.6 + - - +
265B LEU 3.6 6.5 - - - +
266B GLU 3.1 0.6 - - - -
267B ASP* 1.3 78.6 - - - +
269B VAL* 1.3 64.8 + - - +
270B PRO 3.4 0.4 - - - -
271B PHE* 3.2 7.8 + - - +
272B ALA* 3.1 19.6 + - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.3 11.7 - - + -
223B ALA* 6.3 0.2 - - + -
225B PHE* 3.5 43.7 - - + -
232B PHE* 3.7 18.6 - - + -
234B VAL* 4.6 7.9 - - + -
255B PHE* 4.1 9.0 - - + -
265B LEU 3.6 9.6 - - - +
266B GLU 3.4 13.7 - - - +
268B ALA* 1.3 75.5 - - - +
270B PRO* 1.3 72.2 - - + +
272B ALA* 2.8 14.2 + - - +
273B VAL* 2.9 28.9 + - + +
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Residues in contact with PRO 270 (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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232B PHE* 5.1 1.1 - - + -
234B VAL* 5.2 4.0 - - + -
266B GLU 3.6 6.7 - - - +
267B ASP* 3.4 16.6 - - - +
269B VAL* 1.3 95.9 - - + +
271B PHE* 1.3 61.0 + - - +
273B VAL* 3.4 5.9 + - + +
274B ALA* 2.9 24.4 + - - +
295B GLN* 2.9 32.8 - - - +
298B LEU* 4.3 10.0 - - + +
299B GLN* 4.8 10.1 - - + +
302B ILE* 4.6 21.5 - - + -
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.2 7.4 - - + -
254B GLY* 3.1 33.9 - - - -
257B ALA* 4.1 9.4 - - + -
258B ALA* 3.8 10.5 - - + -
263B LYS* 3.8 24.2 - - - +
267B ASP 4.7 0.4 + - - +
268B ALA* 3.2 10.2 + - - +
269B VAL 3.1 0.6 - - - -
270B PRO* 1.3 80.7 - - - +
272B ALA* 1.3 57.3 + - - +
274B ALA* 3.3 6.9 + - - +
275B ALA* 3.0 22.9 + - - +
288B ARG* 2.8 50.5 - - - -
291B VAL* 3.4 31.3 - - + +
292B GLU* 4.4 9.6 - - + -
295B GLN* 4.0 19.5 + - + +
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Residues in contact with ALA 272 (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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215B LEU* 5.0 7.9 - - + -
251B VAL* 3.1 42.0 - - + +
254B GLY* 4.0 2.7 - - - -
255B PHE* 3.4 30.5 - - + +
268B ALA 3.1 7.1 + - - +
269B VAL* 2.8 13.9 + - - +
271B PHE* 1.3 68.8 - - - +
273B VAL* 1.3 65.0 + - - +
274B ALA 3.0 1.8 - - - -
275B ALA* 3.2 1.7 + - - +
276B GLY 3.1 17.3 + - - -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.9 11.2 - - + -
223B ALA* 4.7 20.0 - - + -
234B VAL* 4.7 10.8 - - + +
235B ASN 4.6 5.4 - - - +
236B VAL* 4.7 11.4 - - + -
237B PRO* 4.6 7.4 - - + -
251B VAL* 4.6 7.2 - - + -
269B VAL* 2.9 33.1 + - + +
270B PRO* 3.9 1.8 - - + +
272B ALA* 1.3 75.9 - - - +
274B ALA* 1.3 60.1 + - - +
276B GLY* 3.4 1.0 + - - -
277B SER* 3.0 27.6 + - - +
298B LEU* 3.4 24.9 - - + -
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Residues in contact with ALA 274 (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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270B PRO 2.9 18.5 + - - +
271B PHE 3.3 1.3 - - - +
272B ALA 3.0 0.2 - - - -
273B VAL* 1.3 75.9 - - - +
275B ALA* 1.3 64.5 + - - +
277B SER* 3.9 4.6 + - - -
278B ALA* 3.0 27.4 + - - +
291B VAL* 3.3 35.2 - - + +
294B LEU* 4.4 8.2 - - + +
295B GLN* 3.8 15.0 - - + +
298B LEU* 4.1 5.8 - - + +
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Residues in contact with ALA 275 (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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45B VAL* 5.4 0.2 - - + -
49B LEU* 4.8 5.6 - - + -
250B SER* 3.3 24.5 - - - +
254B GLY* 4.1 11.0 - - - -
271B PHE 3.0 13.5 + - - +
272B ALA 3.2 5.3 + - - +
274B ALA* 1.3 75.6 - - - +
276B GLY* 1.3 62.3 + - - +
278B ALA* 4.4 0.2 - - - -
279B THR* 3.1 28.6 + - - -
286B CYS* 3.4 17.0 - - - -
291B VAL* 3.3 15.0 - - + +
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Residues in contact with GLY 276 (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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247B ALA* 3.7 19.1 - - - +
250B SER* 4.0 0.7 - - - -
251B VAL* 3.5 26.6 - - - +
272B ALA 3.1 9.9 + - - -
273B VAL 3.4 2.0 + - - -
274B ALA 3.1 0.4 - - - -
275B ALA* 1.3 78.6 - - - +
277B SER* 1.3 56.7 + - - +
279B THR* 3.4 4.2 + - - -
280B ALA* 3.2 23.6 + - - +
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Residues in contact with SER 277 (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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236B VAL* 3.8 14.8 - - - +
237B PRO* 2.9 41.8 - - - +
273B VAL 3.0 14.2 + - - -
274B ALA 3.9 1.7 + - - -
276B GLY* 1.3 72.5 - - - +
278B ALA* 1.3 60.0 + - - +
279B THR 3.2 0.9 - - - -
280B ALA* 3.6 8.3 - - - -
281B PHE* 2.8 48.5 + - - -
294B LEU* 4.8 0.4 - - - -
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Residues in contact with ALA 278 (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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274B ALA 3.0 20.6 + - - +
275B ALA* 4.0 1.8 - - - +
276B GLY 3.3 0.2 - - - -
277B SER* 1.3 78.1 + - - +
279B THR* 1.3 59.9 + - - +
281B PHE* 3.9 5.0 + - - +
282B SER* 3.2 23.7 + - - -
286B CYS* 3.5 20.0 - - + +
290B GLU* 3.3 27.2 - - + +
291B VAL 4.5 5.6 - - - +
294B LEU* 4.3 15.7 - - + +
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Residues in contact with THR 279 (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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243B ASN* 4.1 7.6 - - - +
244B SER 5.9 0.4 - - - -
245B VAL 4.7 4.3 - - - +
246B GLY 3.7 26.7 - - - +
247B ALA* 4.1 3.6 - - + +
250B SER* 2.7 21.2 + - - +
275B ALA 3.1 6.0 + - - -
276B GLY 3.6 4.5 - - - -
277B SER 3.2 0.2 - - - -
278B ALA* 1.3 80.3 - - - +
280B ALA* 1.3 63.0 + - - +
282B SER 3.3 12.8 + - - +
284B GLY 3.4 14.0 - - - +
285B PHE* 3.9 17.3 - - + -
286B CYS* 3.0 32.4 + - - +
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Residues in contact with ALA 280 (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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241B VAL* 3.1 22.9 - - + -
242B ARG 2.8 25.6 + - - -
243B ASN 3.2 16.9 + - - +
244B SER* 5.6 0.2 - - - -
247B ALA* 4.6 10.3 - - + -
276B GLY 3.2 16.4 + - - +
277B SER* 3.7 10.3 - - - +
279B THR* 1.3 75.7 - - - +
281B PHE* 1.3 59.5 + - + +
282B SER 2.8 8.3 + - - -
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 4.9 3.4 - - + -
237B PRO* 3.3 26.0 - - + -
238B SER* 3.3 17.9 - - - -
239B GLY* 3.1 42.6 - - - -
240B GLU 3.3 27.0 - - - +
241B VAL* 4.0 6.5 - - + -
242B ARG* 4.1 10.0 - - - -
277B SER* 2.8 35.8 + - - +
278B ALA* 3.9 4.2 + - - +
279B THR 3.4 0.4 - - - -
280B ALA* 1.3 78.2 - - + +
282B SER* 1.3 63.3 + - - +
290B GLU* 6.0 0.2 - - - +
293B ARG* 6.2 0.2 - - - -
294B LEU* 4.1 13.5 - - + -
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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