Contacts of the helix formed by residues 265 - 281 (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 ASP 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU 5.8 1.2 + - - -
263B PRO 3.5 0.6 + - - -
264B GLU* 1.3 83.5 - - - +
266B MET* 1.3 64.6 + - - +
267B ASN* 3.3 10.5 - - - -
268B GLU* 3.2 40.5 + - + +
269B ARG* 3.4 10.0 + - - +
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Residues in contact with MET 266 (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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226B LEU* 4.1 15.3 - - + -
257B LEU* 3.5 31.6 - - + +
258B CYS* 4.4 5.3 + - - +
260B LEU* 4.8 3.5 + - + +
263B PRO* 2.8 58.3 + - + +
264B GLU 4.6 3.8 - - - +
265B ASP* 1.3 74.6 - - - +
267B ASN* 1.3 59.9 + - - +
269B ARG* 3.1 55.5 + - + +
270B VAL* 2.9 31.6 + - + +
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Residues in contact with ASN 267 (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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258B CYS* 3.9 23.8 + - + +
265B ASP* 4.0 10.9 - - - -
266B MET* 1.3 77.7 - - - +
268B GLU* 1.3 61.0 + - - +
270B VAL* 3.3 4.2 - - - +
271B LEU* 2.7 33.3 + - - +
311B ALA 3.8 19.1 - - - +
312B LEU* 2.8 30.3 + - - +
315B PRO* 4.1 16.7 - - + +
316B ALA* 3.7 14.7 + - - +
321B PHE* 3.7 20.6 - - - -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 3.2 36.3 + - + +
266B MET 3.1 0.6 - - - -
267B ASN* 1.3 87.3 + - - +
269B ARG* 1.3 55.0 + - - +
271B LEU* 3.2 7.2 + - - +
272B GLU* 2.8 36.9 + - - +
316B ALA* 5.6 2.3 - - - +
321B PHE* 3.4 36.3 - - + -
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Residues in contact with ARG 269 (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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226B LEU* 3.3 30.2 + - - +
228B THR 4.7 5.5 + - - -
229B GLU 5.8 0.4 + - - -
232B ILE* 3.3 41.9 - - + +
265B ASP 3.4 6.0 + - - +
266B MET* 3.1 49.8 + - + +
268B GLU* 1.3 77.3 - - - +
270B VAL* 1.3 62.0 + - - +
272B GLU* 4.2 15.7 - - - +
273B ALA* 3.2 23.6 + - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 4.3 18.4 - - + -
236B VAL* 4.6 1.0 - - + +
254B LEU* 4.4 31.2 - - + +
257B LEU* 5.0 8.1 - - + -
258B CYS* 3.9 20.4 - - - -
266B MET* 2.9 20.5 + - + +
267B ASN* 3.3 8.7 - - - +
269B ARG* 1.3 74.1 - - + +
271B LEU* 1.3 55.5 + - - +
273B ALA* 2.9 5.0 + - - +
274B MET* 2.7 45.8 + - + +
308B LEU* 5.1 2.0 - - + -
312B LEU* 3.8 18.6 - - + -
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Residues in contact with LEU 271 (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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267B ASN 2.7 17.8 + - - +
268B GLU* 3.5 8.7 - - - +
270B VAL* 1.3 73.3 - - - +
272B GLU* 1.3 55.2 + - - +
274B MET* 2.8 30.2 + - + +
275B THR* 3.0 13.4 + - - -
285B ARG* 3.4 37.7 - - - +
286B PHE* 3.7 23.3 - - + -
312B LEU* 3.9 24.0 - - + +
321B PHE* 4.3 18.6 - - + -
325B ILE* 3.9 24.9 - - + -
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Residues in contact with GLU 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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268B GLU 2.8 18.2 + - - +
269B ARG* 4.2 18.0 - - - +
271B LEU* 1.3 73.3 - - - +
273B ALA* 1.3 58.2 + - - +
275B THR* 3.0 30.5 + - - -
276B GLU* 3.1 23.3 + - + +
285B ARG* 5.8 0.2 - - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 4.2 18.6 - - + -
233B LEU* 4.2 15.3 - - + +
236B VAL* 3.9 16.7 - - + +
269B ARG* 3.2 18.2 + - + +
270B VAL 2.9 5.2 + - - +
272B GLU* 1.3 74.9 - - - +
274B MET* 1.3 64.5 + - - +
275B THR 3.1 1.3 - - - -
276B GLU* 3.5 27.8 + - - +
277B ARG 3.8 7.6 + - - -
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 3.8 23.9 - - + +
239B MET* 4.9 9.4 - - - +
254B LEU* 5.6 0.9 - - + -
270B VAL* 2.7 34.2 + - + +
271B LEU* 2.8 15.1 + - + +
273B ALA* 1.3 71.9 - - - +
275B THR* 1.3 60.3 + - - +
277B ARG* 3.9 6.2 + - - +
278B ALA* 3.4 19.6 + - - +
285B ARG* 3.5 32.0 - - + +
286B PHE* 3.7 27.1 - - + -
288B PRO* 5.0 7.4 - - + -
289B LEU* 4.4 15.9 - - + -
308B LEU* 4.8 10.1 - - + -
312B LEU* 4.0 19.7 - - - -
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Residues in contact with THR 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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271B LEU 3.0 11.9 + - - -
272B GLU* 3.0 19.2 + - - -
274B MET* 1.3 76.6 - - - +
276B GLU* 1.3 63.3 + - - +
278B ALA* 2.8 25.5 + - + +
279B GLU* 3.0 24.0 + - + +
285B ARG* 3.6 27.8 + - - +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.4 32.8 - - + +
272B GLU* 3.1 22.8 + - + +
273B ALA* 3.5 25.2 - - - +
274B MET 3.5 0.6 - - - -
275B THR* 1.3 80.2 - - - +
277B ARG* 1.3 60.9 + - - +
279B GLU* 3.5 15.3 + - - +
280B MET* 3.3 26.6 + - + +
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Residues in contact with ARG 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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233B LEU* 4.2 15.9 - - + +
236B VAL* 3.1 43.4 + - + +
237B ARG* 3.7 25.5 - - + +
239B MET* 3.7 12.9 + - - +
241B PRO* 6.0 0.4 - - - +
273B ALA 3.8 5.4 + - - +
274B MET 4.1 6.1 - - - +
275B THR 3.2 0.4 - - - -
276B GLU* 1.3 74.8 - - - +
278B ALA* 1.3 67.3 + - - +
279B GLU 3.1 2.8 + - - -
280B MET* 3.4 13.8 - - + +
281B ASP* 3.3 27.9 + - - +
285B ARG 6.1 0.2 - - - -
288B PRO* 3.3 42.2 - - - +
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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 MET 3.4 5.0 + - - +
275B THR* 2.8 15.5 + - + +
277B ARG* 1.3 82.2 - - - +
279B GLU* 1.3 55.8 + - + +
281B ASP 2.7 17.9 - - - +
282B GLU* 3.3 2.1 - - - -
283B VAL 2.9 33.3 + - - +
285B ARG* 3.6 30.3 - - + +
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Residues in contact with GLU 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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275B THR* 3.0 36.8 + - + +
276B GLU* 3.6 11.5 - - - +
277B ARG 3.1 0.2 - - - -
278B ALA* 1.3 77.9 - - + +
280B MET* 1.3 68.5 + - - +
281B ASP 3.0 3.0 + - - -
282B GLU* 3.0 27.3 + - + +
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 4.4 17.3 - - + -
237B ARG* 3.6 42.8 - - - +
276B GLU* 3.3 22.2 + - + +
277B ARG* 3.4 17.5 - - - +
279B GLU* 1.3 75.8 - - - +
281B ASP* 1.3 61.7 + - - +
282B GLU* 4.1 2.3 + - - +
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Residues in contact with ASP 281 (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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277B ARG* 3.3 13.0 + - - +
278B ALA* 2.7 11.3 - - - +
279B GLU 3.2 1.6 - - - -
280B MET* 1.3 79.4 - - + +
282B GLU* 1.3 54.6 + - - +
283B VAL* 2.7 32.7 + - + +
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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
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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