Contacts of the helix formed by residues 265 - 281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU 5.8 0.6 + - - -
264A GLU* 1.3 81.6 - - - +
266A MET* 1.3 59.6 + - - +
267A ASN* 3.1 16.7 + - - +
268A GLU* 2.8 58.6 + - + +
269A ARG* 3.4 6.7 + - - +
315A PRO 5.3 4.0 - - - +
317A GLU* 6.0 1.0 + - - +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.7 28.0 - - + -
232A ILE* 5.5 2.0 - - - -
257A LEU* 3.3 43.7 - - + +
258A CYS* 3.9 7.8 + - - +
260A LEU* 4.8 4.5 + - + +
263A PRO* 3.4 43.2 + - + +
264A GLU 3.3 3.7 - - - +
265A ASP* 1.3 76.6 - - - +
267A ASN* 1.3 58.7 + - - +
269A ARG* 3.2 38.9 + - - +
270A VAL* 3.0 35.3 + - + +
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A CYS* 4.2 9.3 - - - +
265A ASP* 3.6 19.1 + - - +
266A MET* 1.3 78.8 + - - +
268A GLU* 1.3 70.8 + - - +
270A VAL* 4.3 0.2 - - - -
271A LEU* 3.0 28.8 + - - +
311A ALA 4.1 13.0 - - - +
312A LEU* 3.5 29.9 - - + +
315A PRO* 3.8 25.2 - - + +
316A ALA* 4.2 25.5 - - - +
321A PHE* 4.8 9.7 - - + -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 2.8 43.6 + - + +
267A ASN* 1.3 87.2 + - - +
269A ARG* 1.3 55.8 + - - +
271A LEU* 3.3 4.5 + - - +
272A GLU* 2.9 42.9 + - + +
321A PHE* 5.0 16.9 - - + -
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.0 46.3 + - - +
228A THR 4.5 5.3 + - - -
232A ILE* 3.7 38.6 - - + +
264A GLU 5.9 1.3 - - - +
265A ASP 3.4 6.3 + - - +
266A MET* 3.2 37.3 + - - +
268A GLU* 1.3 78.1 - - + +
270A VAL* 1.3 57.2 + - + +
272A GLU* 3.6 14.5 + - - +
273A ALA* 3.0 31.5 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 5.0 8.3 - - + -
236A VAL* 4.5 2.6 - - + +
254A LEU* 4.2 33.7 - - + +
257A LEU* 4.8 3.1 - - + -
258A CYS* 4.0 20.9 - - - +
266A MET* 3.0 25.0 + - + +
267A ASN 3.8 4.9 - - - +
269A ARG* 1.3 73.2 - - + +
271A LEU* 1.3 56.2 + - - +
273A ALA* 3.5 5.7 + - - +
274A MET* 2.7 55.7 + - + +
308A LEU* 4.7 1.6 - - + -
312A LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASN 3.0 19.7 + - - +
268A GLU* 3.3 4.7 + - - +
270A VAL* 1.3 74.0 - - - +
272A GLU* 1.3 57.9 + - - +
274A MET* 3.2 7.8 + - + +
275A THR* 2.5 33.2 + - - -
285A ARG* 3.4 30.5 + - - +
286A PHE* 3.8 30.7 - - + -
312A LEU* 3.9 23.1 - - + +
321A PHE* 3.6 31.9 - - + -
325A ILE* 4.3 7.6 - - + -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU* 2.9 25.7 + - + +
269A ARG* 3.6 16.5 - - - +
271A LEU* 1.3 74.8 - - - +
273A ALA* 1.3 63.3 + - - +
275A THR* 2.9 25.5 + - - -
276A GLU* 3.2 18.8 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE* 4.4 12.1 - - + -
233A LEU* 3.5 44.6 - - + +
236A VAL* 4.3 11.2 - - + +
269A ARG 3.0 14.5 + - - +
270A VAL* 3.8 5.6 - - - +
272A GLU* 1.3 79.3 - - - +
274A MET* 1.3 62.9 + - - +
275A THR 3.2 0.7 + - - -
276A GLU* 3.3 23.7 + - - +
277A ARG 3.8 1.9 + - - -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 3.8 20.6 - - + +
239A MET* 5.2 4.0 - - + +
254A LEU* 4.8 8.7 - - + -
270A VAL* 2.7 35.3 + - + +
271A LEU* 3.4 9.4 - - + +
272A GLU 3.2 0.4 - - - -
273A ALA* 1.3 72.6 - - - +
275A THR* 1.3 62.9 + - - +
277A ARG* 3.2 21.4 - - + +
278A ALA 4.2 0.2 + - - -
285A ARG* 3.6 25.3 - - + +
286A PHE* 3.8 28.3 - - + -
289A LEU* 4.3 10.8 - - - -
308A LEU* 4.8 10.8 - - + -
312A LEU* 3.6 26.2 - - + -
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU 2.5 25.3 + - - -
272A GLU* 2.9 12.0 + - - -
274A MET* 1.3 76.3 - - - +
276A GLU* 1.3 52.3 + - - +
278A ALA* 2.7 20.0 + - + +
279A GLU* 2.5 29.4 - - - +
285A ARG* 3.7 37.6 + - + +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 4.1 21.3 - - + +
272A GLU* 3.2 16.5 + - - +
273A ALA* 3.3 30.9 + - - +
275A THR* 1.3 76.3 - - - +
277A ARG* 1.3 57.2 + - - +
279A GLU* 2.9 25.5 - - - +
280A MET* 3.8 18.1 - - + +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 4.5 1.5 - - + +
236A VAL* 3.6 33.7 + - + +
237A ARG* 4.6 20.1 + - + +
239A MET* 3.3 26.8 + - - +
240A ASP* 5.5 3.4 - - - +
273A ALA 3.8 4.7 + - - +
274A MET* 3.2 20.9 - - - +
275A THR 2.9 1.4 + - - -
276A GLU* 1.3 73.8 - - - +
278A ALA* 1.3 60.5 + - + +
279A GLU 3.0 11.7 + - - -
280A MET* 3.7 32.8 + - + +
281A ASP* 3.7 5.7 + - - +
285A ARG* 5.9 1.8 - - - +
288A PRO* 3.4 34.1 - - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A MET 4.6 0.9 - - - +
275A THR* 2.7 22.3 + - + +
277A ARG* 1.3 73.2 - - + +
279A GLU* 1.3 61.2 + - - +
281A ASP 2.9 12.7 - - - +
282A GLU* 3.2 10.0 - - - +
283A VAL 2.9 28.7 - - - +
284A GLU* 4.0 1.6 - - - +
285A ARG* 3.7 28.5 - - + +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A THR* 2.5 32.7 - - - +
276A GLU* 2.9 21.4 + - - +
277A ARG 3.0 0.4 + - - -
278A ALA* 1.3 81.7 + - + +
280A MET* 1.3 68.6 + - - +
281A ASP 3.1 3.4 + - - -
282A GLU* 3.3 24.8 - - + +
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Residues in contact with MET 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 5.6 0.9 - - - +
233A LEU* 4.3 18.6 - - + -
237A ARG* 3.8 46.7 - - - +
276A GLU* 3.8 20.2 - - + +
277A ARG* 3.9 20.9 - - - +
279A GLU* 1.3 75.7 - - - +
281A ASP* 1.3 59.8 + - - +
282A GLU* 5.4 1.6 - - - +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG 3.7 5.2 + - - +
278A ALA* 2.9 20.4 - - - +
279A GLU 3.4 2.7 - - - -
280A MET* 1.3 77.0 - - - +
282A GLU* 1.3 64.9 + - - +
283A VAL* 3.0 19.7 + - + +
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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