Contacts of the helix formed by residues 256 - 273 (chain A) in PDB entry 1B3U
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 TRP 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LYS 3.5 4.8 + - - -
255A SER* 1.3 71.4 + - - +
257A ARG* 1.3 78.3 + - + +
259A ARG* 3.3 21.0 + - - +
260A TYR* 2.7 50.0 + + + +
294A GLU* 3.6 44.8 + - + -
296A GLU* 3.7 47.3 + - + -
297A VAL* 3.6 7.0 - - + +
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Residues in contact with ARG 257 (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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217A ASP* 4.9 17.3 - - + +
218A SER* 4.9 15.9 - - - +
221A LEU* 4.0 29.8 - - + +
255A SER* 3.1 12.0 - - - +
256A TRP* 1.3 114.0 - - + +
258A VAL* 1.3 61.1 + - + +
260A TYR* 3.5 4.9 - - - +
261A MET* 3.2 26.7 + - - +
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Residues in contact with VAL 258 (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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217A ASP* 4.6 3.4 - - - +
220A ARG* 4.2 18.4 - - + +
221A LEU* 4.1 25.6 - - + +
224A VAL* 4.5 8.1 - - + -
250A ALA* 3.8 20.4 - - + +
253A ASP* 3.7 41.5 - - + +
255A SER* 3.1 17.2 + - - +
257A ARG* 1.3 76.2 - - + +
259A ARG* 1.3 65.2 + - - +
261A MET* 3.0 14.8 + - - +
262A VAL* 3.1 11.8 + - - +
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Residues in contact with ARG 259 (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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250A ALA 4.0 9.9 - - - +
251A ALA 3.3 25.8 - - - +
252A GLU* 4.5 2.7 - - - +
253A ASP 2.7 39.0 + - - +
254A LYS* 3.2 21.4 + - - +
255A SER 3.5 1.8 - - - +
256A TRP* 3.3 28.8 + - - +
258A VAL* 1.3 72.5 - - - +
260A TYR* 1.3 68.2 + - - +
262A VAL* 3.0 16.2 + - - +
263A ALA* 3.0 14.0 + - - +
289A LEU* 4.1 11.0 - - + +
292A ASP* 2.6 42.5 + - - +
293A CYS* 4.0 16.6 - - - -
294A GLU* 4.1 1.4 - - - +
297A VAL* 4.4 7.2 - - + -
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Residues in contact with TYR 260 (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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256A TRP* 2.7 40.2 + + + +
257A ARG* 3.5 8.5 - - - +
258A VAL 3.2 0.2 - - - -
259A ARG* 1.3 73.3 - - - +
261A MET* 1.3 73.6 + - - +
263A ALA* 3.1 5.5 + - - +
264A ASP* 2.8 47.8 + - + +
296A GLU* 3.6 36.3 - - + -
297A VAL* 4.0 9.4 - - + +
300A ALA* 3.7 18.6 - - + +
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Residues in contact with MET 261 (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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221A LEU* 3.6 38.4 - - + +
222A LEU* 6.2 2.2 - - + -
224A VAL* 3.7 25.4 - - + +
225A GLU* 5.8 2.2 - - + -
257A ARG 3.4 13.5 - - - +
258A VAL* 3.0 9.7 + - - +
260A TYR* 1.3 97.0 - - - +
262A VAL* 1.3 62.3 + - - +
264A ASP* 3.2 12.5 + - - +
265A LYS* 3.1 50.2 + - + +
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Residues in contact with VAL 262 (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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224A VAL* 4.0 15.5 - - + -
247A LEU* 4.8 9.4 - - + -
250A ALA* 3.8 29.2 - - + +
251A ALA* 3.9 23.8 - - + +
258A VAL 3.1 12.7 + - - +
259A ARG* 3.0 9.8 + - - +
261A MET* 1.3 75.1 - - - +
263A ALA* 1.3 62.8 + - - +
265A LYS 3.2 3.8 + - - -
266A PHE* 3.1 42.1 + - + -
269A LEU* 3.8 11.8 - - + +
289A LEU* 4.3 8.7 - - + -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG 3.0 10.8 + - - +
260A TYR 3.5 7.4 - - - +
262A VAL* 1.3 77.6 - - - +
264A ASP* 1.3 63.1 + - - +
265A LYS 3.1 1.0 + - - -
266A PHE* 3.2 17.7 + - - +
286A PHE* 6.2 0.9 - - + -
289A LEU* 4.2 19.3 - - + -
297A VAL* 4.5 10.1 - - + +
300A ALA* 3.9 19.9 - - + +
301A ALA* 4.1 15.0 - - + +
304A LYS* 3.6 15.2 - - - +
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Residues in contact with ASP 264 (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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260A TYR* 2.8 42.0 + - + +
261A MET* 3.2 17.2 + - - +
263A ALA* 1.3 73.7 - - - +
265A LYS* 1.3 73.7 + - - +
266A PHE 3.6 0.2 - - - -
268A GLU* 4.4 3.8 - - - +
300A ALA* 4.6 6.5 - - + +
304A LYS* 3.1 24.7 + - - +
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Residues in contact with LYS 265 (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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224A VAL* 4.1 22.0 - - + -
225A GLU* 2.7 43.3 + - - +
228A VAL* 4.5 14.6 - - + -
261A MET* 3.1 37.2 + - + +
262A VAL 3.5 3.6 - - - +
263A ALA 3.1 0.6 - - - -
264A ASP* 1.3 88.7 + - - +
266A PHE* 1.3 65.8 + - - +
267A THR 3.3 2.6 + - - -
268A GLU* 3.3 28.3 + - - +
269A LEU* 3.0 22.8 + - + +
304A LYS* 5.0 0.2 - - - +
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Residues in contact with PHE 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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262A VAL* 3.1 24.2 + - + -
263A ALA* 3.2 14.3 + - - +
264A ASP 3.6 0.8 - - - -
265A LYS* 1.3 77.6 - - - +
267A THR* 1.3 53.2 + - + +
269A LEU* 3.3 9.0 + - + +
270A GLN* 2.7 34.1 + - - +
282A LEU* 3.4 44.8 - - + +
285A ALA* 4.3 5.8 - - + -
286A PHE* 3.8 28.5 - + + -
289A LEU* 3.8 25.4 - - + -
304A LYS* 4.5 10.9 - - + +
308A PHE* 3.3 42.4 - + + -
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Residues in contact with THR 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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266A PHE* 1.3 73.1 + - + +
268A GLU* 1.3 70.7 + - - +
270A GLN* 3.2 19.0 + - - +
271A LYS* 2.9 46.0 + - - +
304A LYS* 3.4 27.9 - - + +
307A GLU* 3.1 46.8 + - + +
308A PHE* 4.5 2.9 - - + +
311A ASN* 5.0 2.0 - - - +
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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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225A GLU* 5.1 3.3 - - - +
228A VAL* 4.0 25.1 - - + +
232A GLN* 5.4 4.1 + - - +
264A ASP 4.4 3.5 - - - +
265A LYS* 3.3 40.3 + - - +
267A THR* 1.3 80.9 + - - +
269A LEU* 1.3 61.8 + - - +
271A LYS* 3.3 12.8 + - + +
272A ALA* 2.8 32.7 + - - +
304A LYS* 5.5 0.7 - - - -
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Residues in contact with LEU 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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224A VAL* 4.7 7.6 - - + +
227A CYS* 4.2 15.7 - - + +
228A VAL* 3.7 25.1 - - + -
231A ALA* 6.1 2.0 - - + -
247A LEU* 3.9 40.2 - - + -
262A VAL* 3.8 31.6 - - + +
265A LYS 3.0 21.3 + - - +
266A PHE* 3.5 9.6 - - + +
268A GLU* 1.3 76.0 - - - +
270A GLN* 1.3 65.2 + - - +
272A ALA* 3.3 5.9 + - + +
273A VAL* 2.9 28.6 + - - +
282A LEU* 4.3 9.9 - - + -
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Residues in contact with GLN 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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266A PHE 2.7 12.5 + - - +
267A THR* 3.2 19.7 + - - +
269A LEU* 1.3 77.0 - - - +
271A LYS* 1.3 64.6 + - + +
273A VAL* 3.5 2.9 - - - +
274A GLY* 3.1 20.8 + - - -
278A THR* 3.6 28.4 + - + +
282A LEU* 3.7 13.4 - - + +
307A GLU 4.2 1.0 + - - -
308A PHE* 3.1 59.9 - - + +
311A ASN* 3.6 31.8 - - + +
312A LEU* 3.9 1.4 - - - +
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Residues in contact with LYS 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 THR* 2.9 31.7 + - - +
268A GLU* 3.8 10.9 - - + +
270A GLN* 1.3 77.8 - - + +
272A ALA* 1.3 62.9 + - - +
273A VAL 3.4 0.2 + - - -
274A GLY* 3.6 8.9 + - - -
307A GLU* 5.7 1.6 + - - -
311A ASN* 4.1 28.7 - - + +
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Residues in contact with ALA 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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228A VAL* 4.3 5.8 - - + +
231A ALA* 4.0 30.2 - - + +
232A GLN* 4.0 26.3 - - + +
236A GLN* 4.5 2.3 - - - +
239A LEU* 3.8 11.3 - - - +
268A GLU 2.8 19.5 + - - +
269A LEU* 3.8 6.1 - - - +
271A LYS* 1.3 78.5 - - - +
273A VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 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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231A ALA* 5.5 3.1 - - + -
236A GLN* 2.9 20.1 + - - +
239A LEU* 3.8 10.8 - - + +
243A VAL* 6.3 0.9 - - + -
244A MET* 3.9 15.7 - - + -
247A LEU* 5.5 4.3 - - + -
269A LEU 2.9 16.2 + - - +
270A GLN 3.5 4.5 - - - +
272A ALA* 1.3 77.5 - - - +
274A GLY* 1.3 74.3 + - - +
277A ILE* 3.2 46.1 - - + +
278A THR* 3.5 13.0 - - - +
282A LEU* 3.7 14.8 - - + -
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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