Contacts of the helix formed by residues 247 - 261 (chain A) in PDB entry 1W57
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.3 20.8 + - - +
229A LEU* 3.3 3.6 - - - -
230A ALA 2.7 21.4 + - - -
231A GLY* 2.6 32.2 + - - -
245A ASP* 3.2 18.5 + - - +
246A GLY* 1.3 70.9 - - - +
248A VAL* 1.3 65.0 + - - +
249A LEU 3.6 0.7 + - - -
250A ALA* 3.0 24.0 + - + +
251A HIS* 3.1 27.6 + - - -
282A SER* 3.6 15.6 + - - -
283A MET* 4.3 2.9 - - - +
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Residues in contact with VAL 248 (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* 3.7 31.2 - - - +
219A HIS* 3.2 37.2 - - + +
229A LEU* 3.6 16.7 - - + +
240A LEU* 3.3 27.8 - - + -
246A GLY 2.8 4.0 + - - -
247A ASP* 1.3 67.9 - - - +
249A LEU* 1.3 67.3 + - - +
251A HIS* 3.5 0.9 + - - +
252A SER* 3.0 23.4 + - - -
355A MET* 3.8 18.8 - - + +
357A VAL* 3.8 9.3 - - + +
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Residues in contact with LEU 249 (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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229A LEU* 4.1 9.2 - - + +
230A ALA* 3.7 33.4 - - + +
247A ASP* 3.2 9.3 + - - +
248A VAL* 1.3 79.6 - - - +
250A ALA* 1.3 70.2 + - - +
252A SER* 2.9 14.0 + - - -
253A LEU* 2.9 17.0 + - + +
283A MET* 5.7 0.4 - - - -
305A ILE* 3.9 43.3 - - + -
307A VAL* 4.4 6.3 - - + -
321A MET* 4.2 11.2 - - - -
325A ILE* 4.0 5.8 - - + -
338A VAL* 4.2 20.0 - - + -
357A VAL* 3.8 14.5 - - + +
359A SER* 4.5 0.3 + - - -
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Residues in contact with ALA 250 (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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247A ASP* 3.0 28.8 + - + +
249A LEU* 1.3 85.8 - - - +
251A HIS* 1.3 59.1 + - - +
253A LEU* 3.6 3.8 + - - +
254A THR* 2.9 32.2 + - - -
282A SER* 3.9 17.7 - - - +
283A MET* 3.8 23.1 - - - -
286A LEU* 4.0 6.2 - - + +
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Residues in contact with HIS 251 (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* 3.8 8.2 - - - +
219A HIS* 3.5 6.1 + - - -
243A HIS* 3.3 28.1 - + - -
244A SER* 3.3 10.8 + - - -
246A GLY 4.6 0.4 - - - -
247A ASP 3.1 20.8 + - - +
248A VAL 4.2 0.4 - - - +
250A ALA* 1.3 75.7 - - - +
252A SER* 1.3 67.1 + - - +
254A THR* 3.6 1.7 - - - -
255A ASP* 3.1 25.8 + - - +
266A ILE* 3.9 31.7 - - + +
282A SER* 2.6 35.1 + - - -
285A LEU* 5.4 5.9 - - + +
1371A ZN 2.5 32.5 - - - -
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Residues in contact with SER 252 (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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215A GLY* 2.9 22.7 + - - -
216A PHE 4.9 0.2 - - - -
217A ASP* 4.2 13.0 - - - +
248A VAL 3.0 17.4 + - - -
249A LEU 2.9 4.8 + - - -
251A HIS* 1.3 79.9 - - - +
253A LEU* 1.3 62.4 + - - +
255A ASP* 3.3 6.5 + - - +
256A ALA 3.2 15.8 + - - -
357A VAL* 2.8 35.4 + - - -
359A SER* 3.0 13.8 + - - -
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Residues in contact with LEU 253 (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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249A LEU* 2.9 19.9 + - + +
250A ALA 3.9 3.1 - - - +
252A SER* 1.3 75.0 - - - +
254A THR* 1.3 65.5 + - - +
256A ALA* 3.0 3.5 + - - +
257A ILE* 2.9 40.7 + - + +
286A LEU* 3.9 19.5 - - + -
303A ILE* 3.8 31.9 - - + -
305A ILE* 4.2 11.4 - - + -
325A ILE* 3.9 31.0 - - + -
329A LEU* 4.3 0.7 - - + -
359A SER* 3.2 15.0 + - - +
361A VAL* 3.9 11.4 - - + -
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Residues in contact with THR 254 (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 2.9 22.9 + - - -
251A HIS* 3.6 5.1 - - - -
253A LEU* 1.3 77.8 - - - +
255A ASP* 1.3 62.5 + - - +
257A ILE* 3.2 3.9 + - - +
258A LEU* 2.9 45.7 + - + +
266A ILE* 3.4 28.6 - - + +
270A TYR* 5.3 2.7 - - + -
282A SER 4.9 0.7 + - - -
285A LEU* 5.0 1.9 - - - +
286A LEU* 3.2 33.8 + - - +
289A ALA* 3.9 15.0 - - + +
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Residues in contact with ASP 255 (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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214A ASN 4.0 3.9 - - - +
215A GLY* 4.0 11.7 - - - -
216A PHE 4.1 14.7 + - - +
217A ASP* 5.0 4.0 - - - +
251A HIS 3.1 9.3 + - - +
252A SER* 3.4 10.1 - - - +
254A THR* 1.3 77.4 - - - +
256A ALA* 1.3 58.4 + - - +
258A LEU* 3.1 5.3 + - - +
259A GLY* 2.7 30.3 + - - -
264A GLY 4.7 1.2 - - - +
265A ASP* 3.2 14.6 - - - +
266A ILE* 2.6 47.6 + - - +
1372A C5P 5.0 1.2 + - - -
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Residues in contact with ALA 256 (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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213A GLY* 3.7 8.8 - - - +
214A ASN 3.3 28.9 + - - -
215A GLY 3.7 3.1 - - - +
252A SER 3.2 1.6 + - - -
253A LEU 3.0 9.6 + - - +
255A ASP* 1.3 77.4 - - - +
257A ILE* 1.3 62.4 + - - +
260A ALA* 3.1 26.9 + - - +
359A SER* 3.8 21.8 - - - +
361A VAL* 3.8 17.7 - - + +
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Residues in contact with ILE 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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253A LEU* 2.9 42.1 + - + +
254A THR* 3.7 4.9 - - - +
256A ALA* 1.3 77.7 - - - +
258A LEU* 1.3 61.5 + - - +
260A ALA* 3.6 6.3 + - - +
261A ALA* 3.5 10.9 + - - +
286A LEU* 3.9 9.6 - - + -
289A ALA* 4.9 3.4 - - + +
290A TYR* 3.9 26.7 - - + +
293A VAL* 3.6 27.5 - - + +
300A LEU* 3.8 25.4 - - + -
329A LEU* 3.8 28.9 - - + -
361A VAL* 4.3 5.4 - - + -
363A LEU* 4.0 3.0 - - + +
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Residues in contact with LEU 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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254A THR* 2.9 45.6 + - + +
255A ASP* 3.6 3.1 - - - +
257A ILE* 1.3 71.1 - - - +
259A GLY* 1.3 59.7 + - - +
261A ALA* 2.8 19.9 + - - +
263A LEU* 3.0 45.5 + - + +
264A GLY 3.7 13.2 - - - +
265A ASP* 3.7 27.4 - - - +
266A ILE* 3.8 3.6 - - - +
269A LEU* 4.2 19.5 - - + -
289A ALA* 4.2 26.5 - - + +
292A LYS* 5.3 2.0 - - + -
293A VAL* 4.5 2.0 - - + -
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Residues in contact with GLY 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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212A THR 4.5 1.6 - - - +
213A GLY* 4.6 4.7 - - - -
214A ASN 5.2 4.9 - - - -
255A ASP 2.7 18.6 + - - -
256A ALA* 3.9 1.6 - - - -
258A LEU* 1.3 73.0 - - - +
260A ALA* 1.3 59.6 + - - +
262A GLY* 3.3 12.6 + - - -
263A LEU 4.9 0.4 - - - -
264A GLY 3.7 11.6 + - - -
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Residues in contact with ALA 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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211A PHE* 3.7 32.9 - - - +
212A THR 3.4 30.2 - - - +
213A GLY* 3.7 2.1 - - - -
256A ALA 3.1 18.3 + - - +
257A ILE* 3.9 2.0 - - - +
259A GLY* 1.3 75.7 - - - +
261A ALA* 1.3 58.1 + - - +
262A GLY 3.3 0.9 - - - -
298A PHE* 4.8 0.3 - - - -
361A VAL* 5.2 4.3 - - + +
363A LEU* 3.5 27.2 - - + +
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Residues in contact with ALA 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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59A TYR* 4.6 5.4 + - - -
257A ILE 3.5 1.9 + - - +
258A LEU 2.8 6.7 + - - +
260A ALA* 1.3 77.7 - - - +
262A GLY* 1.3 64.9 + - - +
263A LEU* 3.1 19.6 + - + +
293A VAL* 3.5 32.1 - - + -
296A ILE* 3.8 14.8 - - + +
298A PHE* 4.2 12.9 - - + -
363A LEU* 4.0 9.4 - - + -
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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