Contacts of the helix formed by residues 228 - 248 (chain A) in PDB entry 2C6E
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LYS 4.2 0.4 + - - -
227A PHE* 1.3 75.3 - - - +
229A GLU* 1.3 63.0 + - - +
230A GLN* 3.0 11.0 + - - +
231A ARG* 2.8 32.7 + - - +
232A THR* 3.1 22.7 + - - -
322A LEU* 4.5 1.3 - - - -
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Residues in contact with GLU 229 (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 ASP* 1.3 74.8 - - - +
230A GLN* 1.3 64.1 + - - +
232A THR* 3.9 0.4 - - - -
233A ALA* 2.9 28.4 + - - +
322A LEU* 4.4 12.5 - - + +
352A THR* 3.3 31.3 + - - +
355A ALA* 4.9 0.6 - - + +
381A TRP* 2.9 37.9 + - + -
385A ASN* 4.0 22.4 + - - +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP* 3.0 9.8 + - - +
229A GLU* 1.3 79.4 - - - +
231A ARG* 1.3 64.1 + - - +
234A THR* 3.0 28.6 + - - +
385A ASN* 3.3 26.1 + - + +
386A SER 5.8 0.2 - - - -
387A SER* 4.1 27.2 + - - +
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 3.0 22.1 + - - -
224A LEU* 4.1 16.6 - - - +
227A PHE* 3.5 38.1 - - + +
228A ASP* 2.8 27.3 + - - +
230A GLN* 1.3 74.7 - - - +
232A THR* 1.3 58.4 + - - +
234A THR* 3.3 6.7 + - - -
235A TYR* 3.0 59.2 + - + -
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Residues in contact with THR 232 (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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227A PHE* 3.6 15.4 - - - +
228A ASP 3.1 17.8 + - - -
229A GLU 3.9 3.4 - - - -
231A ARG* 1.3 76.1 - - - +
233A ALA* 1.3 58.2 + - - +
235A TYR* 3.1 8.8 + - - +
236A ILE* 2.9 33.7 + - + +
318A CYS* 4.0 13.9 - - - -
321A PHE* 3.7 30.6 - - + +
322A LEU* 3.6 23.1 - - + +
381A TRP* 4.0 17.0 - - + -
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Residues in contact with ALA 233 (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 GLU 2.9 19.5 + - - +
230A GLN 3.9 0.2 - - - +
232A THR* 1.3 77.5 - - - +
234A THR* 1.3 60.5 + - - +
236A ILE* 3.6 2.1 + - - +
237A THR* 3.0 27.7 + - - -
381A TRP* 4.3 21.5 - - + -
382A ILE* 4.3 15.8 - - + +
385A ASN* 3.8 28.0 - - + -
386A SER* 3.9 5.9 - - - +
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Residues in contact with THR 234 (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 GLN* 3.0 19.7 + - - +
231A ARG* 3.6 6.3 - - - -
233A ALA* 1.3 76.5 - - - +
235A TYR* 1.3 67.8 + - + +
237A THR* 3.3 4.5 + - - -
238A GLU* 3.2 39.5 + - + +
386A SER* 4.0 10.5 - - - +
387A SER* 3.0 38.4 + - - +
388A LYS 5.2 8.1 - - - +
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Residues in contact with TYR 235 (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 VAL* 4.6 5.8 - - + -
220A GLU* 3.0 27.7 + - - -
227A PHE* 3.6 28.3 - + - -
231A ARG* 3.0 40.0 + - + -
232A THR 3.5 6.5 - - - +
234A THR* 1.3 83.2 - - + +
236A ILE* 1.3 62.8 + - - +
238A GLU* 3.2 9.1 + - - -
239A LEU* 3.1 27.2 + - - +
263A LEU* 3.8 13.8 - - + +
267A GLY 4.1 17.2 + - - -
269A LEU* 3.5 31.4 - - + +
321A PHE* 3.9 28.5 - + + -
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Residues in contact with ILE 236 (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 THR* 2.9 30.6 + - + +
233A ALA* 4.0 5.8 - - - +
235A TYR* 1.3 75.8 - - - +
237A THR* 1.3 57.7 + - - +
239A LEU* 3.5 13.2 + - + +
240A ALA* 3.0 27.5 + - - +
314A LEU* 4.3 21.3 - - + +
317A LEU* 5.0 0.7 - - + -
318A CYS* 3.9 37.0 - - + +
321A PHE* 4.4 14.8 - - + -
358A LEU* 5.0 4.9 - - + -
362A LEU* 6.0 1.3 - - + -
376A VAL* 4.2 16.8 - - + -
381A TRP* 5.2 0.2 - - + -
382A ILE* 4.0 20.9 - - + -
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Residues in contact with THR 237 (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 ALA 3.0 15.3 + - - -
234A THR 3.5 9.6 - - - -
235A TYR 3.2 0.4 - - - -
236A ILE* 1.3 74.5 - - - +
238A GLU* 1.3 67.2 + - + +
240A ALA 3.5 0.5 + - - -
241A ASN* 3.2 36.6 + - - +
376A VAL* 6.5 0.2 - - - -
377A LEU* 3.9 19.8 - - + +
382A ILE* 3.6 20.6 - - - +
386A SER* 3.7 15.5 + - - +
388A LYS* 6.1 4.3 - - - -
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Residues in contact with GLU 238 (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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191A ASN* 3.8 29.2 + - - +
234A THR* 3.2 32.5 + - + +
235A TYR* 3.2 13.3 + - - +
237A THR* 1.3 82.8 - - + +
239A LEU* 1.3 61.1 + - - +
241A ASN* 3.5 8.6 + - - +
242A ALA* 3.1 22.2 + - - +
267A GLY 5.0 1.2 - - - +
268A GLU* 3.8 10.8 - - - +
269A LEU* 2.9 43.7 + - + +
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Residues in contact with LEU 239 (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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235A TYR 3.1 23.5 + - - +
236A ILE* 3.9 9.4 - - + +
237A THR 3.3 0.2 - - - -
238A GLU* 1.3 74.6 - - - +
240A ALA* 1.3 54.7 + - - +
242A ALA* 3.2 4.4 + - - +
243A LEU* 2.7 43.5 + - + +
256A ILE* 3.7 25.6 - - + -
261A LEU* 4.1 16.8 - - + -
269A LEU* 4.0 18.8 - - + -
271A ILE* 4.1 11.7 - - + -
314A LEU* 4.0 21.3 - - + -
317A LEU* 3.4 32.1 - - + -
321A PHE* 4.8 2.7 - - + -
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Residues in contact with ALA 240 (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 ILE 3.0 18.3 + - - +
237A THR 4.0 0.2 - - - +
239A LEU* 1.3 75.8 - - - +
241A ASN* 1.3 63.7 + - - +
243A LEU* 3.4 8.3 + - - +
244A SER* 2.9 25.9 + - - -
314A LEU* 4.6 8.3 - - + +
373A LEU* 4.0 22.6 - - + +
376A VAL* 4.7 6.1 - - + -
377A LEU* 3.7 30.7 - - + -
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Residues in contact with ASN 241 (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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189A HIS* 4.2 16.2 - - + +
191A ASN* 4.8 4.4 - - - +
237A THR* 3.2 30.1 + - - +
238A GLU* 3.7 9.5 - - - +
240A ALA* 1.3 78.9 - - - +
242A ALA* 1.3 62.3 + - - +
244A SER* 3.1 8.9 + - - -
245A TYR* 3.1 22.5 + - - +
377A LEU* 3.8 19.6 - - - +
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Residues in contact with ALA 242 (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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189A HIS* 3.8 15.4 + - + -
191A ASN* 4.0 20.9 - - + +
192A ILE* 4.3 5.5 - - + +
238A GLU 3.1 14.4 + - - +
239A LEU* 3.2 4.9 + - - +
241A ASN* 1.3 80.2 - - - +
243A LEU* 1.3 61.6 + - - +
245A TYR* 3.4 3.5 + - - +
246A CYS* 3.1 28.3 + - - -
271A ILE* 3.8 23.6 - - + -
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Residues in contact with LEU 243 (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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239A LEU* 2.7 26.5 + - + +
240A ALA* 3.9 4.0 - - - +
242A ALA* 1.3 70.4 - - - +
244A SER* 1.3 60.1 + - - +
246A CYS* 3.3 5.8 + - + +
247A HIS* 3.0 39.2 + - + +
253A HIS* 4.0 26.2 - - + -
256A ILE* 4.8 14.4 - - + -
271A ILE* 4.8 7.0 - - + -
310A ASP* 4.2 35.9 - - + +
313A SER* 6.4 0.2 - - - -
314A LEU* 3.9 31.4 - - + -
373A LEU* 4.0 13.7 - - + -
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Residues in contact with SER 244 (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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240A ALA 2.9 19.0 + - - -
241A ASN* 3.4 8.5 - - - -
243A LEU* 1.3 73.7 - - - +
245A TYR* 1.3 64.3 - - - +
247A HIS* 3.4 4.5 + - - +
248A SER* 3.2 22.3 + - - -
373A LEU* 3.6 20.2 - - - +
377A LEU* 5.8 4.0 - - - -
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Residues in contact with TYR 245 (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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186A HIS 3.9 5.5 + - - -
187A LEU* 3.6 20.9 - - + -
188A ARG* 3.1 40.1 + - - +
189A HIS* 3.9 28.3 - + + +
192A ILE* 4.0 16.4 - - + -
241A ASN 3.1 11.7 + - - +
242A ALA 3.7 6.1 - - - +
243A LEU 3.3 0.2 - - - -
244A SER* 1.3 76.2 - - - +
246A CYS* 1.3 65.4 + - - +
248A SER* 2.6 24.4 + - - -
249A LYS* 3.3 49.9 + - + +
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Residues in contact with CYS 246 (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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187A LEU* 4.9 5.8 - - - -
192A ILE* 3.6 24.0 - - - -
242A ALA 3.1 20.1 + - - -
243A LEU* 3.6 11.2 - - + +
244A SER 3.2 0.2 - - - -
245A TYR* 1.3 80.2 - - - +
247A HIS* 1.3 56.2 + - + +
249A LYS* 2.7 25.5 + - - +
251A VAL* 3.0 44.8 + - + +
253A HIS* 3.9 26.7 - - + +
271A ILE* 5.7 1.3 - - - -
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Residues in contact with HIS 247 (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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243A LEU* 3.0 22.2 + - + +
244A SER* 3.4 5.8 + - - +
246A CYS* 1.3 76.6 - - + +
248A SER* 1.3 59.0 + - - +
250A ARG* 3.0 20.5 + - - +
251A VAL 3.7 16.2 - - - +
252A ILE* 4.3 5.6 - - + +
307A GLU* 2.9 51.9 + - + +
310A ASP* 2.5 35.5 + - + -
311A LEU* 5.1 0.7 - - + -
373A LEU* 3.9 21.7 - - + +
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Residues in contact with SER 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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244A SER 3.2 11.7 + - - -
245A TYR* 2.6 26.5 + - - -
247A HIS* 1.3 76.9 - - - +
249A LYS* 1.3 73.4 + - - +
250A ARG* 3.4 4.4 - - - +
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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
------------------------------------------------------------
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