Contacts of the helix formed by residues 229 - 249 (chain D) in PDB entry 4C3P
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 229 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU* 5.7 1.9 - - - +
228D PHE* 1.3 76.2 - - - +
230D GLU* 1.3 65.2 + - - +
231D GLN* 3.2 21.8 + - - +
232D ARG* 3.2 37.4 + - - +
233D THR* 3.2 24.8 + - - -
323D LEU* 4.1 1.3 - - - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ASP* 1.3 74.1 - - - +
231D GLN* 1.3 61.4 + - - +
233D THR* 4.1 0.5 - - - -
234D ALA* 3.1 27.9 + - - +
323D LEU* 4.0 16.9 - - + +
353D THR* 2.6 45.9 + - + +
356D ALA* 4.5 1.4 - - - +
382D TRP* 2.8 26.8 + - + -
386D ASN* 3.5 26.4 + - - +
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Residues in contact with GLN 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ASP* 3.2 16.9 + - - +
230D GLU* 1.3 79.6 - - - +
232D ARG* 1.3 61.8 + - - +
235D THR* 2.6 33.5 + - - -
386D ASN* 3.0 29.0 - - + +
388D SER* 3.6 30.0 - - - +
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D GLU* 3.0 25.3 + - - -
225D LEU* 3.1 25.1 - - - +
228D PHE* 3.6 37.5 - - + -
229D ASP* 3.2 27.9 + - - +
231D GLN* 1.3 78.4 + - - +
233D THR* 1.3 61.2 + - - +
235D THR* 3.2 6.5 + - - -
236D TYR* 2.9 52.3 + - + +
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Residues in contact with THR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D PHE* 3.5 7.6 - - - +
229D ASP 3.2 16.0 + - - -
230D GLU 4.1 2.5 - - - -
232D ARG* 1.3 79.2 - - - +
234D ALA* 1.3 57.1 + - - +
235D THR 3.1 0.2 + - - -
236D TYR* 3.4 1.8 + - - +
237D ILE* 2.8 35.0 + - + +
319D CYS* 3.9 27.8 - - - -
322D PHE* 3.3 42.6 - - + +
323D LEU* 3.7 21.3 - - + +
382D TRP* 4.0 4.3 - - + -
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU 3.1 20.0 + - - +
233D THR* 1.3 77.5 - - - +
235D THR* 1.3 56.3 - - - +
237D ILE* 3.6 2.3 + - - +
238D THR* 2.8 32.3 + - - -
382D TRP* 4.0 20.0 - - + -
383D ILE* 3.7 20.7 - - - +
386D ASN* 3.8 6.7 - - + -
387D SER* 3.7 22.9 - - - +
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLN 2.6 22.2 + - - -
232D ARG* 3.2 6.0 + - - -
233D THR 3.1 0.4 - - - -
234D ALA* 1.3 75.8 - - - +
236D TYR* 1.3 71.3 + - + +
238D THR* 3.1 4.3 + - - -
239D GLU* 3.1 46.1 + - - +
387D SER* 3.4 12.8 - - - +
388D SER* 2.8 39.7 + - - +
389D LYS* 4.7 6.7 - - + +
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Residues in contact with TYR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D VAL* 4.3 9.2 - - + -
221D GLU* 2.4 30.7 + - - -
228D PHE* 3.6 32.5 - + - -
232D ARG* 2.9 34.8 + - + +
233D THR 3.6 3.6 - - - +
235D THR* 1.3 80.5 - - + +
237D ILE* 1.3 59.9 + - - +
239D GLU* 3.3 11.5 + - - +
240D LEU* 3.0 33.7 + - - +
264D LEU* 3.6 17.7 - - + +
268D GLY 4.1 17.0 + - - -
270D LEU* 3.6 21.7 - - + +
322D PHE* 4.0 19.5 - + + -
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Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D THR* 2.8 34.2 + - + +
234D ALA* 3.9 5.4 - - - +
236D TYR* 1.3 73.2 - - - +
238D THR* 1.3 58.0 + - - +
240D LEU* 3.8 13.3 - - + +
241D ALA* 3.0 26.7 + - - +
315D LEU* 4.1 19.7 - - + +
318D LEU* 4.5 0.9 - - + -
319D CYS* 4.0 36.8 - - + +
322D PHE* 4.0 17.0 - - + -
359D LEU* 5.2 3.8 - - + -
363D LEU* 6.1 2.0 - - + -
377D VAL* 4.1 18.6 - - + -
383D ILE* 3.9 18.8 - - + -
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ALA 2.8 19.1 + - - -
235D THR 3.1 8.9 + - - -
237D ILE* 1.3 77.0 - - - +
239D GLU* 1.3 59.1 + - + +
241D ALA* 3.3 2.9 + - - +
242D ASN* 3.0 33.1 + - - +
377D VAL* 6.4 0.2 - - - -
378D LEU* 3.7 21.8 - - + -
383D ILE* 3.1 22.5 - - + +
387D SER* 3.5 9.9 + - - -
389D LYS 4.5 2.5 - - - +
390D PRO* 3.7 31.4 - - + +
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Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ASN* 3.2 37.6 + - - +
235D THR* 3.1 42.2 + - - +
236D TYR* 3.8 12.2 - - - +
238D THR* 1.3 75.2 - - + +
240D LEU* 1.3 63.1 + - - +
242D ASN* 4.6 2.2 - - - +
243D ALA* 3.1 24.9 + - - +
268D GLY 4.7 0.2 - - - +
269D GLU* 3.9 8.8 - - - -
270D LEU* 2.9 40.8 + - + +
389D LYS* 5.5 1.4 - - - +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D TYR 3.0 21.2 + - - +
237D ILE* 3.8 15.3 - - + +
239D GLU* 1.3 74.2 - - - +
241D ALA* 1.3 58.3 + - - +
243D ALA* 3.4 3.3 + - - +
244D LEU* 2.8 36.5 + - + +
257D ILE* 4.3 13.7 - - + -
262D LEU* 3.8 33.7 - - + -
270D LEU* 4.5 9.9 - - + -
272D ILE* 3.9 20.4 - - + -
315D LEU* 3.6 19.1 - - + -
318D LEU* 3.7 24.7 - - + -
322D PHE* 4.4 5.6 - - + -
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Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ILE 3.0 19.0 + - - +
238D THR 3.3 3.8 + - - +
240D LEU* 1.3 76.8 - - - +
242D ASN* 1.3 57.3 + - - +
244D LEU* 3.7 1.4 - - - +
245D SER* 2.9 32.7 + - - -
315D LEU* 4.2 14.5 - - + +
374D LEU* 4.0 17.8 - - + +
377D VAL* 4.4 7.9 - - + -
378D LEU* 3.7 24.9 - - + -
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Residues in contact with ASN 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D HIS* 3.8 16.7 + - + +
192D ASN* 4.4 6.0 - - - +
238D THR* 3.0 36.2 + - - +
239D GLU* 4.1 5.6 - - - +
240D LEU 3.3 0.2 - - - -
241D ALA* 1.3 73.0 - - - +
243D ALA* 1.3 65.0 + - - +
245D SER* 3.3 7.3 + - - -
246D TYR* 3.0 23.4 + - - +
378D LEU* 3.4 21.7 - - - +
390D PRO 3.8 11.7 + - - -
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D HIS* 3.6 13.6 - - - -
192D ASN* 3.9 12.1 - - + +
193D ILE* 3.8 17.5 - - + +
239D GLU 3.1 17.1 + - - +
240D LEU 3.8 0.2 - - - +
242D ASN* 1.3 78.8 - - - +
244D LEU* 1.3 57.2 + - - +
246D TYR* 3.5 3.3 + - - +
247D CYS* 3.0 32.2 + - - -
272D ILE* 3.7 25.4 - - + -
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D LEU 2.8 20.9 + - - +
241D ALA 3.7 4.3 - - - +
243D ALA* 1.3 75.0 - - - +
245D SER* 1.3 66.1 + - - +
247D CYS* 3.3 7.5 + - + +
248D HIS* 3.1 32.3 + - - +
254D HIS* 4.1 26.5 - - + -
257D ILE* 4.4 14.8 - - + -
272D ILE* 4.5 10.5 - - + -
311D ASP* 3.7 33.2 - - + +
315D LEU* 3.7 29.2 - - + -
374D LEU* 3.7 20.6 - - + -
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA 2.9 21.9 + - - -
242D ASN* 3.5 10.5 - - - -
244D LEU* 1.3 73.0 - - - +
246D TYR* 1.3 66.0 + - - +
248D HIS* 3.0 6.0 + - - +
249D SER* 2.9 23.8 + - - -
374D LEU* 3.4 24.2 - - - +
378D LEU* 4.3 9.2 - - - +
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Residues in contact with TYR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D HIS 4.5 0.2 + - - -
188D LEU* 3.7 20.0 - - + -
189D ARG* 2.8 49.4 + - - +
190D HIS* 3.6 37.0 - + + +
193D ILE* 4.2 9.2 - - + -
242D ASN 3.0 5.0 + - - +
243D ALA 3.6 6.3 - - - +
245D SER* 1.3 78.2 - - - +
247D CYS* 1.3 69.2 + - - +
249D SER* 2.4 32.3 + - - -
250D LYS* 3.1 41.5 + - + +
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Residues in contact with CYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.3 15.0 - - - -
193D ILE* 3.5 22.9 - - - -
243D ALA 3.0 19.4 + - - +
244D LEU* 3.4 19.7 - - + +
246D TYR* 1.3 80.3 - - - +
248D HIS* 1.3 59.8 + - + +
250D LYS* 3.1 11.5 + - - +
252D VAL* 2.9 47.7 + - + +
254D HIS* 5.3 7.6 - - - +
272D ILE* 5.6 1.6 - - - -
275D PHE* 4.8 7.2 - - - -
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D LEU* 3.1 20.9 + - - +
245D SER* 3.0 9.4 + - - +
247D CYS* 1.3 74.7 - - + +
249D SER* 1.3 54.8 + - - +
250D LYS 2.8 6.1 + - - -
251D ARG* 2.6 26.6 + - - +
252D VAL 3.2 20.6 - - - +
253D ILE* 4.4 3.9 - - + -
308D GLU* 2.9 58.3 + - + +
311D ASP* 2.6 35.1 + - + +
312D LEU* 5.1 0.2 - - + -
374D LEU* 4.1 11.8 - - + +
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Residues in contact with SER 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D SER 2.9 12.2 + - - -
246D TYR* 2.4 34.6 + - - -
248D HIS* 1.3 74.5 - - - +
250D LYS* 1.3 64.1 - - - +
251D ARG* 3.5 3.7 - - - +
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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
------------------------------------------------------------
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