Contacts of the helix formed by residues 233 - 251 (chain E) in PDB entry 4CDC
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 SER 233 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E GLN* 3.6 5.5 - - - +
231E CYS* 2.9 21.4 + - - -
232E GLY* 1.3 72.1 - - - +
234E CYS* 1.3 65.3 + - - +
235E TYR* 3.2 10.1 - - - -
236E SER* 2.8 19.8 + - - -
237E PHE* 3.3 22.0 + - - -
265E VAL* 3.7 21.5 - - - -
273E GLY 4.6 0.2 - - - -
300E TYR* 2.7 24.0 + - - -
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Residues in contact with CYS 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E GLN* 3.6 18.0 - - - +
232E GLY* 4.9 5.4 - - - -
233E SER* 1.3 75.4 - - - +
235E TYR* 1.3 70.2 + - - +
237E PHE* 3.1 5.2 + - - +
238E ALA* 2.9 30.1 + - - +
276E GLY* 6.1 1.1 - - - -
277E GLY 5.9 0.7 - - - -
380F ASN 4.3 6.3 - - - -
381F HIS* 3.3 39.3 - - + +
382F ALA* 3.5 28.3 - - - +
404F SER* 4.4 4.0 + - - +
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Residues in contact with TYR 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E GLY 3.5 13.5 - - - -
233E SER* 3.9 6.5 - - - -
234E CYS* 1.3 84.5 - - - +
236E SER* 1.3 75.4 + - - +
238E ALA* 4.1 1.0 - - - +
239E SER* 3.1 30.3 + - - -
264E VAL* 3.9 9.7 + - + +
265E VAL* 4.2 10.8 - - + +
271E ALA* 3.5 26.8 - - + +
273E GLY* 2.9 38.2 + - - -
276E GLY* 3.3 15.7 - - - -
277E GLY 3.2 37.5 - - - +
278E PHE 4.7 0.2 - - - -
279E PRO* 3.9 12.7 - - + +
282E ILE* 3.8 24.5 - - + -
382F ALA* 3.7 13.9 - - + -
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Residues in contact with SER 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E SER* 2.8 17.8 + - - -
235E TYR* 1.3 96.7 - - - +
237E PHE* 1.3 56.2 - - - +
239E SER* 3.5 5.1 - - - -
240E MET* 2.9 35.5 + - - +
261E PRO* 3.0 36.4 + - - +
264E VAL* 3.2 20.1 - - - +
265E VAL* 4.5 1.6 - - - -
282E ILE* 5.0 0.2 - - - -
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Residues in contact with PHE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E ARG* 3.7 39.5 - - + -
227E ASN 4.0 7.0 - - - -
228E GLN* 3.7 14.6 - - + -
233E SER* 3.3 34.5 - - - -
234E CYS 3.1 7.2 + - - +
236E SER* 1.3 78.4 - - - +
238E ALA* 1.3 60.3 + - - +
240E MET* 4.0 5.6 - - + +
241E GLY* 3.0 25.8 + - - -
261E PRO* 3.8 24.9 - - + -
300E TYR* 3.7 37.2 - + - -
384F LEU* 5.8 0.2 - - - +
402F LYS* 5.7 1.0 + - - -
404F SER* 3.9 25.8 - - - -
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Residues in contact with ALA 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E CYS 2.9 15.7 + - - +
235E TYR 4.1 1.1 - - - +
237E PHE* 1.3 77.2 - - - +
239E SER* 1.3 63.9 + - - +
242E MET* 3.0 21.7 + - - +
279E PRO* 4.8 0.4 - - + -
347E ALA* 4.3 10.4 - - + +
382F ALA* 3.7 24.2 + - + +
383F VAL* 3.7 28.0 - - - +
384F LEU* 3.7 13.7 - - - +
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E TYR 3.1 21.7 + - - -
236E SER 3.5 4.5 - - - -
238E ALA* 1.3 72.8 - - - +
240E MET* 1.3 78.8 + - - +
242E MET* 3.4 6.8 + - - +
243E LEU* 3.3 27.5 + - - +
279E PRO* 3.3 18.0 - - - +
282E ILE* 3.6 5.8 - - - +
283E ALA* 3.3 34.1 + - - +
347E ALA* 4.7 2.4 - - - +
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Residues in contact with MET 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E SER 2.9 26.2 + - - +
237E PHE* 4.0 5.6 - - - +
238E ALA 3.4 0.2 - - - -
239E SER* 1.3 88.5 - - - +
241E GLY* 1.3 53.1 + - - +
243E LEU* 3.2 3.9 + - + +
244E GLU* 2.8 53.6 + - - +
259E LEU* 3.6 35.8 - - + +
260E SER 3.9 11.4 - - - +
261E PRO* 3.9 17.9 - - + -
264E VAL* 4.0 9.0 - - + -
282E ILE* 3.9 16.6 - - + -
292E LEU* 3.7 28.0 - - + -
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Residues in contact with GLY 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E SER* 4.3 6.2 + - - -
237E PHE 3.0 18.1 + - - -
238E ALA 3.8 1.1 - - - -
240E MET* 1.3 74.2 - - - +
242E MET* 1.3 63.0 + - - +
244E GLU* 3.9 13.7 - - - +
245E ALA* 3.0 25.6 + - - +
384F LEU* 3.5 17.6 - - - +
402F LYS* 4.6 6.1 - - - -
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Residues in contact with MET 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E ALA 3.0 12.1 + - - +
239E SER 3.8 1.6 - - - +
240E MET 3.3 0.2 - - - -
241E GLY* 1.3 75.4 - - - +
243E LEU* 1.3 61.0 + - + +
245E ALA* 3.9 1.9 - - - +
246E ARG* 3.0 39.8 + - - +
283E ALA* 3.4 32.8 - - + -
345E PRO 3.3 13.9 - - - +
346E MET* 3.7 12.1 - - - -
347E ALA* 4.1 13.5 - - + +
384F LEU* 3.5 20.7 - - + +
431F VAL* 3.5 30.1 - - + +
432F ALA* 4.0 1.6 - - - -
433F ALA* 3.6 26.9 - - + +
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Residues in contact with LEU 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E SER 3.4 14.4 - - - +
240E MET 3.2 7.0 + - - +
242E MET* 1.3 78.8 - - + +
244E GLU* 1.3 60.0 + - - +
247E ILE* 2.9 38.4 + - + +
259E LEU* 4.0 10.3 - - + -
283E ALA* 4.0 20.0 - - + +
287E ALA* 4.3 0.4 - - + -
292E LEU* 3.3 32.5 - - + -
317E TYR 6.3 0.2 - - - -
318E SER* 3.8 18.6 - - - +
433F ALA* 4.0 22.4 - - + +
435F PRO* 3.7 28.8 - - + +
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Residues in contact with GLU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E SER* 2.5 43.1 + - - +
224E PRO 5.3 0.3 - - - +
226E ARG* 5.3 6.8 + - - -
240E MET* 2.8 36.3 + - - +
241E GLY* 3.9 5.7 - - - +
243E LEU* 1.3 72.9 - - - +
245E ALA* 1.3 63.4 + - - +
247E ILE* 3.5 9.5 + - - +
248E ARG* 3.2 27.7 + - - +
257E PRO* 3.5 22.1 - - - +
258E ILE* 3.6 14.4 - - - +
259E LEU* 2.9 41.7 + - + +
402F LYS* 4.8 0.9 + - - -
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Residues in contact with ALA 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E PHE 3.3 20.9 - - - +
222E VAL* 4.3 9.6 - - + +
223E SER* 5.0 0.9 + - - +
241E GLY 3.0 19.5 + - - +
242E MET 3.9 1.8 - - - +
244E GLU* 1.3 77.1 - - - +
246E ARG* 1.3 57.6 + - - +
248E ARG* 3.2 5.8 + - - +
249E ILE* 3.0 31.7 + - - +
345E PRO* 3.7 29.8 - - + -
384F LEU* 4.9 2.2 - - + -
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Residues in contact with ARG 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E MET* 3.0 30.9 + - - +
244E GLU 3.3 0.2 - - - -
245E ALA* 1.3 73.4 - - - +
247E ILE* 1.3 61.0 + - - +
249E ILE* 3.8 5.7 - - + +
250E LEU* 2.9 37.5 + - + +
339E GLU* 2.8 38.1 + - - +
343E HIS* 3.5 28.6 + - - +
344E GLY* 2.8 26.3 + - - -
345E PRO 2.8 19.5 + - - +
346E MET* 4.0 6.3 - - - +
432F ALA* 4.0 1.6 - - - +
433F ALA 3.0 37.5 + - - +
434F THR* 4.4 6.6 + - - +
435F PRO* 3.6 20.0 - - + -
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Residues in contact with ILE 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E LEU 2.9 26.7 + - - +
244E GLU* 3.6 5.8 - - - +
246E ARG* 1.3 76.3 - - - +
248E ARG* 1.3 55.9 + - - +
250E LEU* 3.5 5.2 + - - -
251E THR* 2.7 35.3 + - - +
255E GLN* 3.8 22.4 - - + +
257E PRO* 3.7 39.7 - - + -
259E LEU* 4.6 9.4 - - + -
316E TYR* 4.0 24.5 - - + -
435F PRO* 3.7 20.9 - - + -
437F PRO* 4.6 15.7 - - + -
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Residues in contact with ARG 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ASN* 4.2 14.5 + - - +
221E PHE* 3.0 27.6 - - + +
222E VAL 4.0 9.8 + - - -
223E SER* 3.8 30.7 - - - +
224E PRO* 4.0 11.1 - - - +
244E GLU 3.2 16.5 + - - +
245E ALA* 3.4 7.6 - - - +
246E ARG 3.2 0.2 - - - -
247E ILE* 1.3 73.5 - - - +
249E ILE* 1.3 64.4 + - - +
251E THR* 3.4 1.1 + - - -
252E ASN* 3.0 5.5 + - - -
253E ASN* 2.9 53.5 + - - +
255E GLN 3.5 19.3 - - - +
256E THR* 3.9 33.4 + - + +
257E PRO 5.2 1.6 + - - -
258E ILE* 4.7 3.6 - - - +
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Residues in contact with ILE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E TRP* 3.7 36.1 - - + -
221E PHE* 3.9 21.0 - - + -
245E ALA 3.0 19.5 + - - +
246E ARG* 3.3 7.2 + - - +
248E ARG* 1.3 74.2 - - - +
250E LEU* 1.3 69.3 + - + +
251E THR 3.1 1.4 + - - -
252E ASN* 3.2 7.4 + - - -
343E HIS 4.5 7.4 - - - +
344E GLY* 3.7 13.2 - - - -
345E PRO* 3.5 31.2 - - + -
206K HIS* 3.0 25.9 + - + +
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Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.3 16.5 - - - +
56A ASN* 4.1 16.9 + - - +
246E ARG* 2.9 27.6 + - + +
247E ILE 3.9 3.6 - - - +
249E ILE* 1.3 80.8 - - + +
251E THR* 1.3 57.7 + - - +
252E ASN 3.6 0.2 - - - -
434F THR* 4.7 11.0 - - + -
435F PRO* 3.5 34.5 - - + +
437F PRO* 4.2 18.2 - - + -
206K HIS* 3.4 12.3 + - - +
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Residues in contact with THR 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.7 15.1 - - + +
247E ILE 2.7 22.7 + - - +
248E ARG 3.6 2.9 + - - -
249E ILE 3.2 0.2 - - - -
250E LEU* 1.3 80.7 - - - +
252E ASN* 1.3 68.1 + - - +
254E SER* 2.9 29.4 + - - -
255E GLN* 3.3 48.1 + - + +
437F PRO* 3.8 20.0 - - + -
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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