Contacts of the helix formed by residues 241 - 256 (chain C) in PDB entry 2Q41
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 HIS 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C MSE 3.2 46.1 + - + +
55C TRP* 5.3 3.7 - + - -
204C ASP* 5.6 1.0 + - - -
236C GLU* 3.1 40.7 - - + +
237C SER* 2.8 24.0 + - - +
240C LEU* 1.3 104.1 + - + +
242C MSE 1.3 65.2 + - - +
243C ASP* 3.3 9.4 - - - -
244C ILE* 4.0 24.3 - - + +
245C ILE* 2.9 26.9 + - - +
271C PRO* 5.9 1.8 - - - +
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Residues in contact with MSE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 3.1 47.6 - - - +
239C TRP 5.7 0.4 - - - -
240C LEU 3.9 1.2 - - - -
241C HIS* 1.3 75.5 - - - +
243C ASP* 1.3 63.9 + - - +
245C ILE* 3.4 4.6 + - + +
246C GLU* 3.0 24.4 + - - +
324C PHE* 3.7 11.2 - - + +
325C ALA* 3.4 36.8 - - + +
328C VAL* 4.2 17.8 - - + +
329C ILE* 3.8 23.8 - - + -
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C LEU 4.8 1.6 - - - +
241C HIS* 3.8 7.3 - - - -
242C MSE 1.3 80.1 + - - +
244C ILE* 1.3 86.6 + - - +
246C GLU* 3.0 24.6 + - - +
247C ASP* 3.3 13.7 + - - +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C MSE 5.0 15.3 - - + -
205C PRO* 5.2 12.3 - - + -
213C PHE* 5.7 0.9 - - + -
236C GLU* 5.5 4.0 - - + -
241C HIS* 3.8 28.0 - - + +
242C MSE 3.4 0.2 - - - -
243C ASP* 1.3 96.9 - - - +
245C ILE* 1.3 64.0 + - + +
247C ASP* 2.9 23.4 + - + +
248C ILE* 2.9 36.7 + - + +
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ALA* 4.0 13.9 - - + +
236C GLU* 4.6 4.0 - - + -
237C SER 3.5 25.8 - - - +
238C LEU* 3.7 13.2 - - + +
241C HIS* 2.9 30.3 + - + +
242C MSE 3.6 5.8 - - - +
243C ASP 3.3 0.2 - - - -
244C ILE* 1.3 75.6 - - - +
246C GLU* 1.3 56.5 + - - +
248C ILE* 3.7 10.9 - - + +
249C VAL* 2.9 36.5 + - + +
262C TYR* 3.4 38.8 - - + +
329C ILE* 3.6 29.4 - - + -
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C MSE 3.0 11.3 + - - +
243C ASP* 3.0 15.5 + - - +
245C ILE* 1.3 79.1 - - - +
247C ASP* 1.3 55.2 + - - +
249C VAL* 3.4 7.6 + - + +
250C SER* 2.6 41.0 + - - +
328C VAL* 3.1 37.9 - - + +
329C ILE* 5.5 7.0 - - + +
330C GLU* 5.6 2.4 - - - +
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Residues in contact with ASP 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ASP* 3.6 14.4 - - - +
244C ILE* 2.9 13.5 + - + +
246C GLU* 1.3 75.3 - - - +
248C ILE* 1.3 66.9 + - + +
250C SER* 3.2 9.3 + - - -
251C ASN* 3.0 35.7 + - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PHE* 3.5 41.1 - - + +
218C PHE* 4.5 19.0 - - + -
233C THR* 5.2 1.6 - - - +
235C ALA* 4.8 17.0 - - + -
236C GLU* 5.1 2.0 - - + +
244C ILE* 2.9 32.2 + - + +
245C ILE* 3.7 14.4 - - + +
247C ASP* 1.3 77.9 - - + +
249C VAL* 1.3 62.2 + - + +
251C ASN* 3.5 9.2 + - - +
252C CYS* 3.3 22.2 + - - -
278C MSE 4.0 22.2 - - + -
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 2.9 38.8 + - + +
246C GLU* 3.6 8.1 - - + +
248C ILE* 1.3 75.0 - - + +
250C SER* 1.3 65.7 + - - +
252C CYS* 3.2 4.0 + - - +
253C ARG* 3.0 56.0 + - + +
260C VAL* 4.6 4.5 - - + -
262C TYR* 4.6 2.9 - - + -
278C MSE 3.3 30.4 - - + +
329C ILE* 4.3 20.4 - - + -
330C GLU* 5.8 0.2 - - - +
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Residues in contact with SER 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU* 2.6 30.6 + - - +
247C ASP* 3.4 11.1 + - - -
249C VAL* 1.3 77.6 - - - +
251C ASN* 1.3 64.7 + - - -
253C ARG* 3.0 24.8 + - - +
254C GLU* 3.4 15.9 + - - +
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Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PHE 3.4 21.0 + - - -
214C GLU* 4.6 4.2 + - - +
215C LYS* 3.0 50.5 + - + +
218C PHE* 4.3 12.3 - - + -
247C ASP* 3.0 27.7 + - - +
248C ILE* 3.7 6.0 - - - +
250C SER* 1.3 79.5 - - - +
252C CYS* 1.3 57.2 + - - +
254C GLU* 3.3 5.1 + - - +
255C ILE* 3.0 33.3 + - - +
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Residues in contact with CYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE* 4.1 22.2 - - - -
248C ILE 3.3 7.8 + - - -
249C VAL 3.2 2.2 + - - -
251C ASN* 1.3 76.4 - - - +
253C ARG* 1.3 57.5 + - - +
254C GLU 3.0 5.4 - - - -
256C PHE* 2.8 54.0 + - + +
260C VAL* 3.8 5.1 - - + +
278C MSE 3.4 33.0 - - + -
280C CYS* 3.3 31.0 - - - -
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL* 3.0 41.0 + - + +
250C SER* 3.0 15.7 + - - +
252C CYS* 1.3 76.4 - - - +
254C GLU* 1.3 60.0 + - + +
256C PHE 3.7 7.5 - - - +
257C LYS* 5.5 4.3 - - - +
260C VAL* 4.0 23.5 - - + +
329C ILE* 3.1 26.5 + - - +
330C GLU* 3.2 30.3 + - - +
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LYS* 3.9 23.6 + - + +
250C SER* 3.4 12.5 + - - +
251C ASN* 3.3 7.4 + - - +
252C CYS 3.0 0.2 - - - -
253C ARG* 1.3 82.9 - - + +
255C ILE* 1.3 71.6 + - + +
256C PHE 3.9 3.4 - - - +
257C LYS* 5.2 3.5 - - - +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LYS* 3.3 39.0 - - + +
218C PHE* 3.1 39.0 - - + +
219C GLN* 3.3 35.4 + - + +
222C ALA* 3.7 16.3 - - + +
251C ASN 3.0 17.5 + - - +
254C GLU* 1.3 81.8 - - + +
256C PHE* 1.3 67.0 + - + +
257C LYS* 3.7 3.1 + - - +
283C GLU* 5.1 3.8 - - - +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE* 3.3 53.8 - + + -
221C VAL* 3.9 2.9 - - + -
222C ALA* 3.7 24.7 - - + -
231C VAL* 3.4 31.6 - - + -
252C CYS* 2.8 46.7 + - + +
253C ARG* 3.7 13.3 - - - +
254C GLU 3.9 1.3 - - - +
255C ILE* 1.3 76.8 - - + +
257C LYS* 1.3 60.7 + - - +
258C GLY 3.5 1.1 - - - +
260C VAL* 4.6 5.4 - - + +
280C CYS* 3.7 17.5 - - + -
281C SER 3.5 13.9 - - - +
282C THR* 3.7 21.3 - - + +
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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