Contacts of the helix formed by residues 240 - 253 (chain C) in PDB entry 7CE1
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 PRO 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C GLU 3.5 6.0 - - - +
239C THR* 1.3 93.8 - - + +
241C LEU* 1.3 61.2 + - + +
242C ASP* 3.2 14.8 - - - +
243C LYS* 3.1 44.2 + - + +
244C ILE* 3.1 11.3 + - - +
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Residues in contact with LEU 241 (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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90C LEU* 3.9 37.5 - - + -
237C ILE 5.8 1.6 - - - +
239C THR 4.8 2.5 - - - +
240C PRO* 1.3 70.6 - - - +
242C ASP* 1.3 64.8 + - - +
243C LYS 3.3 0.2 - - - -
244C ILE* 3.8 9.4 - - + -
245C ARG* 3.1 24.3 + - - +
267C SER* 3.1 37.0 - - - +
268C SER* 3.8 7.2 - - - -
270C ILE* 5.9 1.1 - - + -
271C ALA* 3.7 20.9 - - + +
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Residues in contact with ASP 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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240C PRO* 4.1 8.3 - - - +
241C LEU* 1.3 81.0 - - - +
243C LYS* 1.3 119.8 + - - +
245C ARG* 3.5 9.6 + - - +
246C ASP* 2.8 24.5 + - - +
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Residues in contact with LYS 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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235C ILE* 4.4 2.9 - - + +
239C THR* 3.9 11.0 - - + -
240C PRO* 3.1 36.0 + - + +
242C ASP* 1.3 116.6 + - - +
244C ILE* 1.3 61.9 + - - +
246C ASP* 3.9 5.6 + - - +
247C PHE* 3.3 22.2 + - - +
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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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202C ILE* 5.7 2.2 - - + -
235C ILE* 3.8 27.1 - - + -
236C THR 4.0 6.7 - - - +
237C ILE 4.6 0.7 - - - +
239C THR* 3.3 33.7 - - + +
240C PRO 3.1 9.3 + - - +
241C LEU* 3.8 11.4 - - + +
242C ASP 3.3 0.4 - - - -
243C LYS* 1.3 77.1 - - - +
245C ARG* 1.3 65.6 + - - +
247C PHE* 3.3 3.1 + - - +
248C GLY* 3.0 19.9 + - - -
268C SER* 3.7 32.1 - - - +
271C ALA* 4.2 1.6 - - + -
272C LEU* 3.8 38.7 - - + +
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Residues in contact with ARG 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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241C LEU 3.1 17.4 + - - +
242C ASP* 3.8 6.5 - - - +
243C LYS 3.5 0.4 - - - -
244C ILE* 1.3 76.7 - - - +
246C ASP* 1.3 62.9 + - - +
248C GLY 3.0 11.4 + - - -
249C LYS* 3.4 1.9 + - - +
271C ALA* 3.4 21.7 + - + +
274C ALA* 5.0 5.6 - - + -
275C GLY* 3.0 29.3 - - - +
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Residues in contact with ASP 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 ASP* 2.8 22.4 + - - +
243C LYS* 4.4 4.8 - - - +
244C ILE 3.4 0.4 - - - -
245C ARG* 1.3 75.7 - - - +
247C PHE* 1.3 64.7 + - - +
249C LYS* 3.2 9.4 + - - +
250C ARG* 3.1 22.7 + - - +
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Residues in contact with PHE 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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232C LEU* 4.5 25.6 - - + -
234C ALA* 3.6 28.7 - - + -
235C ILE* 3.3 29.2 - - + -
243C LYS 3.3 19.0 + - - +
244C ILE 3.3 4.7 + - - +
245C ARG 3.2 0.2 - - - -
246C ASP* 1.3 77.5 - - - +
248C GLY* 1.3 62.3 + - - +
250C ARG* 3.2 7.5 + - + +
251C LEU* 2.9 56.9 + - + +
272C LEU* 4.4 11.0 - - + -
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Residues in contact with GLY 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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244C ILE 3.0 12.6 + - - -
245C ARG 3.0 6.2 + - - -
247C PHE* 1.3 80.1 - - - +
249C LYS* 1.3 60.4 + - - +
251C LEU* 3.7 0.6 - - - +
252C MET* 3.2 19.1 + - - +
272C LEU* 4.0 7.4 - - - -
275C GLY* 4.0 3.8 - - - -
276C PHE* 3.4 39.6 - - - -
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Residues in contact with LYS 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 ARG 3.4 7.5 + - - +
246C ASP* 3.2 11.9 + - - +
248C GLY* 1.3 74.4 - - - +
250C ARG* 1.3 55.8 + - - +
253C GLN* 2.7 40.6 + - + +
275C GLY* 3.6 13.5 + - - +
278C ALA* 5.2 4.3 - - + -
279C ALA* 3.6 23.1 - - + +
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Residues in contact with ARG 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 ASP 3.1 15.6 + - - +
247C PHE* 3.8 7.6 - - + +
249C LYS* 1.3 76.1 - - - +
251C LEU* 1.3 61.7 + - - +
253C GLN* 4.0 4.4 - - - -
254C SER* 3.2 25.3 + - - -
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Residues in contact with LEU 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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230C PHE* 4.0 19.7 - - + -
232C LEU* 5.6 8.1 - - + -
247C PHE* 2.9 45.1 + - + +
248C GLY 3.7 4.9 - - - +
249C LYS 3.2 0.2 - - - -
250C ARG* 1.3 79.3 - - - +
252C MET* 1.3 61.3 + - - +
254C SER* 3.4 11.2 + - - +
256C ASP 3.4 32.9 - - - +
257C ARG* 4.3 1.6 - - - +
258C PRO* 3.6 29.8 - - + -
261C ILE* 5.3 2.2 - - + -
272C LEU* 5.9 0.7 - - + -
276C PHE* 4.5 17.0 - - + -
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Residues in contact with MET 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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248C GLY 3.2 17.0 + - - +
249C LYS 4.2 1.3 - - - +
251C LEU* 1.3 74.9 - - - +
253C GLN* 1.3 61.2 + - - +
254C SER 3.1 12.8 + - - +
257C ARG* 4.1 25.6 - - + +
258C PRO* 4.6 6.5 - - - +
276C PHE* 3.6 27.4 - - + -
279C ALA* 4.2 13.5 - - + -
281C VAL* 3.6 32.8 - - + -
286C ASP* 5.5 1.1 - - + -
287C ILE* 4.5 24.0 - - + -
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Residues in contact with GLN 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 LYS* 2.7 24.6 + - + +
250C ARG* 4.0 5.4 - - - +
252C MET* 1.3 72.2 - - - +
254C SER* 1.3 59.0 + - - +
279C ALA* 4.6 8.6 - - + +
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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