Contacts of the helix formed by residues 240 - 253 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B GLU 3.5 5.4 - - - +
239B THR* 1.3 89.9 - - + +
241B LEU* 1.3 62.5 + - + +
242B ASP* 4.1 8.1 - - + +
243B LYS* 2.8 35.7 + - + +
244B ILE* 2.8 12.1 + - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TRP* 3.5 32.2 - - + +
90B LEU* 5.3 20.6 - - + +
237B ILE 4.9 6.7 - - - +
239B THR 4.3 7.4 - - - +
240B PRO* 1.3 74.7 - - + +
242B ASP* 1.3 59.6 + - - +
243B LYS 3.1 0.4 - - - -
244B ILE* 3.0 21.1 - - + +
245B ARG* 3.5 7.8 + - - +
267B SER* 3.0 42.2 - - - +
268B SER* 4.9 2.5 - - - +
270B ILE* 5.2 4.3 - - + -
271B ALA* 3.7 20.9 - - + +
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Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A TRP* 3.8 20.8 - - - -
346A MET* 5.4 6.4 - - - +
240B PRO* 4.7 7.9 - - + -
241B LEU* 1.3 78.7 - - - +
243B LYS* 1.3 56.7 + - + +
245B ARG* 4.0 11.8 - - - +
246B ASP* 4.7 7.1 - - - +
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ILE* 5.6 1.4 - - - +
239B THR* 5.3 3.1 - - - -
240B PRO* 2.8 27.6 + - + +
242B ASP* 1.3 77.6 - - - +
244B ILE* 1.3 64.8 + - - +
245B ARG 2.8 6.6 + - - -
246B ASP* 3.6 14.2 + - - +
247B PHE* 3.7 9.0 + - - +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 5.4 5.4 - - + -
235B ILE* 3.7 30.7 - - + -
236B THR 5.1 2.7 - - - +
237B ILE 6.1 0.2 - - - +
239B THR* 4.3 16.5 + - - +
240B PRO 2.8 8.1 + - - +
241B LEU* 3.0 40.2 - - + +
243B LYS* 1.3 73.4 - - - +
245B ARG* 1.3 63.3 + - - +
247B PHE* 3.4 7.6 - - - +
248B GLY* 3.1 14.2 + - - -
268B SER* 3.9 34.1 - - - +
271B ALA* 3.5 10.5 - - + -
272B LEU* 4.2 20.2 - - + +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TRP* 4.2 17.5 - - + -
241B LEU 3.7 13.7 - - - +
242B ASP* 4.0 12.8 - - - +
243B LYS 2.8 1.2 - - - -
244B ILE* 1.3 75.2 - - - +
246B ASP* 1.3 69.4 + - - +
247B PHE 3.0 0.9 - - - -
248B GLY* 2.5 30.1 + - - -
249B LYS* 3.1 22.1 + - - +
271B ALA 4.1 7.9 - - - -
274B ALA* 4.0 18.7 + - - +
275B GLY* 3.7 23.8 - - - +
278B ALA* 4.0 27.3 - - - +
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Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ASP 4.7 7.9 - - - +
243B LYS* 3.6 8.0 + - - +
245B ARG* 1.3 93.6 + - - +
247B PHE* 1.3 53.5 + - - +
249B LYS* 3.9 14.6 - - - +
250B ARG* 2.6 38.7 + - + +
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 5.8 0.2 - - + -
232B LEU* 3.7 42.8 - - + -
234B ALA* 3.8 24.9 - - + -
235B ILE* 3.4 46.7 - - + -
243B LYS 3.7 7.3 + - - +
244B ILE* 3.4 14.6 + - - +
245B ARG 3.0 0.6 - - - -
246B ASP* 1.3 77.5 - - - +
248B GLY* 1.3 59.4 + - - +
250B ARG* 4.0 5.1 - - + +
251B LEU* 2.9 44.6 + - + +
272B LEU* 4.1 15.3 - - + -
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ILE 3.1 6.3 + - - -
245B ARG 2.5 16.8 + - - -
247B PHE* 1.3 82.6 - - - +
249B LYS* 1.3 58.5 + - - -
251B LEU* 3.9 1.0 - - - +
252B MET* 3.5 16.3 + - - +
272B LEU* 4.1 19.1 - - - -
275B GLY* 3.8 7.1 - - - +
276B PHE* 3.6 21.9 - - - -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ARG* 3.1 20.6 + - - +
246B ASP* 3.2 16.8 + - + +
248B GLY* 1.3 75.3 - - - +
250B ARG* 1.3 62.9 + - + +
252B MET 3.8 0.2 + - - -
253B GLN* 3.0 51.4 + - - +
275B GLY* 3.3 21.7 - - - +
278B ALA* 3.6 30.6 + - - +
279B ALA* 3.8 13.7 - - + +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ASP* 2.6 24.1 + - + +
247B PHE* 4.0 5.4 - - + +
249B LYS* 1.3 76.9 - - + +
251B LEU* 1.3 62.7 + - - +
253B GLN* 3.6 21.3 - - - +
254B SER* 3.8 5.5 - - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LEU* 3.3 46.9 - - + -
247B PHE* 2.9 30.7 + - + +
248B GLY* 3.9 3.6 - - - +
249B LYS 3.3 0.2 - - - -
250B ARG* 1.3 74.8 - - - +
252B MET* 1.3 82.8 - - + +
254B SER* 2.5 31.3 + - - +
256B ASP 4.0 2.5 - - - +
257B ARG* 4.3 0.7 - - - +
258B PRO* 3.4 32.5 - - + -
276B PHE* 4.5 7.2 - - + -
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Residues in contact with MET 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLY 3.5 7.0 + - - +
251B LEU* 1.3 85.2 - - + +
253B GLN* 1.3 56.5 + - - +
254B SER* 2.9 16.2 + - - +
257B ARG* 3.4 26.3 - - - +
258B PRO* 4.0 9.9 - - + +
261B ILE* 6.0 0.2 - - + -
276B PHE* 3.4 51.8 - - + -
279B ALA* 4.4 15.5 - - + -
281B VAL* 4.2 23.1 - - + -
287B ILE* 3.9 25.6 - - + -
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LYS* 3.0 45.5 + - - +
250B ARG* 3.6 11.5 - - - +
251B LEU 3.2 0.2 - - - -
252B MET* 1.3 73.3 - - - +
254B SER* 1.3 58.0 + - - +
278B ALA 5.8 0.2 + - - -
279B ALA* 4.6 15.9 + - + +
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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