Contacts of the helix formed by residues 230 - 250 (chain B) in PDB entry 3C7N
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 GLY 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLY 3.3 4.2 + - - -
202B GLY* 3.5 2.2 + - - -
229B GLY* 1.3 68.3 - - - -
231B GLU* 1.3 54.2 + - - -
232B ASP 2.6 13.2 + - - -
233B PHE* 2.7 20.3 + - - +
234B ASP* 3.1 12.2 + - - +
271B LYS* 3.2 17.9 - - - -
340B SER* 3.0 27.3 + - - -
560B ADP 3.6 11.4 - - - -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLY 2.8 17.7 + - - +
203B GLY* 5.3 2.0 - - - -
229B GLY 2.6 3.8 + - - -
230B GLY* 1.3 69.0 - - - -
232B ASP* 1.3 60.3 + - - +
234B ASP* 3.4 14.6 - - - +
235B ASN* 3.0 36.9 + - - +
264B ARG* 4.9 13.7 - - - +
560B ADP 4.0 4.8 + - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLY* 5.4 1.6 - - - -
227B HIS 3.2 24.1 - - - +
228B LEU* 3.4 12.4 - - + -
229B GLY 2.5 28.9 + - - +
230B GLY 2.6 0.8 + - - -
231B GLU* 1.3 70.4 - - - +
233B PHE* 1.3 66.3 + - + +
234B ASP 3.0 1.1 - - - -
235B ASN* 3.1 28.1 + - - +
236B ARG* 3.3 11.8 + - - +
309B LEU* 3.8 21.2 - - + +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.9 18.8 - - + -
228B LEU* 4.5 9.9 - - + -
229B GLY* 3.5 9.0 - - - -
230B GLY* 2.7 44.3 + - - +
232B ASP* 1.3 72.5 - - - +
234B ASP* 1.3 63.0 + - - +
236B ARG* 3.5 1.4 + - - +
237B MET* 3.5 20.9 + - - +
271B LYS* 3.8 10.8 - - + -
302B PHE* 4.0 18.1 - - + -
306B ASN* 3.1 25.7 - - - +
309B LEU* 4.0 22.4 - - + -
310B PHE* 3.2 40.6 - + - -
313B THR* 5.6 0.9 - - + -
340B SER* 3.6 13.7 - - - -
343B ILE* 5.2 3.8 - - + -
346B ILE* 4.2 3.8 - - + -
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLY 3.1 8.3 + - - -
231B GLU* 3.4 19.4 + - - +
233B PHE* 1.3 73.7 - - - +
235B ASN* 1.3 67.8 + - - +
237B MET* 2.9 24.7 + - + +
238B VAL* 2.9 18.2 + - + +
264B ARG* 4.3 18.7 - - + +
267B CYS* 5.1 1.1 - - + -
268B GLU* 3.5 34.6 - - - +
271B LYS* 3.0 32.3 - - - +
560B ADP 4.8 2.1 + - - -
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Residues in contact with ASN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLU* 3.0 26.3 + - - +
232B ASP* 3.1 16.9 + - - +
234B ASP* 1.3 78.3 - - - +
236B ARG* 1.3 63.3 + - - +
238B VAL* 3.1 8.2 + - - +
239B ASN* 2.8 32.3 + - - +
264B ARG* 3.0 29.5 + - - +
556B CL 4.2 12.6 - - + -
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Residues in contact with ARG 236 (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 ASP* 3.3 7.2 + - - +
233B PHE 3.7 1.6 - - - +
234B ASP 3.1 1.4 + - - -
235B ASN* 1.3 77.0 - - - +
237B MET* 1.3 58.5 + - - +
239B ASN* 3.5 9.2 + - - +
240B HIS* 2.9 31.0 + - - +
305B LEU* 3.2 33.4 + - + +
306B ASN* 3.3 27.4 - - - +
308B ASP* 2.6 43.6 + - - -
309B LEU* 3.6 22.6 - - + +
556B CL 3.0 28.2 - - - +
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Residues in contact with MET 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE 3.5 13.2 + - - +
234B ASP* 2.9 13.8 + - - +
236B ARG* 1.3 77.2 - - - +
238B VAL* 1.3 67.9 + - - +
240B HIS* 3.1 3.7 + - - +
241B PHE* 2.8 31.1 + - + -
267B CYS* 3.0 53.8 - - + +
270B ALA* 4.7 5.8 - - - -
271B LYS* 3.9 12.1 - - + -
274B LEU* 5.5 0.9 - - - -
297B ILE* 4.3 22.7 - - + -
302B PHE* 3.9 35.4 - - + -
305B LEU* 3.6 9.1 - - + +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASP 2.9 25.5 + - - +
235B ASN* 3.5 4.7 - - - +
237B MET* 1.3 75.2 - - - +
239B ASN* 1.3 70.0 + - - +
241B PHE* 2.9 8.1 + - - +
242B ILE* 2.9 33.7 + - + +
260B VAL* 4.4 21.5 - - + +
263B LEU* 3.7 16.4 - - + -
264B ARG* 3.8 40.8 - - + +
267B CYS* 3.9 10.5 - - + -
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN* 2.8 27.7 + - - +
236B ARG* 3.6 11.1 - - - +
238B VAL* 1.3 78.1 - - - +
240B HIS* 1.3 54.6 + - - +
242B ILE* 2.8 29.1 + - - +
243B ALA* 3.1 10.2 + - - +
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Residues in contact with HIS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG 2.9 22.1 + - - +
237B MET* 3.3 2.9 - - - +
239B ASN* 1.3 72.2 - - - +
241B PHE* 1.3 89.9 + + - +
243B ALA* 3.0 27.1 - - + +
244B GLU* 3.3 15.2 + - + +
247B ARG* 5.9 4.0 - - - -
297B ILE* 4.4 11.7 - - + +
301B ARG* 5.7 8.2 - - + +
305B LEU* 3.2 31.2 - - + +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B MET* 2.8 29.9 + - + +
238B VAL 3.7 2.9 - - - +
240B HIS* 1.3 86.6 - + - +
242B ILE* 1.3 61.4 + - - +
243B ALA 3.2 1.3 - - - -
244B GLU* 3.1 21.3 + - - +
245B PHE* 2.7 29.9 + - - +
263B LEU* 3.8 23.1 - - + -
267B CYS* 3.7 21.8 - - - -
282B ILE* 3.9 24.0 - - + -
293B PHE* 4.1 17.2 - + + -
295B THR* 3.8 13.7 - - - -
296B SER 3.9 8.3 - - - -
297B ILE* 3.7 38.6 - - + -
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Residues in contact with ILE 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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238B VAL* 2.9 49.2 + - + +
239B ASN* 2.8 14.3 + - - +
241B PHE* 1.3 71.3 - - - +
243B ALA* 1.3 65.8 + - - +
245B PHE* 4.4 5.6 - - - +
246B LYS* 2.9 25.4 + - + +
252B ASP* 4.2 12.8 - - - +
253B ILE* 3.9 24.5 - - + +
254B SER* 3.6 25.4 - - - +
260B VAL* 4.8 10.8 - - + -
263B LEU* 3.7 12.6 - - + -
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Residues in contact with ALA 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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239B ASN 3.1 8.2 + - - +
240B HIS* 3.0 22.7 - - - +
242B ILE* 1.3 74.3 - - - +
244B GLU* 1.3 59.1 + - - +
246B LYS* 3.8 3.5 - - - +
247B ARG* 2.9 48.2 + - - +
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Residues in contact with GLU 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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240B HIS* 3.3 15.8 + - - +
241B PHE* 3.1 26.3 + - - +
243B ALA* 1.3 80.9 - - - +
245B PHE* 1.3 57.6 + - - +
247B ARG* 3.5 20.3 + - - +
248B LYS* 2.9 44.7 + - + +
293B PHE* 3.8 15.5 - - + -
295B THR* 2.8 34.0 - - - +
296B SER 5.1 0.9 - - - +
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Residues in contact with PHE 245 (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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241B PHE 2.7 18.9 + - - +
242B ILE* 4.2 5.6 - - - +
244B GLU* 1.3 70.8 - - - +
246B LYS* 1.3 65.7 + - - +
249B HIS* 3.1 49.7 + + + +
251B LYS* 3.7 23.3 - - + -
253B ILE* 3.3 33.7 - - + -
263B LEU* 6.4 1.1 - - + -
287B LEU* 4.3 11.4 - - + -
288B TYR* 3.8 22.7 - - + -
291B ILE* 4.1 29.2 - - + -
293B PHE* 3.7 43.1 - + + -
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Residues in contact with LYS 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 ILE* 2.9 23.7 + - + +
243B ALA* 3.8 3.8 - - - +
245B PHE* 1.3 72.9 - - - +
247B ARG* 1.3 55.9 + - - +
250B LYS* 2.7 38.8 + - - +
251B LYS 3.0 13.4 + - - +
252B ASP* 3.5 43.5 - - + +
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Residues in contact with ARG 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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240B HIS* 5.0 4.4 + - - -
243B ALA* 2.9 30.1 + - - +
244B GLU* 3.5 35.3 + - - +
246B LYS* 1.3 75.4 - - - +
248B LYS* 1.3 68.1 + - + +
249B HIS 2.8 11.9 + - - -
250B LYS* 3.6 15.8 + - - -
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 2.9 37.0 + - + +
247B ARG* 1.3 80.8 - - + +
249B HIS* 1.3 90.0 + - + +
250B LYS* 5.4 2.0 - - - -
293B PHE* 5.8 1.8 - - + -
295B THR* 5.4 6.3 - - + -
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Residues in contact with HIS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.1 37.8 + + + +
247B ARG 2.8 4.4 + - - -
248B LYS* 1.3 113.7 + - + +
250B LYS* 1.3 67.7 + - - +
251B LYS* 2.5 29.6 + - - +
291B ILE* 3.2 48.0 - - + +
292B ASP 4.1 10.9 + - - -
293B PHE* 4.9 6.6 - + - -
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Residues in contact with LYS 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 LYS* 2.7 26.9 + - - +
247B ARG 3.6 14.3 + - - +
248B LYS 5.4 0.7 - - - -
249B HIS* 1.3 75.6 - - - +
251B LYS* 1.3 69.2 + - - +
252B ASP* 3.9 1.2 + - - +
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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