Contacts of the helix formed by residues 241 - 256 (chain X) in PDB entry 3N5N
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 241 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237X ALA* 5.7 0.4 - - - -
238X ASP* 2.7 29.3 + - - -
239X PRO 3.4 0.3 - - - +
240X SER* 1.3 81.2 + - - +
242X THR* 1.3 65.4 + - - +
243X LEU* 3.3 15.6 + - - +
244X VAL* 3.7 12.4 + - - +
245X SER* 2.9 28.1 + - - -
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Residues in contact with THR 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240X SER 3.6 1.8 + - - -
241X SER* 1.3 72.2 + - - +
243X LEU* 1.3 71.2 + - + +
245X SER* 3.5 4.9 + - - -
246X GLN* 3.0 42.7 + - - +
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Residues in contact with LEU 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241X SER* 3.3 7.9 + - - +
242X THR* 1.3 84.4 - - + +
244X VAL* 1.3 64.0 + - + +
246X GLN* 3.5 5.1 + - + +
247X GLN* 2.9 47.3 + - + +
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Residues in contact with VAL 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X CYS* 5.0 2.0 - - - -
235X ILE* 4.1 22.2 - - + -
237X ALA* 3.5 34.1 - - + +
238X ASP 3.6 17.0 - - - +
239X PRO* 3.7 22.0 - - + +
241X SER* 3.6 7.9 + - - +
242X THR 3.3 0.4 - - - -
243X LEU* 1.3 81.6 - - + +
245X SER* 1.3 66.8 + - - +
247X GLN* 3.1 7.4 + - + +
248X LEU* 2.8 35.6 + - + +
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Residues in contact with SER 245 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239X PRO 3.4 11.4 + - - -
240X SER* 4.4 3.6 + - - -
241X SER 2.9 22.5 + - - -
242X THR* 3.9 6.1 - - - -
243X LEU 3.4 0.2 - - - -
244X VAL* 1.3 76.0 - - - +
246X GLN* 1.3 73.3 + - - +
248X LEU* 3.1 9.2 + - - +
249X TRP* 2.9 38.9 + - - -
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Residues in contact with GLN 246 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203X ARG* 3.1 29.8 + - - +
242X THR* 3.0 28.6 + - - +
243X LEU* 3.9 6.1 - - + +
245X SER* 1.3 89.1 - - - +
247X GLN* 1.3 56.7 + - - +
249X TRP* 3.5 3.5 + - - +
250X GLY* 3.0 23.7 + - - -
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Residues in contact with GLN 247 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X SER* 5.6 5.7 + - - +
71X HIS* 5.3 2.4 - - - +
72X LEU* 3.6 26.5 - - - +
235X ILE* 5.1 12.6 - - + +
243X LEU* 2.9 34.6 + - + +
244X VAL* 3.1 11.4 + - + +
246X GLN* 1.3 74.5 - - - +
248X LEU* 1.3 60.8 + - - +
250X GLY* 3.3 2.3 + - - -
251X LEU* 2.9 34.4 + - + +
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Residues in contact with LEU 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X VAL* 4.0 17.5 - - + -
226X ALA* 4.0 25.1 - - + -
229X LEU* 3.6 27.9 - - + +
230X CYS* 4.1 15.3 - - - -
235X ILE* 3.7 27.8 - - + -
239X PRO* 5.2 6.5 - - + +
244X VAL* 2.8 36.7 + - + +
245X SER* 3.6 9.2 - - - +
247X GLN* 1.3 69.8 - - - +
249X TRP* 1.3 61.0 + - - +
251X LEU* 3.2 6.3 + - + +
252X ALA* 2.8 30.3 + - - +
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Residues in contact with TRP 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203X ARG* 3.3 72.1 - - + +
204X TYR* 4.0 12.8 - - + -
218X THR* 5.7 0.4 - - - -
219X GLY 3.4 26.9 - - - +
220X VAL* 3.7 15.7 - - + -
221X VAL* 3.4 50.0 + - + +
245X SER* 2.9 37.6 + - - +
246X GLN* 3.9 5.6 - - - +
248X LEU* 1.3 77.5 - - - +
250X GLY* 1.3 55.9 + - - +
252X ALA* 3.4 1.7 + - - +
253X GLN* 2.9 30.6 + - - +
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Residues in contact with GLY 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246X GLN 3.0 15.2 + - - -
247X GLN* 3.3 3.8 + - - -
248X LEU 3.1 0.4 - - - -
249X TRP* 1.3 73.8 - - - +
251X LEU* 1.3 63.9 + - - +
253X GLN* 3.2 6.7 + - - +
254X GLN* 3.0 24.0 + - - +
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Residues in contact with LEU 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X HIS 4.0 16.2 - - - +
72X LEU* 4.4 9.0 - - + -
73X PHE* 3.5 36.8 - - + +
229X LEU* 4.0 18.8 - - + -
233X ARG* 3.8 20.4 - - + -
235X ILE* 4.1 19.3 - - + -
247X GLN* 2.9 18.9 + - - +
248X LEU* 3.2 13.7 + - + +
250X GLY* 1.3 71.7 - - - +
252X ALA* 1.3 62.3 + - - +
254X GLN* 3.1 16.2 + - - +
255X LEU* 2.8 34.8 + - - +
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Residues in contact with ALA 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X GLY* 3.8 5.1 - - - -
220X VAL 4.1 17.9 - - - +
221X VAL* 3.5 22.7 - - + -
225X VAL* 5.0 2.2 - - + -
229X LEU* 4.1 8.7 - - + +
248X LEU 2.8 16.4 + - - +
249X TRP* 3.7 4.0 - - + +
251X LEU* 1.3 75.7 - - - +
253X GLN* 1.3 58.2 + - - +
255X LEU* 4.0 5.3 - - - +
256X VAL* 3.0 32.7 + - - +
264X PHE* 4.8 4.7 - - + -
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Residues in contact with GLN 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X ALA 3.1 21.4 - - - +
218X THR* 3.5 9.8 + - - +
219X GLY* 2.9 32.6 + - - +
249X TRP* 2.9 18.5 + - - +
250X GLY* 3.6 7.4 - - - +
251X LEU 3.2 0.2 - - - -
252X ALA* 1.3 77.7 - - - +
254X GLN* 1.3 61.7 + - - +
256X VAL* 3.7 11.3 - - - +
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Residues in contact with GLN 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X LEU* 5.7 1.6 - - - +
73X PHE* 2.8 52.0 + - - +
79X VAL* 3.8 16.3 - - + +
83X ARG* 3.1 22.7 + - - -
250X GLY 3.0 14.6 + - - +
251X LEU* 3.1 17.0 + - - +
253X GLN* 1.3 79.4 - - - +
255X LEU* 1.3 58.4 + - - +
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Residues in contact with LEU 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X PHE* 3.7 42.2 - - + -
79X VAL* 4.2 18.8 - - + +
82X PHE* 4.1 31.9 - - + -
83X ARG* 2.9 25.0 + - + +
229X LEU* 3.6 31.4 - - + -
251X LEU 2.8 19.7 + - - +
252X ALA* 4.0 3.1 - - - +
254X GLN* 1.3 79.3 - - + +
256X VAL* 1.3 66.2 + - - +
257X ASP 3.2 1.4 + - - -
264X PHE* 3.5 17.9 - - + -
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Residues in contact with VAL 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X ARG* 3.4 11.4 + - - -
217X ALA* 4.0 23.5 - - + +
218X THR 3.9 7.9 - - - +
219X GLY* 3.7 16.8 - - - +
252X ALA 3.0 13.5 + - - +
253X GLN* 3.7 17.4 - - - +
254X GLN 4.3 0.3 - - - +
255X LEU* 1.3 77.3 - - - +
257X ASP* 1.3 64.3 + - - +
258X PRO* 3.4 4.9 - - - +
261X PRO* 3.8 26.7 - - + +
264X PHE* 3.6 14.1 - - + -
265X ASN* 3.8 20.9 - - - +
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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