Contacts of the helix formed by residues 241 - 256 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237Y ALA* 5.9 0.2 - - - -
238Y ASP* 2.7 28.0 + - - -
239Y PRO 3.0 0.2 - - - -
240Y SER* 1.3 84.7 + - - +
242Y THR* 1.3 62.4 + - - +
243Y LEU* 3.4 15.1 + - - +
244Y VAL* 3.6 12.7 + - - +
245Y SER* 3.0 25.8 + - - -
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Residues in contact with THR 242 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240Y SER 3.7 0.8 + - - -
241Y SER* 1.3 73.1 + - - +
243Y LEU* 1.3 71.7 - - + +
244Y VAL 3.2 0.2 - - - -
245Y SER* 4.0 3.3 - - - -
246Y GLN* 3.0 41.0 + - + +
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Residues in contact with LEU 243 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241Y SER* 3.4 8.1 + - - +
242Y THR* 1.3 84.7 - - + +
244Y VAL* 1.3 63.9 + - + +
246Y GLN* 3.9 3.6 - - + +
247Y GLN* 3.0 46.7 + - + +
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Residues in contact with VAL 244 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230Y CYS* 5.1 0.9 - - - -
235Y ILE* 4.1 24.0 - - + -
237Y ALA* 3.6 27.4 - - + +
238Y ASP 3.5 21.5 - - - +
239Y PRO* 3.6 22.2 - - + -
241Y SER* 3.6 9.2 + - - +
242Y THR 3.2 0.6 - - - -
243Y LEU* 1.3 83.7 - - + +
245Y SER* 1.3 65.9 + - - +
247Y GLN* 3.0 7.8 + - + +
248Y LEU* 2.9 34.4 + - + +
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Residues in contact with SER 245 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239Y PRO 3.0 13.9 + - - -
240Y SER* 4.3 3.6 + - - -
241Y SER 3.0 20.6 + - - -
242Y THR* 4.0 4.7 - - - -
244Y VAL* 1.3 73.6 - - - +
246Y GLN* 1.3 75.9 + - - +
248Y LEU* 3.0 10.2 + - - +
249Y TRP* 2.9 35.2 + - - -
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Residues in contact with GLN 246 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Y ARG* 2.8 30.9 + - - +
242Y THR* 3.0 29.5 + - + +
243Y LEU* 4.1 3.8 - - + +
245Y SER* 1.3 82.7 - - - +
247Y GLN* 1.3 57.0 + - - +
249Y TRP* 3.5 3.9 + - - +
250Y GLY* 2.9 24.9 + - - -
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Residues in contact with GLN 247 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Y HIS* 5.4 1.2 - - - +
72Y LEU* 3.8 23.9 - - - +
235Y ILE* 5.0 14.0 - - + +
243Y LEU* 3.0 41.8 + - + +
244Y VAL* 3.0 12.4 + - + +
246Y GLN* 1.3 77.0 - - - +
248Y LEU* 1.3 58.4 - - - +
250Y GLY* 3.2 2.6 + - - -
251Y LEU* 2.9 33.8 + - + +
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Residues in contact with LEU 248 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221Y VAL* 3.6 18.7 - - + +
226Y ALA* 4.2 20.0 - - + -
229Y LEU* 3.7 27.3 - - + +
230Y CYS* 4.0 22.7 - - - -
235Y ILE* 3.7 27.6 - - + -
239Y PRO* 5.0 7.6 - - + +
244Y VAL* 2.9 29.7 + - + +
245Y SER* 3.6 9.2 - - - +
247Y GLN* 1.3 71.9 - - - +
249Y TRP* 1.3 62.1 + - + +
251Y LEU* 3.3 7.9 + - + +
252Y ALA* 2.9 29.5 + - - +
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Residues in contact with TRP 249 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Y ARG* 3.4 70.3 - - + +
204Y TYR* 4.0 19.7 - - + -
218Y THR* 5.7 0.7 - - - -
219Y GLY 3.2 28.2 - - - +
220Y VAL* 3.7 8.1 - - + -
221Y VAL* 3.6 47.8 + - + +
245Y SER* 2.9 35.9 + - - +
246Y GLN* 3.9 5.6 - - - +
248Y LEU* 1.3 73.4 - - + +
250Y GLY* 1.3 64.7 + - - +
252Y ALA* 3.5 1.2 + - - +
253Y GLN* 3.0 26.0 + - - +
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Residues in contact with GLY 250 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246Y GLN 2.9 15.8 + - - -
247Y GLN* 3.2 4.7 + - - -
248Y LEU 3.2 0.4 - - - -
249Y TRP* 1.3 75.4 - - - +
251Y LEU* 1.3 60.6 + - - +
253Y GLN* 3.1 7.5 + - - +
254Y GLN* 3.0 23.9 + - - +
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Residues in contact with LEU 251 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Y HIS 3.8 17.0 - - - +
72Y LEU* 4.2 15.7 - - + -
73Y PHE* 3.6 31.9 - - + -
229Y LEU* 4.4 15.5 - - + -
233Y ARG* 3.8 20.6 - - + -
235Y ILE* 4.0 19.7 - - + -
247Y GLN* 2.9 17.9 + - - +
248Y LEU* 3.3 14.8 + - + +
250Y GLY* 1.3 73.7 - - - +
252Y ALA* 1.3 58.5 + - - +
254Y GLN* 3.3 15.5 + - - +
255Y LEU* 2.9 36.1 + - + +
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Residues in contact with ALA 252 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y GLY* 3.8 4.2 - - - -
220Y VAL 4.1 20.6 - - - +
221Y VAL* 3.7 20.2 - - + -
225Y VAL* 4.9 1.6 - - + -
229Y LEU* 4.2 9.5 - - + +
248Y LEU 2.9 16.5 + - - +
249Y TRP* 3.8 4.3 - - - +
251Y LEU* 1.3 76.5 - - - +
253Y GLN* 1.3 58.4 + - - +
255Y LEU* 3.8 4.8 - - - +
256Y VAL* 2.9 33.8 + - - +
264Y PHE* 4.8 5.3 - - + -
265Y ASN* 5.9 0.2 - - - +
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Residues in contact with GLN 253 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217Y ALA 2.9 21.7 - - - +
218Y THR* 3.5 10.5 + - - +
219Y GLY* 2.8 33.5 + - - +
249Y TRP* 3.0 18.4 + - - +
250Y GLY* 3.1 6.5 + - - +
252Y ALA* 1.3 77.5 - - - +
254Y GLN* 1.3 63.2 + - - +
256Y VAL* 3.3 16.0 - - - +
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Residues in contact with GLN 254 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Y LEU* 5.6 2.2 - - - +
73Y PHE* 2.6 49.8 + - - +
79Y VAL* 3.8 14.0 - - + +
83Y ARG* 2.9 23.6 + - - -
250Y GLY 3.0 11.9 + - - +
251Y LEU* 3.6 23.7 + - - +
253Y GLN* 1.3 79.0 - - - +
255Y LEU* 1.3 58.3 + - - +
256Y VAL 3.5 0.2 + - - -
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Residues in contact with LEU 255 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Y PHE* 3.7 44.6 - - + -
79Y VAL* 4.5 14.8 - - + +
82Y PHE* 4.0 34.3 - - + -
83Y ARG* 2.9 17.5 + - + +
229Y LEU* 3.7 30.1 - - + -
251Y LEU* 2.9 23.4 + - + +
252Y ALA* 4.1 3.1 - - - +
254Y GLN* 1.3 72.4 - - + +
256Y VAL* 1.3 66.9 + - - +
257Y ASP 3.1 1.7 + - - -
264Y PHE* 3.4 23.8 - - + -
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Residues in contact with VAL 256 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Y ARG* 3.5 7.3 + - - -
217Y ALA* 3.8 21.4 - - + +
218Y THR 4.2 6.7 - - - +
219Y GLY* 3.8 18.6 - - - +
252Y ALA 2.9 14.0 + - - +
253Y GLN* 3.3 18.6 - - - +
254Y GLN 3.4 0.7 - - - +
255Y LEU* 1.3 75.9 - - - +
257Y ASP* 1.3 64.7 + - - +
258Y PRO* 3.3 8.5 - - - +
261Y PRO* 3.6 37.0 - - + +
264Y PHE* 3.7 15.7 - - + -
265Y ASN* 4.1 8.1 - - - +
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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