Contacts of the helix formed by residues 225 - 241 (chain N) in PDB entry 5NSS
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 ASN 225 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44N LEU* 5.1 14.6 - - + -
222N TRP* 3.3 14.8 + - - +
223N PRO 3.1 7.9 + - - +
224N GLY* 1.3 80.5 - - - +
226N ILE* 1.3 62.7 + - - +
227N ARG 3.4 0.2 + - - -
228N GLU 3.9 4.5 + - - -
229N LEU* 3.9 12.1 + - - +
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Residues in contact with ILE 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N ASN* 1.3 77.3 - - - +
227N ARG* 1.3 58.4 + - - +
228N GLU 3.5 0.2 - - - -
229N LEU* 5.0 2.2 - - - -
230N LYS* 2.5 47.3 + - + +
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Residues in contact with ARG 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224N GLY* 3.1 14.2 + - - +
226N ILE* 1.3 76.5 - - - +
228N GLU* 1.3 56.5 + - - +
230N LYS* 4.9 0.2 - - - -
231N ASN* 2.6 40.7 + - - +
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Residues in contact with GLU 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F ALA* 5.8 7.9 - - + -
222N TRP* 4.7 11.7 - - + -
224N GLY* 3.8 23.8 + - - +
225N ASN 3.9 2.6 + - - +
226N ILE 3.5 0.2 - - - -
227N ARG* 1.3 76.5 - - - +
229N LEU* 1.3 60.0 + - - +
231N ASN* 3.9 2.0 - - - +
232N VAL* 2.9 31.7 + - - +
252N ILE 4.6 6.1 - - - +
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Residues in contact with LEU 229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N ILE* 6.2 4.0 - - + -
217N LEU* 5.8 11.3 - - + +
222N TRP* 4.7 12.9 - - + +
225N ASN 3.9 12.2 + - - +
226N ILE* 4.9 2.7 - - - +
228N GLU* 1.3 75.8 - - - +
230N LYS* 1.3 62.2 + - - +
232N VAL* 3.3 4.2 + - - +
233N VAL* 2.9 34.5 + - - +
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Residues in contact with LYS 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N PHE* 5.6 10.5 - - + -
226N ILE* 2.5 31.7 + - + +
227N ARG* 4.9 0.2 - - - -
229N LEU* 1.3 79.6 - - - +
231N ASN* 1.3 54.2 + - - +
233N VAL* 5.1 1.1 - - - -
234N GLU* 2.5 41.7 + - + +
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Residues in contact with ASN 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ASP* 6.3 2.7 - - + -
227N ARG* 2.6 25.6 + - - +
228N GLU* 4.1 2.0 - - - +
230N LYS* 1.3 77.8 - - - +
232N VAL* 1.3 58.5 + - - +
234N GLU* 4.8 0.4 - - - -
235N ARG* 2.5 40.0 + - + +
254N PRO* 4.1 5.8 - - + +
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Residues in contact with VAL 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217N LEU* 5.7 7.2 - - + -
228N GLU 2.9 20.6 + - - +
229N LEU* 3.9 3.6 - - - +
231N ASN* 1.3 77.5 - - - +
233N VAL* 1.3 58.4 + - - +
235N ARG* 4.8 0.4 - - - -
236N SER* 2.9 32.6 + - - -
250N ILE* 4.4 6.6 - - + +
251N ILE 3.3 26.1 - - - +
252N ILE* 3.8 15.7 + - - +
254N PRO* 5.0 7.6 - - - +
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Residues in contact with VAL 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190N ALA* 4.8 19.5 - - + +
213N ALA* 6.4 1.8 - - + -
217N LEU* 5.8 7.4 - - + +
229N LEU 2.9 15.5 + - - +
230N LYS* 5.1 1.1 - - - -
232N VAL* 1.3 75.3 - - - +
234N GLU* 1.3 60.9 + - - +
236N SER* 3.9 3.1 - - - -
237N VAL* 2.9 32.9 + - - +
250N ILE* 4.8 8.7 - - + +
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Residues in contact with GLU 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N PHE* 5.8 7.9 - - + +
194N ALA* 6.3 4.5 - - - +
197N MET* 5.4 11.9 - - + -
230N LYS* 2.5 27.0 + - + +
231N ASN* 4.8 0.4 - - - -
233N VAL* 1.3 78.9 - - - +
235N ARG* 1.3 57.1 + - - +
237N VAL* 4.4 2.6 - - - +
238N TYR* 2.9 31.0 + - - +
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Residues in contact with ARG 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231N ASN* 2.5 27.9 + - + +
234N GLU* 1.3 75.7 - - - +
236N SER* 1.3 60.5 + - - +
238N TYR* 3.8 5.4 - - - +
239N ARG* 2.9 29.6 + - - +
254N PRO* 3.7 22.9 - - + -
255N PHE* 5.3 2.3 + - - +
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Residues in contact with SER 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N VAL 2.9 22.0 + - - -
233N VAL* 3.9 2.5 - - - -
235N ARG* 1.3 75.4 - - - +
237N VAL* 1.3 61.4 + - - +
239N ARG* 3.3 6.8 + - - +
240N HIS* 2.9 28.5 + - - +
247N LEU* 5.8 4.3 - - - -
249N ASP 5.1 2.9 - - - -
250N ILE* 4.2 23.1 - - - -
251N ILE 5.5 0.9 - - - -
254N PRO* 6.0 0.2 - - - -
255N PHE* 5.2 10.7 - - - +
258N ARG 5.8 2.5 - - - -
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Residues in contact with VAL 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N ALA* 5.6 10.3 - - + -
207N PRO* 4.6 21.5 - - + -
233N VAL 2.9 16.8 + - - +
234N GLU* 4.4 2.7 - - - +
236N SER* 1.3 77.2 - - - +
238N TYR* 1.3 58.8 + - - +
240N HIS* 3.9 6.0 - - - +
241N GLY* 2.9 27.0 + - - -
242N THR 4.9 0.3 + - - -
247N LEU* 4.8 11.3 - - + +
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Residues in contact with TYR 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N GLU 2.9 23.0 + - - +
235N ARG* 3.9 6.5 - - - +
237N VAL* 1.3 78.0 - - - +
239N ARG* 1.3 60.7 + - - +
240N HIS 3.6 0.2 + - - -
241N GLY* 4.1 6.6 + - - -
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Residues in contact with ARG 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235N ARG 2.9 19.9 + - - +
236N SER* 3.7 5.4 - - - +
238N TYR* 1.3 76.7 - - - +
240N HIS* 1.3 64.5 + - - +
255N PHE* 4.6 18.8 - - + -
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Residues in contact with HIS 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N SER 2.9 15.5 + - - +
237N VAL* 3.9 6.5 - - - +
238N TYR 3.3 0.4 - - - -
239N ARG* 1.3 81.0 - - - +
241N GLY* 1.3 65.4 + - - +
242N THR* 3.5 11.3 - - - +
247N LEU* 5.9 5.2 - - + -
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Residues in contact with GLY 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237N VAL 2.9 19.3 + - - -
238N TYR* 4.6 5.8 - - - -
239N ARG 3.8 0.4 - - - -
240N HIS* 1.3 76.1 - - - +
242N THR* 1.3 59.2 + - - +
243N SER 4.3 0.6 + - - -
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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