Contacts of the helix formed by residues 227 - 243 (chain A) in PDB entry 3NA0
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLN* 4.6 11.0 + - - +
220A GLY 4.9 2.4 + - - -
221A MET* 3.6 9.0 - - - +
225A VAL 4.3 0.4 + - - -
226A VAL* 1.3 78.7 - - - +
228A PRO* 1.4 70.0 - - - +
229A GLU* 3.1 21.5 + - - +
230A ALA* 3.3 23.5 + - + +
231A GLN 3.1 16.8 + - - -
280A TYR* 5.4 4.0 + - - -
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Residues in contact with PRO 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A VAL* 3.1 11.4 - - + +
227A ASN* 1.4 91.3 - - - +
229A GLU* 1.3 66.2 + - + +
231A GLN* 3.4 9.6 + - + +
232A ARG* 3.0 28.2 + - - +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASN* 3.1 14.2 + - - +
228A PRO* 1.3 84.4 - - + +
230A ALA* 1.3 64.6 + - - +
232A ARG* 3.0 38.9 + - - +
233A PHE 3.2 16.6 + - - -
276A LYS* 3.0 35.9 + - - +
280A TYR* 5.1 1.3 - - - +
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 4.0 12.1 - - + -
219A GLN* 5.5 3.8 - - + +
221A MET* 3.5 29.4 - - + -
227A ASN* 3.3 19.3 + - + +
229A GLU* 1.3 74.5 - - - +
231A GLN* 1.3 66.5 + - - +
233A PHE* 3.2 8.0 + - - +
234A ILE* 3.0 23.8 + - - +
280A TYR* 3.9 21.9 + - - +
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP* 5.5 3.2 + - - +
203A PHE* 5.8 0.4 - - - +
204A ARG* 3.0 43.3 + - - +
221A MET* 3.5 5.2 - - + +
226A VAL* 4.1 9.4 - - + +
227A ASN 3.1 13.1 + - - +
228A PRO* 3.5 13.5 - - + +
229A GLU 3.3 0.2 - - - -
230A ALA* 1.3 77.0 - - - +
232A ARG* 1.3 55.7 + - - +
234A ILE* 3.1 21.8 + - - +
235A ASP* 3.0 64.6 + - - +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PRO 3.0 12.3 + - - +
229A GLU* 3.0 38.0 + - - +
231A GLN* 1.3 75.8 - - - +
233A PHE* 1.3 57.8 + - - +
235A ASP* 3.6 8.1 + - + +
236A ALA* 3.0 28.4 + - - +
272A VAL* 3.7 34.8 - - - +
275A SER* 6.2 1.4 - - - -
276A LYS* 3.7 19.2 - - - +
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Residues in contact with PHE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 3.3 33.2 - + + -
229A GLU 3.2 6.5 + - - +
230A ALA* 3.2 11.4 + - - +
232A ARG* 1.3 73.2 - - - +
234A ILE* 1.3 65.2 + - - +
236A ALA* 3.1 12.0 + - - +
237A ILE* 3.2 37.4 + - + +
272A VAL* 3.9 9.1 - - - +
273A ILE* 3.3 47.3 - - + +
276A LYS* 3.7 29.2 - - + -
277A ALA* 4.3 7.4 - - + -
280A TYR* 4.9 6.3 - + - +
324A LEU* 4.1 31.4 - - + -
325A ALA 4.7 1.3 - - - -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE* 3.7 29.4 - - + -
204A ARG* 3.8 28.0 - - + -
207A PHE* 3.8 38.8 - - + -
221A MET* 3.9 20.0 - - + -
230A ALA 3.0 13.3 + - - +
231A GLN* 3.1 20.2 + - - +
233A PHE* 1.3 73.9 - - - +
235A ASP* 1.3 64.3 + - - +
237A ILE* 3.2 25.2 + - - +
238A TYR* 3.6 6.9 + - - +
328A VAL* 4.0 10.5 - - + +
329A ASP* 4.7 0.7 - - - +
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLN* 3.0 43.9 + - - +
232A ARG* 3.9 7.6 - - - +
234A ILE* 1.3 73.6 - - - +
236A ALA* 1.3 66.8 + - - +
237A ILE 3.1 2.0 + - - -
238A TYR* 3.3 9.1 + - - +
239A GLN* 3.0 27.3 + - + +
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG 3.0 19.0 + - - +
233A PHE 3.1 6.2 + - - +
235A ASP* 1.3 75.8 - - - +
237A ILE* 1.3 53.2 + - - +
239A GLN* 3.1 8.6 + - - +
240A MET* 2.7 36.0 + - - +
269A ALA* 3.6 16.2 - - - +
272A VAL* 3.6 30.7 - - + -
273A ILE* 4.3 6.1 - - + -
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A PHE* 3.2 44.7 + - + +
234A ILE* 3.4 9.2 - - - +
235A ASP 3.1 0.6 - - - -
236A ALA* 1.3 77.2 - - - +
238A TYR* 1.3 63.6 + - - +
240A MET* 3.4 4.1 + - + +
241A PHE* 3.3 29.0 + - + -
273A ILE* 4.0 20.2 - - + -
325A ALA* 3.7 33.7 - - + +
328A VAL* 3.5 24.7 - - + -
329A ASP* 3.6 25.1 - - - +
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE* 5.0 10.5 - + + -
234A ILE 3.6 6.6 + - - +
235A ASP* 3.3 11.7 + - - +
237A ILE* 1.3 80.1 - - - +
239A GLN* 1.3 71.6 + - - +
241A PHE* 3.2 4.6 + - + +
242A HIS* 2.9 52.6 + + + +
329A ASP* 3.3 20.9 - - - +
498A ASN* 3.7 17.4 + - + -
502A MET* 3.3 41.5 - - + +
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP* 3.0 19.7 + - + +
236A ALA* 3.4 9.6 - - - +
238A TYR* 1.3 88.2 - - + +
240A MET* 1.3 59.7 + - - +
242A HIS* 4.3 18.0 - - - -
243A THR* 2.8 57.9 + - + +
265A ASP* 4.9 8.2 - - - +
269A ALA* 3.9 12.8 - - + -
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Residues in contact with MET 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 3.2 32.8 - - + -
236A ALA 2.7 17.1 + - - +
237A ILE* 3.4 8.7 - - + +
239A GLN* 1.3 73.8 - - - +
241A PHE* 1.3 75.1 + - + +
243A THR* 4.0 2.5 - - - -
244A SER* 2.7 26.7 + - - -
266A HIS* 3.2 11.6 + - - -
269A ALA* 3.6 10.2 - - + +
270A TRP* 3.4 46.7 - - + +
273A ILE* 3.9 15.0 - - + -
325A ALA* 5.5 0.7 - - + -
602A 2DC 3.5 32.3 - - + -
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Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 3.5 37.2 - + - -
237A ILE* 3.3 35.4 + - + -
238A TYR* 3.2 7.9 + - + +
239A GLN 3.2 0.2 - - - -
240A MET* 1.3 78.7 - - + +
242A HIS* 1.3 69.0 + - - +
244A SER* 3.0 20.7 + - - -
245A VAL* 3.8 2.3 + - - +
325A ALA 4.5 4.3 - - - -
326A GLY* 5.5 0.7 - - - -
329A ASP* 3.5 26.7 - - + +
330A THR* 5.8 1.8 - - + -
498A ASN* 3.3 22.4 - - + +
499A LEU* 3.6 15.4 - - + +
500A ILE* 4.1 20.0 - - + -
602A 2DC 3.8 37.5 - - + -
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Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A HIS* 4.3 15.3 - + - -
238A TYR* 2.9 42.6 + + + +
239A GLN* 4.0 18.8 - - - +
241A PHE* 1.3 76.9 - - - +
243A THR* 1.3 68.9 + - + +
244A SER 3.1 1.2 + - - -
245A VAL* 3.3 17.3 + - - +
246A PRO* 3.8 4.5 - - - +
498A ASN* 3.2 31.4 + - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLN* 2.8 48.5 + - - +
242A HIS* 1.3 76.0 - - + +
244A SER* 1.3 63.2 + - - +
245A VAL 3.2 0.4 + - - -
246A PRO* 3.7 5.1 - - - +
247A MET* 4.3 3.8 - - - +
262A THR* 3.2 30.6 - - + +
265A ASP* 4.0 22.9 - - + +
266A HIS* 2.8 42.9 + - - +
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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