Contacts of the helix formed by residues 222 - 238 (chain B) in PDB entry 2NUD
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 TYR 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B VAL 5.3 1.3 + - - -
173B ILE* 3.5 31.0 - - + -
174B PRO* 3.6 38.6 - - + +
218B THR* 4.6 1.8 - - + -
219B ASN* 2.9 40.5 + - + +
221B SER* 1.3 80.3 - - - +
223B LEU* 1.3 66.2 + - - +
224B PRO* 3.3 2.0 - - - -
225B ILE* 2.9 33.1 - - + +
226B ILE* 3.0 28.3 + - + +
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Residues in contact with LEU 223 (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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116B GLU* 4.3 12.8 - - + +
117B ARG* 3.5 36.6 - - + +
218B THR* 5.8 0.9 - - + -
219B ASN 4.1 1.3 + - - +
220B ALA* 2.9 26.6 + - - +
222B TYR* 1.3 77.1 - - - +
224B PRO* 1.3 55.4 - - + +
226B ILE* 3.1 4.4 + - + -
227B LYS* 2.6 49.1 + - + +
261B ALA* 3.9 28.3 - - + +
263B PRO* 3.7 41.5 - - + +
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Residues in contact with PRO 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 5.9 1.6 - - - +
220B ALA 3.7 4.3 - - - +
221B SER* 3.4 17.3 - - - +
222B TYR 3.4 0.9 - - - -
223B LEU* 1.3 93.8 - - + +
225B ILE* 1.3 67.5 + - + +
227B LYS* 3.3 12.9 + - + +
228B ASP* 2.8 32.1 + - - +
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Residues in contact with ILE 225 (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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168B LEU* 4.3 11.1 - - + +
169B HIS* 5.2 11.3 - - + +
173B ILE* 5.3 5.2 - - + -
221B SER 3.4 21.1 - - - +
222B TYR* 2.9 37.5 - - + +
224B PRO* 1.3 79.0 - - + +
226B ILE* 1.3 63.0 + - + +
228B ASP* 3.4 11.9 + - - +
229B HIS* 3.2 21.0 + - - +
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Residues in contact with ILE 226 (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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168B LEU* 5.0 1.6 - - + -
173B ILE* 4.9 8.5 - - + -
175B LEU* 4.3 16.2 - - + -
218B THR* 4.4 4.5 - - + -
222B TYR* 3.0 39.0 + - + +
223B LEU* 3.7 6.7 - - + +
225B ILE* 1.3 77.9 - - + +
227B LYS* 1.3 60.2 + - + +
229B HIS* 3.0 8.4 + - - +
230B LEU* 2.9 40.6 + - + +
257B TRP* 3.9 36.1 - - + +
261B ALA* 3.8 33.7 - - + -
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Residues in contact with LYS 227 (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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88B PHE* 5.3 3.5 - - + +
89B GLU* 3.0 35.5 + - + +
116B GLU* 2.7 39.1 + - - +
223B LEU* 2.6 40.7 + - + +
224B PRO* 3.7 12.6 - - - +
226B ILE* 1.3 73.7 - - + +
228B ASP* 1.3 62.0 + - - +
230B LEU* 3.3 15.5 + - + +
231B ASN* 3.1 27.3 + - - +
263B PRO* 5.3 10.5 - - + -
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Residues in contact with ASP 228 (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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169B HIS* 6.3 1.8 - - + -
224B PRO* 2.8 27.5 + - - +
225B ILE* 3.6 11.8 - - - +
226B ILE 3.1 0.2 - - - -
227B LYS* 1.3 76.7 - - - +
229B HIS* 1.3 62.9 + - - +
231B ASN* 3.1 17.8 + - - +
232B ASP* 3.2 18.5 + - - +
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Residues in contact with HIS 229 (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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168B LEU* 3.6 42.0 - - + +
169B HIS* 4.7 6.9 - - + +
225B ILE 3.2 2.9 + - - +
226B ILE* 3.0 9.7 + - + +
228B ASP* 1.3 80.8 - - - +
230B LEU* 1.3 55.9 + - - +
232B ASP* 3.1 17.2 + - + +
233B LEU* 3.0 53.7 + - + +
257B TRP* 3.4 44.8 + + + -
305B GLU* 5.1 2.5 - - - -
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Residues in contact with LEU 230 (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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88B PHE* 3.7 40.6 - - + +
226B ILE* 2.9 27.8 + - + +
227B LYS* 3.7 15.9 - - + +
228B ASP 3.3 0.4 - - - -
229B HIS* 1.3 75.1 - - - +
231B ASN* 1.3 58.1 + - - +
233B LEU* 3.4 8.0 + - + +
234B TYR* 2.9 29.3 + - - +
254B THR* 3.6 41.3 - - + +
257B TRP* 3.7 19.3 - - + -
258B ALA* 3.8 15.9 - - - +
263B PRO* 5.3 8.3 - - + -
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Residues in contact with ASN 231 (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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86B THR 4.7 1.4 + - - -
87B SER* 3.4 18.6 - - - +
88B PHE* 3.2 34.0 + - - +
89B GLU* 4.1 13.0 + - - +
227B LYS* 3.1 15.7 + - - +
228B ASP* 3.1 14.2 + - - +
230B LEU* 1.3 79.3 - - - +
232B ASP* 1.3 59.1 + - - +
234B TYR* 3.4 2.7 + - - +
235B ARG* 2.9 29.8 + - - +
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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
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169B HIS* 5.6 2.9 + - - -
228B ASP* 3.2 14.6 + - - +
229B HIS* 3.1 22.5 + - + +
231B ASN* 1.3 78.9 - - - +
233B LEU* 1.3 64.8 + - + +
235B ARG* 3.5 11.0 + - - +
236B GLN* 3.0 38.7 + - - +
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Residues in contact with LEU 233 (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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229B HIS* 3.0 46.3 + - + +
230B LEU* 3.7 10.8 - - + +
231B ASN 3.3 0.2 - - - -
232B ASP* 1.3 76.2 - - + +
234B TYR* 1.3 58.0 + - - +
236B GLN* 3.2 17.2 + - - +
237B ALA* 2.8 31.7 + - - +
250B LEU* 4.0 22.7 - - + +
253B ARG* 4.5 10.8 - - + -
254B THR* 3.7 32.5 - - - +
257B TRP* 3.8 19.7 - - + -
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Residues in contact with TYR 234 (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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80B ILE* 3.8 14.2 - - + +
85B ILE* 2.5 37.7 + - + +
86B THR 3.6 10.3 - - - -
87B SER* 3.5 30.3 - - - -
88B PHE* 3.6 20.8 - + + -
91B LEU* 4.2 18.8 - - + -
230B LEU 2.9 18.2 + - - +
231B ASN* 3.5 6.3 - - - +
233B LEU* 1.3 76.8 - - - +
235B ARG* 1.3 66.7 + - + +
237B ALA* 2.9 16.9 + - + +
238B ILE* 3.0 44.2 + - + +
254B THR* 4.8 1.5 + - - -
279B ILE* 4.1 25.6 - - + -
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Residues in contact with ARG 235 (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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231B ASN 2.9 17.0 + - - +
232B ASP* 3.8 11.2 + - - +
233B LEU 3.4 0.2 - - - -
234B TYR* 1.3 79.1 - - + +
236B GLN* 1.3 64.5 + - + +
238B ILE* 3.2 28.2 + - + +
239B SER* 3.8 7.4 + - - -
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Residues in contact with GLN 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* 3.0 31.6 + - - +
233B LEU* 3.5 18.0 - - - +
235B ARG* 1.3 78.6 - - + +
237B ALA* 1.3 64.1 + - - +
239B SER* 3.2 24.4 + - - -
242B LEU* 3.4 9.0 - - - +
250B LEU* 3.9 23.8 - - + +
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Residues in contact with ALA 237 (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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233B LEU 2.8 16.9 + - - +
234B TYR* 2.9 9.1 + - - +
236B GLN* 1.3 78.4 - - - +
238B ILE* 1.3 51.0 + - + +
239B SER 3.1 3.7 + - - +
242B LEU* 4.3 2.7 - - - -
247B LEU* 3.9 7.3 - - + +
250B LEU* 3.9 21.3 - - + -
251B ILE* 5.5 1.3 - - + -
254B THR* 5.3 3.4 - - - +
279B ILE* 3.9 26.2 - - + +
283B HIS* 2.6 33.8 + - - -
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Residues in contact with ILE 238 (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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26B PHE* 3.4 43.0 - - + -
27B ARG 5.0 0.2 - - - +
29B LEU* 4.1 8.2 - - + +
80B ILE* 3.8 19.3 - - + +
83B GLY* 6.5 0.9 - - - -
85B ILE 4.8 4.3 - - - +
86B THR* 4.9 5.6 - - - +
234B TYR* 3.0 57.6 + - + +
235B ARG* 3.2 22.4 - - + +
236B GLN 3.2 0.4 - - - -
237B ALA* 1.3 78.0 - - + +
239B SER* 1.3 60.6 + - - +
240B SER 4.2 0.2 + - - -
279B ILE* 5.5 3.1 - - + -
283B HIS* 4.1 4.9 - - - +
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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