Contacts of the helix formed by residues 234 - 248 (chain F) in PDB entry 2CNW
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 GLN 234 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C MET 4.4 7.8 + - - +
40C ASP* 3.9 32.4 - - - +
42C ASP* 2.7 24.1 + - - +
224C GLN* 5.9 2.6 - - - +
43F ASP* 3.0 38.8 + - - +
44F VAL 4.3 1.6 - - - +
45F GLY* 3.3 25.9 + - - -
233F GLY* 1.3 72.7 - - - -
235F ASN* 1.3 59.9 + - - +
236F GLY 3.1 1.9 + - - -
237F LEU* 3.3 20.5 + - - +
238F GLU* 3.9 2.6 + - - +
265F VAL* 4.1 8.4 - - - +
268F PRO* 5.0 3.3 - - - +
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Residues in contact with ASN 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP* 4.1 6.0 + - - +
221C MET* 4.2 14.2 - - + +
250C ASP* 2.8 29.5 + - - -
251C ALA* 3.5 35.1 + - + +
110F VAL* 5.6 0.2 - - - +
196F LEU* 6.0 1.6 - - - +
197F HIS* 3.4 15.7 - - - -
232F THR* 4.7 1.1 - - + -
233F GLY 3.2 1.0 + - - -
234F GLN* 1.3 74.1 - - - +
236F GLY* 1.3 58.9 + - - +
238F GLU* 3.1 13.3 + - - +
239F GLN* 2.9 49.1 + - - +
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Residues in contact with GLY 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F LEU* 3.8 15.5 - - - +
232F THR* 3.4 19.4 - - - +
233F GLY 3.0 11.9 + - - -
235F ASN* 1.3 77.3 - - - +
237F LEU* 1.3 56.3 + - - +
239F GLN* 3.3 7.0 - - - +
240F ALA* 2.9 26.9 + - - +
265F VAL* 4.2 4.9 - - - -
269F ILE* 3.7 9.7 - - - +
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F GLN* 3.3 11.0 + - - +
235F ASN 3.3 0.6 - - - -
236F GLY* 1.3 71.7 - - - +
238F GLU* 1.3 62.9 + - - +
240F ALA* 3.1 3.5 + - + +
241F LYS* 2.8 53.8 + - + +
265F VAL* 3.9 11.7 - - + +
268F PRO* 3.6 43.5 - - + +
269F ILE* 3.8 16.8 - - + -
271F ARG* 5.8 1.8 - - - +
272F THR* 3.9 18.2 - - + +
273F LEU* 5.6 1.3 - - + -
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Residues in contact with GLU 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ASP* 3.9 22.6 - - - +
197F HIS* 3.9 8.5 - - + +
234F GLN 3.9 2.1 + - - +
235F ASN* 3.1 24.5 + - - +
237F LEU* 1.3 81.0 - - - +
239F GLN* 1.3 57.5 + - - +
241F LYS* 3.2 23.3 + - - +
242F LYS* 2.9 63.2 + - - +
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Residues in contact with GLN 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C MET* 2.9 34.8 - - - +
110F VAL* 3.5 36.9 + - + +
113F VAL* 4.9 1.6 - - - +
197F HIS* 3.8 12.7 - - - +
226F LEU* 4.8 5.3 - - + +
227F VAL 4.8 5.2 - - - +
228F LEU* 3.8 18.6 - - + +
229F ASP 5.4 0.2 + - - -
232F THR* 3.9 7.5 + - - +
235F ASN* 2.9 32.0 + - - +
236F GLY* 3.3 12.8 - - - +
238F GLU* 1.3 74.5 - - - +
240F ALA* 1.3 56.7 + - - +
242F LYS 3.9 0.2 - - - -
243F PHE* 2.9 43.1 + - + +
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Residues in contact with ALA 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F LEU* 3.9 21.3 - - + +
236F GLY 2.9 14.2 + - - +
237F LEU* 3.1 7.6 + - + +
239F GLN* 1.3 75.2 - - - +
241F LYS* 1.3 62.7 + - - +
244F HIS* 3.0 28.2 + - - +
249F LEU* 3.8 2.6 - - + +
269F ILE* 3.8 25.4 - - + -
273F LEU* 3.4 19.5 - - + +
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Residues in contact with LYS 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F LEU* 2.8 46.7 + - + +
238F GLU* 3.6 26.5 - - - +
240F ALA* 1.3 72.5 - - - +
242F LYS* 1.3 62.0 + - + +
244F HIS* 3.6 4.9 - - - +
245F GLU* 3.0 29.3 + - - +
272F THR* 4.5 19.3 - - + +
273F LEU* 4.5 10.8 - - + +
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Residues in contact with LYS 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F HIS* 3.6 45.3 - - + +
203F MET* 3.6 6.0 - - + +
238F GLU* 2.9 39.0 + - - +
241F LYS* 1.3 79.3 - - + +
243F PHE* 1.3 62.7 + - - +
245F GLU* 3.5 10.8 + - + +
246F ALA* 3.2 23.2 + - - +
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Residues in contact with PHE 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F VAL* 4.0 10.1 - - + -
109F GLY* 3.7 22.7 - - - -
110F VAL* 3.8 20.4 - - + -
195F ARG* 3.6 29.6 - - + -
197F HIS* 4.0 14.4 - - + -
203F MET* 3.6 22.4 - - + -
206F LEU* 3.6 29.6 - - + -
226F LEU* 4.0 20.0 - - + -
239F GLN* 2.9 31.3 + - + +
240F ALA 4.4 1.1 - - - +
242F LYS* 1.3 74.8 - - - +
244F HIS* 1.3 58.2 + - - +
246F ALA* 3.2 0.7 + - - -
247F VAL* 3.0 37.1 + - + +
249F LEU* 4.2 11.4 - - + -
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Residues in contact with HIS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F ALA 3.0 19.4 + - - +
241F LYS 3.6 4.0 - - - +
243F PHE* 1.3 75.5 - - - +
245F GLU* 1.3 63.3 + - - +
248F GLY* 3.0 29.2 + - - -
249F LEU* 3.0 49.5 + - + +
273F LEU* 3.4 40.0 + - + +
275F VAL* 4.6 7.9 - - + -
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Residues in contact with GLU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F LYS* 4.5 12.7 + - - -
241F LYS 3.0 18.1 + - - +
242F LYS* 3.7 12.3 - - + +
243F PHE 3.4 0.2 - - - -
244F HIS* 1.3 77.4 - - - +
246F ALA* 1.3 65.3 + - - +
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Residues in contact with ALA 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F MET* 3.7 32.1 - - + +
206F LEU* 5.7 0.4 - - + -
207F LYS* 3.4 40.1 - - - +
210F LYS* 5.6 0.3 - - - +
242F LYS 3.2 16.7 + - - +
243F PHE 3.8 2.2 - - - +
244F HIS 3.2 0.2 - - - -
245F GLU* 1.3 81.0 - - - +
247F VAL* 1.3 66.6 + - + +
248F GLY 3.9 0.2 - - - -
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Residues in contact with VAL 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 5.1 3.1 - - + -
108F VAL* 4.4 13.9 - - + -
206F LEU* 3.9 32.3 - - + +
207F LYS* 4.0 18.2 - - - +
210F LYS* 2.8 44.5 + - + +
224F VAL* 3.7 23.8 - - + +
243F PHE* 3.0 18.5 + - - +
246F ALA* 1.3 85.2 - - + +
248F GLY* 1.3 68.2 + - - +
249F LEU* 4.5 2.2 - - + -
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Residues in contact with GLY 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LYS* 4.6 3.0 + - - -
224F VAL* 3.3 15.3 - - - +
243F PHE 3.8 0.8 + - - -
244F HIS* 3.0 26.7 + - - -
246F ALA 3.9 0.2 - - - -
247F VAL* 1.3 82.9 - - - +
249F LEU* 1.3 65.7 + - - +
250F THR* 3.7 5.6 + - - +
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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