Contacts of the helix formed by residues 242 - 254 (chain F) in PDB entry 1W88
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 ASP 242 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193F GLY 3.2 22.1 + - - +
194F LYS* 3.6 16.6 + - - +
195F ALA* 2.9 36.2 + - + +
235F LEU* 5.2 2.1 + - - +
237F THR 4.9 3.0 + - - -
240F PRO 3.8 1.2 + - - -
241F LEU* 1.3 68.3 - - - +
243F ILE* 1.3 64.5 + - - +
244F GLU* 3.6 9.2 + - - +
245F THR* 2.5 35.5 + - - -
246F ILE* 3.2 27.4 + - - +
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Residues in contact with ILE 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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353E PHE* 3.5 41.2 - - + -
241F LEU* 3.2 22.7 + - + +
242F ASP* 1.3 71.0 + - - +
244F GLU* 1.3 66.2 + - - +
246F ILE* 3.0 9.2 + - + +
247F ILE* 2.9 34.8 + - + +
275F GLU* 4.0 39.3 - - + +
279F ARG* 3.6 35.2 - - - +
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Residues in contact with GLU 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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353E PHE* 5.1 8.9 - - + -
194F LYS* 3.9 19.9 + - - -
242F ASP* 3.4 7.9 + - - +
243F ILE* 1.3 77.7 - - - +
245F THR* 1.3 58.7 + - - +
247F ILE* 4.1 3.1 - - - +
248F GLY* 2.9 28.1 + - - -
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Residues in contact with THR 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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194F LYS* 4.0 12.5 + - - -
195F ALA* 4.1 23.7 + - + +
196F ASP* 4.9 0.4 - - - -
197F ILE* 3.8 27.7 - - + +
233F VAL* 4.4 5.3 - - + +
242F ASP* 2.5 32.0 + - - -
243F ILE 3.4 0.6 - - - -
244F GLU* 1.3 78.3 - - - +
246F ILE* 1.3 62.4 + - - +
248F GLY* 4.0 1.0 - - - -
249F SER* 3.2 22.0 + - - -
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Residues in contact with ILE 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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195F ALA* 5.4 0.4 - - + -
205F THR* 5.0 0.5 - - - +
207F ILE* 3.8 24.5 - - + -
233F VAL* 4.7 12.1 - - + -
235F LEU* 3.7 31.9 - - + -
241F LEU* 4.1 22.7 - - + -
242F ASP* 3.2 23.7 + - + +
243F ILE* 3.0 11.9 + - + +
245F THR* 1.3 74.0 - - - +
247F ILE* 1.3 72.3 + - + +
249F SER* 3.3 6.3 + - - -
250F VAL* 3.2 22.5 + - - +
272F VAL* 4.6 7.2 - - + -
275F GLU* 6.3 2.2 - - + -
276F ILE* 3.9 22.2 - - + -
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Residues in contact with ILE 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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243F ILE* 2.9 36.0 + - + +
244F GLU* 4.1 3.1 - - - +
246F ILE* 1.3 75.4 - - + +
248F GLY* 1.3 57.8 + - - +
250F VAL* 3.1 4.3 + - - +
251F GLU* 2.8 58.7 + - + +
275F GLU* 4.1 4.0 - - + +
276F ILE* 4.0 32.5 - - + +
279F ARG* 3.9 29.8 - - + +
280F ALA* 4.2 14.1 - - + -
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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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244F GLU 2.9 18.1 + - - -
245F THR* 4.0 1.6 - - - -
247F ILE* 1.3 78.2 - - - +
249F SER* 1.3 59.1 + - - +
251F GLU* 3.6 12.1 + - - +
252F LYS* 3.2 21.1 + - - +
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Residues in contact with SER 249 (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 ILE* 5.0 2.0 - - - -
205F THR* 2.9 27.2 + - - +
231F GLU* 2.8 32.6 + - - +
233F VAL* 4.1 13.2 - - - -
245F THR 3.2 17.4 + - - -
246F ILE 3.6 4.9 - - - -
247F ILE 3.2 0.8 - - - -
248F GLY* 1.3 74.4 - - - +
250F VAL* 1.3 59.5 + - - +
252F LYS* 3.2 7.1 + - - +
253F THR* 3.0 24.8 + - - +
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Residues in contact with VAL 250 (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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205F THR* 3.7 16.4 - - + -
207F ILE* 4.7 0.2 - - + -
246F ILE 3.2 14.5 + - - +
247F ILE* 3.1 6.7 + - - +
249F SER* 1.3 71.7 - - - +
251F GLU* 1.3 61.5 + - - +
253F THR* 4.0 2.0 - - - -
254F GLY* 2.8 29.7 + - - -
255F ARG 4.8 4.0 - - - +
256F ALA* 3.7 26.5 - - + -
276F ILE* 4.0 28.0 - - + -
280F ALA* 4.7 9.9 - - + +
283F SER* 4.3 3.1 - - - -
284F LEU* 3.7 31.0 - - + -
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Residues in contact with GLU 251 (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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247F ILE* 2.8 39.2 + - + +
248F GLY* 3.7 10.7 - - - +
250F VAL* 1.3 79.0 - - - +
252F LYS* 1.3 59.9 + - - +
254F GLY* 4.4 1.9 + - - -
279F ARG 4.5 6.8 - - - +
280F ALA* 4.4 6.0 - - + +
283F SER* 3.6 28.1 + - - +
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Residues in contact with LYS 252 (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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200F GLU* 4.3 14.6 + - - +
201F GLY 3.1 23.8 + - - -
202F LYS* 4.3 9.7 - - + +
231F GLU* 2.9 35.1 + - - -
248F GLY 3.2 13.4 + - - +
249F SER* 3.2 8.2 + - - +
250F VAL 3.1 0.6 - - - -
251F GLU* 1.3 79.7 - - - +
253F THR* 1.3 65.4 + - + +
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Residues in contact with THR 253 (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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201F GLY 4.0 12.8 - - - +
202F LYS* 3.6 32.0 - - - +
203F ASP* 3.7 9.2 - - - +
204F ILE 3.7 21.3 - - - +
205F THR* 2.9 24.8 + - - +
231F GLU* 4.6 3.1 - - + -
249F SER 3.0 11.1 + - - +
250F VAL 4.0 0.9 + - - -
252F LYS* 1.3 84.1 - - - +
254F GLY* 1.3 62.6 + - - +
255F ARG* 2.9 21.9 + - - +
285F GLU* 5.0 2.1 - - - +
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Residues in contact with GLY 254 (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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250F VAL 2.8 20.6 + - - -
251F GLU 4.4 2.0 + - - -
252F LYS 3.7 1.0 - - - -
253F THR* 1.3 70.8 + - - +
255F ARG* 1.3 62.9 + - - +
283F SER 3.3 20.2 - - - -
284F LEU* 3.5 10.1 - - - +
285F GLU* 2.8 36.0 + - - +
286F ALA 4.2 0.2 + - - -
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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