Contacts of the strand formed by residues 236 - 243 (chain F) in PDB entry 2HU4
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 SER 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232F CYS* 3.2 1.0 - - - -
233F VAL 2.7 41.1 + - - +
234F ASN* 4.5 2.9 + - - -
235F GLY* 1.3 74.5 - - - +
237F CYS* 1.3 63.8 + - - +
238F PHE* 3.3 24.2 - - - -
256F LYS* 3.6 12.6 + - - -
257F MET 3.6 4.7 - - - -
258F GLU* 2.8 27.3 + - - -
308F GLN* 5.1 5.3 + - - -
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Residues in contact with CYS 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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183F CYS* 4.0 6.7 - - - -
185F ASP* 3.7 18.2 - - - -
190F LEU* 3.8 28.7 - - + -
207F TYR* 6.2 0.9 - - - -
230F CYS* 5.1 0.2 - - - -
231F ALA 3.4 3.6 - - - -
232F CYS* 2.1 44.9 - - - -
235F GLY 5.2 0.7 - - - -
236F SER* 1.3 73.3 - - - +
238F PHE* 1.3 64.4 + - - +
256F LYS* 3.6 2.3 - - - -
257F MET* 2.9 42.9 + - - +
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Residues in contact with PHE 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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226F GLN* 4.0 0.7 + - - -
230F CYS* 3.0 22.8 - - - +
231F ALA* 2.8 28.1 + - - +
232F CYS* 4.8 0.2 - - - -
233F VAL* 4.5 5.6 - - + -
236F SER* 3.3 36.8 - - - -
237F CYS* 1.3 74.7 - - - +
239F THR* 1.3 62.5 + - - +
255F PHE 3.2 11.0 - - - +
256F LYS* 3.8 17.7 - - + -
257F MET* 4.3 0.2 - - - -
280F CYS* 5.4 2.9 - - - +
287F ILE* 3.6 23.8 - - + -
305F PHE* 3.6 34.5 - + + -
306F ASN 4.3 1.6 - - - -
308F GLN* 3.8 32.1 - - + -
310F LEU* 3.7 24.2 - - + -
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Residues in contact with THR 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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181F SER* 3.8 5.0 + - - -
192F ILE* 4.0 10.9 - - + +
225F THR* 3.4 13.3 + - - -
226F GLN* 2.5 27.5 + - - +
230F CYS* 4.3 1.8 - - - -
238F PHE* 1.3 74.6 - - - +
240F VAL* 1.3 67.2 + - - +
241F MET* 4.5 10.3 - - + -
254F ILE* 3.5 5.2 - - - +
255F PHE* 2.8 45.5 + - + +
257F MET* 3.1 27.4 - - + -
280F CYS* 5.5 1.6 - - - -
305F PHE* 5.6 0.4 - - - -
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Residues in contact with VAL 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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225F THR* 2.8 21.1 + - - -
226F GLN* 3.8 10.6 + - - +
239F THR* 1.3 79.4 + - - +
241F MET* 1.3 71.8 + - - +
242F THR* 5.0 4.7 - - - +
252F TYR* 5.1 6.5 - - + -
253F LYS 3.3 14.1 - - - +
254F ILE* 4.5 14.6 - - + -
268F LEU* 5.6 4.9 - - + -
275F TYR* 5.3 4.5 - - + -
276F GLU* 6.6 0.2 - - - -
278F CYS* 3.9 28.5 - - + -
280F CYS* 4.1 2.5 - - - -
289F CYS* 3.9 27.8 - - - -
303F VAL* 5.7 4.7 - - + -
305F PHE* 4.6 5.4 - - + -
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Residues in contact with MET 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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192F ILE* 3.5 32.5 - - + -
194F ILE* 4.1 4.7 - - + -
203F ALA* 3.9 15.7 - - + -
205F LEU* 5.3 0.2 - - + -
215F ILE* 4.2 17.7 - - + -
218F TRP* 4.0 9.6 - - + -
223F LEU* 4.3 16.8 - - + -
224F ARG 3.2 10.3 - - - +
225F THR* 3.9 18.8 - - - +
239F THR* 4.5 10.1 - - + -
240F VAL* 1.3 81.6 - - - +
242F THR* 1.3 63.3 + - - +
251F SER 4.0 0.2 - - - +
252F TYR* 3.5 2.3 - - - -
253F LYS* 2.9 32.8 + - - -
255F PHE* 3.7 32.3 - - + -
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Residues in contact with THR 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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218F TRP* 4.5 1.8 - - - -
223F LEU* 3.6 1.7 - - - +
224F ARG* 2.9 60.9 + - - +
240F VAL* 5.0 2.8 - - - +
241F MET* 1.3 75.3 + - - +
243F ASP* 1.3 67.3 + - - +
250F ALA* 3.8 11.2 - - + -
251F SER 3.2 11.9 - - - +
252F TYR* 3.4 17.3 - - + +
274F HIS* 5.8 0.2 - - - +
275F TYR* 2.9 30.1 + - - +
276F GLU* 4.4 11.1 - - + -
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Residues in contact with ASP 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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217F SER* 2.5 27.5 + - - -
218F TRP* 2.9 30.3 + - + -
219F ARG* 2.8 29.0 + - + +
221F ASN 3.0 31.2 + - - +
222F ILE 4.5 0.2 - - - -
223F LEU* 4.1 8.7 - - + +
224F ARG* 4.3 0.7 - - - +
242F THR* 1.3 77.5 - - - +
244F GLY* 1.3 59.2 + - - +
250F ALA* 4.3 1.6 - - - -
251F SER* 2.9 33.2 + - - -
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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