Contacts of the strand formed by residues 236 - 243 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G CYS* 3.2 0.9 - - - -
233G VAL 2.8 33.5 + - - +
234G ASN 3.4 3.1 + - - -
235G GLY* 1.3 77.7 - - - +
237G CYS* 1.3 62.6 - - - +
238G PHE* 3.2 23.6 - - - -
256G LYS* 3.7 10.9 - - - -
257G MET 3.4 5.6 - - - -
258G GLU* 2.5 34.2 + - - +
308G GLN* 5.1 4.3 + - - -
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Residues in contact with CYS 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G CYS* 4.1 7.9 - - - -
185G ASP* 3.6 19.3 - - - -
190G LEU* 3.9 26.5 - - + -
207G TYR* 6.4 0.7 - - - -
231G ALA 3.4 4.0 - - - +
232G CYS* 2.0 45.5 - - - -
235G GLY 5.5 0.2 - - - -
236G SER* 1.3 74.3 - - - +
238G PHE* 1.3 65.0 + - - +
256G LYS* 3.5 2.3 - - - -
257G MET* 2.7 50.4 + - + +
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Residues in contact with PHE 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G GLN* 4.2 0.3 + - - -
230G CYS* 3.1 22.5 - - - +
231G ALA* 2.9 23.5 + - - +
233G VAL* 4.4 9.2 - - + -
236G SER* 3.2 38.6 - - - -
237G CYS* 1.3 73.0 - - - +
239G THR* 1.3 62.4 + - - +
255G PHE 3.2 7.9 - - - +
256G LYS* 3.8 22.0 - - + -
257G MET* 4.4 1.1 - - - -
280G CYS* 5.7 2.1 - - - +
287G ILE* 3.8 20.4 - - + -
305G PHE* 3.7 28.3 - + + -
306G ASN 4.3 0.7 - - - -
308G GLN* 3.8 39.7 - - + -
310G LEU* 3.7 23.1 - - + -
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Residues in contact with THR 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G SER* 3.9 3.5 + - - -
192G ILE* 4.2 9.4 - - + +
225G THR* 3.6 13.7 + - - -
226G GLN* 2.8 21.8 + - - +
230G CYS* 4.4 3.1 - - - -
238G PHE* 1.3 77.5 - - - +
240G VAL* 1.3 76.8 + - - +
241G MET* 4.9 7.0 - - + -
254G ILE* 3.6 6.6 - - - +
255G PHE* 3.1 44.9 + - + -
257G MET* 3.2 27.6 - - + -
280G CYS* 5.5 2.0 - - - -
305G PHE* 5.0 1.4 - - - -
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Residues in contact with VAL 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G THR* 3.1 25.8 + - - -
226G GLN* 3.9 7.4 + - + +
239G THR* 1.3 85.2 + - - +
241G MET* 1.3 72.8 + - - +
242G THR* 5.2 4.9 - - - +
252G TYR* 5.4 4.0 - - + -
253G LYS 3.5 12.6 - - - +
254G ILE* 5.1 5.6 - - + -
255G PHE* 5.0 0.2 - - - -
268G LEU* 5.7 5.4 - - + -
275G TYR* 5.3 6.5 - - + -
278G CYS* 3.9 28.9 - - + -
280G CYS* 4.0 4.5 - - - -
289G CYS* 3.8 29.4 - - - -
303G VAL* 5.6 5.2 - - + -
305G PHE* 4.9 7.9 - - + -
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Residues in contact with MET 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G ILE* 3.6 35.7 - - + -
194G ILE* 4.4 1.8 - - + -
203G ALA* 3.7 14.1 - - + -
205G LEU* 4.9 0.2 - - + -
215G ILE* 4.0 19.1 - - + -
218G TRP* 3.9 11.2 - - + -
223G LEU* 4.1 24.2 - - + -
224G ARG 3.6 5.8 - - - +
225G THR* 4.0 17.9 - - - +
239G THR* 4.9 6.7 - - + -
240G VAL* 1.3 82.8 - - - +
242G THR* 1.3 61.8 + - - +
252G TYR* 3.5 3.5 - - - +
253G LYS 2.9 33.5 + - - -
255G PHE* 3.6 30.0 - - + -
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Residues in contact with THR 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G LEU* 3.5 4.1 - - - +
224G ARG* 3.0 62.8 + - - +
240G VAL* 5.2 3.1 - - - +
241G MET* 1.3 75.1 + - - +
243G ASP* 1.3 66.3 + - - +
250G ALA* 3.9 15.7 - - + -
251G SER 3.4 11.0 - - - +
252G TYR* 3.7 6.4 - - + +
275G TYR* 2.6 33.2 + - - +
276G GLU* 4.1 12.2 - - - +
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Residues in contact with ASP 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G SER* 2.5 29.3 + - - -
218G TRP* 2.7 39.4 + - + -
219G ARG* 2.8 15.7 + - + +
221G ASN 2.9 35.7 + - - +
223G LEU* 3.9 8.5 + - + -
224G ARG* 4.1 0.4 - - - +
242G THR* 1.3 78.5 - - - +
244G GLY* 1.3 58.9 + - - +
251G SER* 3.1 32.0 + - - -
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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