Contacts of the helix formed by residues 231 - 241 (chain B) in PDB entry 5M7R
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 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLU* 2.5 28.5 + - - -
224B CYS* 4.4 2.5 - - - -
225B TYR 3.3 11.1 + - - -
227B ASN 3.3 16.0 + - - -
228B VAL 3.5 10.6 + - - -
229B SER 3.7 0.8 - - - -
230B GLN* 1.3 74.8 - - - +
232B PRO* 1.4 63.5 - - - +
233B TYR* 3.4 4.9 + - - +
234B LEU* 3.1 22.4 + - - -
235B ARG* 2.9 29.2 + - - +
270B ILE* 3.8 2.5 - - - +
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Residues in contact with PRO 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B SER* 5.9 1.3 - - - -
225B TYR* 3.6 15.7 - - + +
226B PRO* 4.2 5.6 - - + -
230B GLN 3.1 10.5 - - - +
231B SER* 1.4 79.4 - - - +
233B TYR* 1.3 66.7 + - - +
235B ARG* 3.9 16.2 - - + +
236B THR* 2.9 29.8 + - - -
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B HIS* 4.3 14.8 - + + -
190B SER* 5.7 0.4 - - - -
191B PHE* 4.3 5.6 - + + -
192B ALA* 3.6 34.1 - - + +
195B GLN* 2.3 42.5 + - - -
214B PHE* 3.9 1.9 - - - -
216B PRO* 3.4 25.0 - - + +
217B THR* 2.9 27.7 + - - -
218B GLU* 3.6 33.0 - - + +
225B TYR 5.9 0.2 - - - +
231B SER* 3.3 7.8 + - - +
232B PRO* 1.3 81.6 - - - +
234B LEU* 1.3 67.6 + - + +
237B VAL* 3.2 34.0 + - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PRO* 4.6 9.9 - - + -
218B GLU* 4.0 21.1 - - - +
224B CYS* 3.7 25.6 - - - -
228B VAL* 4.0 15.7 - - + +
231B SER* 3.1 18.2 + - - +
233B TYR* 1.3 85.0 - - + +
235B ARG* 1.3 60.4 + - - +
237B VAL* 3.7 6.1 - - + +
238B GLY 2.8 26.2 + - - -
249B TRP* 4.3 4.9 - - + -
267B VAL* 4.3 14.6 - - + -
270B ILE* 3.5 29.8 - - + +
271B ILE* 3.8 19.9 - - + +
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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
----------------------------------------------------------
229B SER 4.7 5.7 + - - -
230B GLN* 4.1 22.2 + - - +
231B SER 2.9 19.3 + - - +
232B PRO* 3.3 14.7 + - - +
234B LEU* 1.3 75.7 - - - +
236B THR* 1.3 57.5 + - - +
238B GLY* 3.3 1.2 + - - -
239B GLU* 3.0 59.7 + - + +
270B ILE* 3.7 25.4 - - + +
272B LYS* 5.3 3.7 - - - -
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Residues in contact with THR 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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190B SER* 4.2 2.4 + - - -
192B ALA* 3.7 22.6 - - + +
193B HIS* 3.5 50.9 + - + +
196B VAL* 4.6 1.5 - - + +
232B PRO* 2.9 18.0 + - - +
235B ARG* 1.3 74.0 - - - +
237B VAL* 1.3 59.3 + - - +
239B GLU* 3.2 8.6 + - - -
240B LYS* 2.8 41.6 + - + +
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Residues in contact with VAL 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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192B ALA* 4.6 3.4 - - + -
196B VAL* 4.1 17.7 - - + -
214B PHE* 4.0 21.5 - - + -
216B PRO* 5.6 0.9 - - + -
233B TYR* 3.2 38.5 + - + +
234B LEU* 3.2 13.4 + - + +
236B THR* 1.3 74.4 - - - +
238B GLY* 1.3 64.0 + - - +
241B LEU* 3.1 49.8 + - + +
247B VAL* 4.3 12.3 - - + -
271B ILE* 4.5 11.2 - - + -
273B ARG* 3.7 1.6 + - - +
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Residues in contact with GLY 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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234B LEU 2.8 15.2 + - - -
235B ARG 3.7 0.4 - - - -
237B VAL* 1.3 75.5 - - - +
239B GLU* 1.3 60.8 + - - +
241B LEU 4.6 0.2 - - - +
270B ILE 3.3 21.8 - - - -
271B ILE* 3.4 18.6 - - - +
272B LYS* 3.7 20.4 - - - +
273B ARG* 3.7 11.2 + - - -
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Residues in contact with GLU 239 (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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235B ARG* 3.0 46.6 + - - +
236B THR* 3.2 5.8 + - - +
238B GLY* 1.3 78.7 - - - +
240B LYS* 1.3 69.0 + - + +
241B LEU 4.0 2.3 + - - +
272B LYS* 4.4 20.7 + - - +
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Residues in contact with LYS 240 (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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193B HIS* 3.9 36.0 + - + +
196B VAL* 3.5 15.7 - - + -
200B ASN* 2.8 22.0 + - - -
236B THR* 2.8 24.2 + - + +
239B GLU* 1.3 82.2 - - + +
241B LEU* 1.3 61.0 + - - +
242B LEU* 3.4 2.4 + - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 3.6 18.2 - - + +
199B THR* 3.8 33.2 - - + -
200B ASN* 3.8 11.0 - - - +
214B PHE* 3.9 19.1 - - + -
237B VAL* 3.1 24.8 + - + +
238B GLY 4.6 1.9 - - - +
239B GLU 4.6 1.6 - - - +
240B LYS* 1.3 76.5 - - - +
242B LEU* 1.3 65.6 + - - +
243B PRO* 3.4 1.6 - - - +
245B ILE* 3.9 22.2 - - + -
247B VAL* 3.5 32.3 - - + -
273B ARG* 2.8 27.2 + - - +
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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