Contacts of the helix formed by residues 207 - 215 (chain B) in PDB entry 2B4M
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 GLY 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLU 3.5 0.6 + - - -
206B ALA* 1.3 74.6 - - - +
208B PRO* 1.3 54.4 - - - +
209B MET 3.7 2.2 - - - +
210B TRP* 3.0 13.9 + - - +
211B THR* 2.7 42.9 + - - -
233B TYR* 3.6 26.2 - - - -
236B LYS* 6.1 1.3 - - - -
237B TYR* 4.8 1.0 - - - -
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Residues in contact with PRO 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 4.0 21.4 - - + +
205B GLU* 3.5 26.5 - - + +
206B ALA 3.3 13.2 - - - +
207B GLY* 1.3 82.6 - - - +
209B MET* 1.3 54.6 + - - +
211B THR* 3.7 8.0 - - - +
212B ALA* 2.9 30.5 + - - +
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Residues in contact with MET 209 (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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102B ILE* 4.6 5.4 - - - -
174B ALA* 4.3 12.2 - - + +
176B VAL* 3.8 19.3 - - + -
204B VAL* 3.7 20.3 - - + +
205B GLU 2.9 19.8 + - - +
206B ALA* 4.2 2.5 - - - -
207B GLY 3.1 0.2 - - - -
208B PRO* 1.3 74.4 - - - +
210B TRP* 1.3 96.4 + - + +
212B ALA* 3.4 4.6 + - - +
213B ILE* 3.2 31.1 + - - +
221B SER* 3.4 26.9 - - - +
223B SER* 3.8 33.9 - - - +
224B ALA* 4.5 0.9 - - - +
230B HIS* 4.4 2.9 - - + -
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Residues in contact with TRP 210 (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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102B ILE* 3.8 24.2 - - + -
206B ALA* 4.7 1.1 - - - -
207B GLY* 3.0 15.3 + - - +
209B MET* 1.3 94.9 - - + +
211B THR* 1.3 61.2 + - - +
213B ILE* 3.4 5.1 + - + +
214B ALA* 2.9 30.7 + - - +
224B ALA* 3.9 19.1 - - + -
226B LEU* 4.2 6.5 - - + -
230B HIS* 3.4 42.4 + - + -
233B TYR* 3.6 40.1 - + + +
234B ALA* 4.0 18.2 - - + -
237B TYR* 3.6 24.6 - + + -
241B TYR* 3.5 36.6 - + + -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLY 2.7 28.7 + - - -
208B PRO* 3.7 8.5 - - - +
210B TRP* 1.3 72.3 - - - +
212B ALA* 1.3 51.1 + - - +
214B ALA 3.2 1.0 + - - -
215B THR* 2.6 57.2 + - + +
236B LYS* 4.8 2.8 + - - -
237B TYR* 2.7 27.2 + - + +
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Residues in contact with ALA 212 (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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174B ALA* 5.1 3.4 - - + -
204B VAL* 5.5 4.7 - - + -
208B PRO 2.9 20.7 + - - +
209B MET* 3.6 7.2 - - - +
210B TRP 3.4 0.2 - - - -
211B THR* 1.3 75.8 - - - +
213B ILE* 1.3 59.9 + - - +
215B THR* 3.8 0.7 - - - -
216B GLY 3.2 2.8 + - - -
217B SER* 2.8 47.7 + - - +
218B ALA* 3.1 19.9 + - + -
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Residues in contact with ILE 213 (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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102B ILE* 4.0 24.0 - - + +
103B THR 3.2 26.5 - - - +
104B ARG* 3.3 16.1 - - - +
105B LYS 4.5 0.3 + - - -
174B ALA* 4.7 1.3 - - + -
209B MET 3.2 14.2 + - - +
210B TRP* 3.7 6.7 - - + +
212B ALA* 1.3 75.5 - - - +
214B ALA* 1.3 63.0 + - - +
216B GLY 3.2 9.7 + - - -
218B ALA* 3.9 17.5 - - + +
219B ASP 4.1 1.3 - - - +
220B ALA* 3.7 41.7 - - - +
221B SER* 3.9 12.1 - - - +
240B LYS 4.3 1.0 - - - +
241B TYR* 3.9 14.1 - - + -
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Residues in contact with ALA 214 (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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105B LYS* 5.9 0.5 - - - +
210B TRP* 2.9 15.4 + - + +
211B THR 3.8 1.3 - - - +
213B ILE* 1.3 77.8 - - - +
215B THR* 1.3 60.6 + - + +
216B GLY 3.4 0.8 + - - -
237B TYR* 3.2 46.9 - - + -
240B LYS* 3.6 33.4 - - + +
241B TYR* 5.1 1.3 - - + -
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Residues in contact with THR 215 (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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211B THR* 2.6 47.4 + - + +
212B ALA* 3.7 5.2 + - - -
214B ALA* 1.3 78.5 - - + +
216B GLY* 1.3 54.6 + - - +
217B SER* 2.8 18.7 + - - -
237B TYR* 5.5 3.1 - - + -
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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