Contacts of the helix formed by residues 210 - 223 (chain A) in PDB entry 2MBG
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 PRO 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.3 17.3 - - + -
197A ALA* 4.2 6.3 - - + -
198A VAL* 3.8 10.7 - - + -
201A THR* 3.2 12.1 - - - +
209A LEU* 1.3 99.4 - - + +
211A ALA* 1.3 66.2 + - - +
212A VAL* 4.4 2.9 - - + +
213A PHE* 3.7 16.5 + - + +
214A ARG* 3.3 15.0 + - - +
270A TYR* 3.1 41.1 - - + +
313A CYS* 6.1 0.7 - - + -
317A LEU* 4.3 6.5 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A THR* 2.8 36.8 + - + +
203A MET* 3.5 23.3 - - + -
210A PRO* 1.3 69.3 - - - +
212A VAL* 1.3 58.3 + - - +
214A ARG* 2.8 17.2 + - - +
215A GLU* 2.7 49.7 + - - +
247A TYR* 6.2 0.2 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ILE* 4.5 7.6 - - + -
190A PHE* 4.8 0.4 - - + -
201A THR* 4.8 8.7 - - + -
210A PRO 3.4 0.2 - - - -
211A ALA* 1.3 76.5 - - - +
213A PHE* 1.3 63.4 + - - +
215A GLU* 3.3 9.8 + - - +
216A CYS* 3.0 35.5 + - - -
247A TYR* 3.4 32.3 - - + -
266A LEU* 3.8 29.6 - - + -
267A LEU* 4.7 1.8 - - + -
270A TYR* 3.9 44.6 - - + +
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.2 11.9 - - + -
210A PRO* 3.7 24.8 + - + +
211A ALA 3.1 0.4 + - - -
212A VAL* 1.3 78.6 - - - +
214A ARG* 1.3 58.6 + - - +
216A CYS* 3.4 0.9 + - - +
217A ILE* 2.9 48.5 + - + +
267A LEU* 3.5 25.8 - - + +
270A TYR* 4.8 3.1 - - + -
271A LEU* 4.3 4.7 - - + -
317A LEU* 3.8 24.7 - - + -
320A TRP* 3.3 37.7 - + + -
321A LEU* 3.3 56.3 - - + -
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR 3.1 23.6 + - - -
202A MET* 4.5 0.6 - - - +
203A MET* 3.3 26.6 - - + +
204A TYR* 5.6 1.3 - - - -
206A GLY* 5.6 3.0 - - - +
207A ILE* 3.9 19.4 - - - +
209A LEU* 2.8 58.1 + - + +
210A PRO 3.3 4.8 + - - +
211A ALA* 2.8 18.6 + - - +
213A PHE* 1.3 72.7 - - - +
215A GLU* 1.3 58.9 + - - +
217A ILE* 3.6 6.5 - - - +
218A ASP* 2.7 39.2 + - - +
320A TRP* 3.6 28.9 - - + -
374A LYS 4.9 1.5 - - - +
376A VAL* 3.7 22.8 - - + +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 4.2 16.4 - - + -
211A ALA* 2.7 41.6 + - - +
212A VAL 3.6 3.8 - - - +
214A ARG* 1.3 73.8 - - - +
216A CYS* 1.3 60.2 + - - +
218A ASP* 4.3 0.9 - - - -
219A TYR* 3.3 9.0 + - - +
247A TYR* 2.7 41.5 + - - +
253A THR* 3.8 11.6 + - - +
255A LEU* 3.5 19.4 - - + +
376A VAL* 5.5 0.4 - - - -
378A LYS* 2.9 41.3 + - + +
379A PRO* 5.6 2.9 - - - +
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.0 38.6 + - - +
213A PHE 3.9 0.2 - - - +
215A GLU* 1.3 74.4 - - - +
217A ILE* 1.3 67.0 + - - +
218A ASP 3.2 0.2 - - - -
219A TYR* 3.5 4.5 + - - +
220A VAL* 3.1 30.5 + - + +
231A TYR* 5.0 1.1 - - - +
247A TYR* 5.1 0.4 - - - -
255A LEU* 4.4 14.4 - - - -
263A VAL* 3.7 30.4 - - + +
264A ALA 5.2 0.2 - - - +
266A LEU* 4.5 4.7 - - - -
267A LEU* 3.8 33.4 - - + -
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 2.9 47.6 + - + +
214A ARG* 3.9 5.8 - - - +
216A CYS* 1.3 76.2 - - - +
218A ASP* 1.3 60.2 + - - +
220A VAL* 3.6 0.4 + - - -
221A GLU* 2.9 29.5 + - + +
231A TYR* 3.9 9.2 - - - +
267A LEU* 3.6 24.5 - - + -
320A TRP* 4.5 12.6 - - + -
324A HIS* 3.4 43.0 + - + +
325A MET* 4.8 4.9 - - + -
373A LEU* 4.3 18.4 - - + -
374A LYS 5.1 4.5 - - - +
375A GLN* 6.0 0.2 - - - -
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG 2.7 23.3 + - - +
215A GLU* 3.7 4.3 - - - +
217A ILE* 1.3 73.8 - - - +
219A TYR* 1.3 65.4 + - - +
221A GLU* 3.2 5.1 + - - +
222A LYS* 2.6 62.9 + - - +
375A GLN* 3.2 11.1 - - - +
376A VAL 3.0 41.1 + - - +
378A LYS* 2.6 27.4 + - + +
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLU 3.3 14.2 + - - +
216A CYS 3.9 4.0 - - - +
217A ILE 3.4 0.2 - - - -
218A ASP* 1.3 84.5 + - - +
220A VAL* 1.3 58.1 + - - +
222A LYS 3.2 0.2 + - - -
223A TYR* 2.7 61.1 + + + +
224A GLY 3.1 6.9 + - - -
255A LEU* 3.2 25.6 - - + -
256A GLU* 3.6 33.2 + - - +
258A TYR 2.7 21.8 + - - -
259A GLU* 4.2 2.0 + - - -
260A PRO* 3.5 42.6 - - + +
263A VAL* 3.8 19.5 - - + -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A CYS* 3.1 17.8 + - + +
219A TYR* 1.3 84.2 - - + +
221A GLU* 1.3 62.7 + - - +
224A GLY* 3.0 49.4 + - - +
225A MET* 3.1 13.6 - - + +
230A ILE* 4.0 10.3 - - + -
231A TYR* 3.7 34.5 - - + +
260A PRO* 5.1 2.2 - - + +
263A VAL* 4.6 9.6 - - + -
264A ALA* 5.3 0.2 - - + -
324A HIS* 3.6 24.2 - - + -
328A VAL* 4.6 1.6 - - + -
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ILE* 2.9 20.4 + - + +
218A ASP* 3.2 7.2 + - - +
220A VAL* 1.3 76.9 - - - +
222A LYS* 1.3 62.1 + - + +
225A MET* 3.2 35.3 - - - +
324A HIS* 2.7 31.5 + - + +
327A HIS* 4.4 12.4 - - - +
373A LEU* 3.6 32.4 - - + +
375A GLN* 5.7 5.2 - - + -
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ASP* 2.6 56.8 + - - +
220A VAL 4.3 0.2 - - - -
221A GLU* 1.3 83.0 - - + +
223A TYR* 1.3 91.3 + - + +
225A MET* 5.1 2.4 - - - +
256A GLU* 2.6 23.8 + - - -
375A GLN* 3.7 26.6 - - + +
376A VAL 4.2 1.8 + - - -
378A LYS* 3.4 9.9 - - - +
404A ARG* 6.1 0.7 - - - +
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 2.7 47.6 + + + +
222A LYS* 1.3 102.5 - - + +
224A GLY* 1.3 56.5 + - - +
225A MET* 3.1 10.4 + - - +
226A LYS* 4.3 5.7 + - - +
227A CYS* 5.1 1.4 + - - +
256A GLU* 3.4 30.8 + - + +
260A PRO* 5.7 0.4 - - - -
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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