Contacts of the helix formed by residues 212 - 223 (chain G) in PDB entry 40ER
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 212 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210G THR 3.6 6.3 - - - +
211G THR* 1.3 93.7 - - + +
213G VAL* 1.3 61.5 + - - +
214G TYR* 4.1 8.5 - - + +
215G VAL* 3.1 38.6 - - + +
216G ALA* 3.5 5.4 + - - +
258G LEU 4.1 4.7 - - - +
259G ASP* 3.7 18.4 - - - +
260G VAL 3.2 10.8 - - - +
261G SER* 4.0 0.4 - - - -
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Residues in contact with VAL 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G PRO* 1.3 70.1 - - - +
214G TYR* 1.3 63.2 + - - +
216G ALA* 3.3 4.3 + - - +
217G LEU* 3.0 27.5 + - + +
241G TYR* 4.2 14.1 - - - +
249G LEU* 4.9 6.7 - - + -
257G ASN 4.5 0.4 - - - +
258G LEU* 3.1 44.9 - - + +
260G VAL* 2.6 29.2 + - + +
261G SER 3.5 19.7 - - - +
262G VAL* 3.8 13.0 - - + -
265G ALA* 3.6 21.5 - - + -
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Residues in contact with TYR 214 (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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96G HIS* 3.2 61.7 + + + -
99G TYR* 3.4 39.1 + + + +
212G PRO* 3.1 4.6 - - + -
213G VAL* 1.3 79.6 - - - +
215G VAL* 1.3 67.0 + - + +
217G LEU* 3.0 12.6 + - + +
218G GLY 2.8 22.0 + - - -
258G LEU* 3.2 31.5 + - + +
259G ASP* 5.8 0.2 - - - +
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Residues in contact with VAL 215 (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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96G HIS* 5.5 0.4 - - - -
207G VAL* 5.2 2.9 - - + -
211G THR* 3.9 24.7 - - + -
212G PRO* 3.1 39.2 + - + +
214G TYR* 1.3 83.7 - - + +
216G ALA* 1.3 64.8 + - - +
218G GLY* 3.1 4.8 + - - +
219G ILE* 3.0 30.4 + - + +
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Residues in contact with ALA 216 (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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207G VAL* 4.0 11.2 - - + -
212G PRO 4.0 0.9 - - - +
213G VAL* 3.3 11.8 + - - +
214G TYR 3.1 0.2 - - - -
215G VAL* 1.3 81.7 - - - +
217G LEU* 1.3 61.9 + - - +
219G ILE 3.2 2.3 + - - -
220G PHE* 3.1 19.9 + - - -
228G LEU* 3.2 30.3 - - + +
241G TYR* 4.2 12.8 - - + -
262G VAL* 3.9 26.2 - - + -
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Residues in contact with LEU 217 (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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92G ILE* 3.7 21.1 - - + +
95G LEU* 3.8 39.7 - - + -
96G HIS* 4.1 12.8 - - + +
213G VAL* 3.0 20.4 + - + +
214G TYR* 3.0 11.3 + - + +
216G ALA* 1.3 75.7 - - - +
218G GLY* 1.3 57.4 + - - +
220G PHE* 3.1 11.3 + - + +
221G VAL* 3.0 32.6 + - - +
241G TYR* 4.8 4.7 - - + +
246G VAL* 3.7 32.3 - - + -
249G LEU* 5.2 3.4 - - + -
258G LEU* 4.3 15.9 - - + -
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Residues in contact with GLY 218 (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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96G HIS* 3.3 29.1 + - - -
214G TYR 2.8 9.8 + - - -
215G VAL* 3.1 8.0 + - - -
216G ALA 3.1 0.6 - - - -
217G LEU* 1.3 78.8 - - - +
219G ILE* 1.3 57.1 + - - +
221G VAL* 3.2 18.3 - - - +
222G GLN* 3.3 14.7 + - - +
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Residues in contact with ILE 219 (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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205G ALA* 4.0 9.2 - - + -
206G MET 3.4 24.9 - - - +
207G VAL* 3.6 17.7 - - + -
215G VAL* 3.0 16.2 + - + +
216G ALA 3.6 6.1 - - - +
217G LEU 3.2 0.4 - - - -
218G GLY* 1.3 75.0 - - - +
220G PHE* 1.3 62.3 + - - +
221G VAL 3.2 0.4 - - - -
222G GLN* 4.3 6.7 - - - +
223G HIS* 2.9 52.8 + - + +
225G VAL* 4.5 0.8 - - + +
228G LEU* 3.5 21.8 - - + -
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Residues in contact with PHE 220 (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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89G THR* 5.6 3.1 - - - +
92G ILE* 3.9 15.5 - - + -
216G ALA 3.1 16.0 + - - -
217G LEU* 3.1 23.0 + - + +
219G ILE* 1.3 78.3 - - - +
221G VAL* 1.3 55.7 + - - +
223G HIS 2.7 20.9 - - - +
224G ARG* 4.9 0.3 - - - -
225G VAL* 3.7 17.9 - - + +
227G ALA* 3.7 16.2 - - - -
228G LEU* 3.5 27.4 - - + -
241G TYR* 3.4 41.7 - + - -
243G LYS* 3.4 46.2 + - + -
246G VAL* 4.1 11.0 - - + -
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Residues in contact with VAL 221 (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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92G ILE* 4.3 6.3 - - + -
93G ASN* 3.3 41.5 + - - +
96G HIS* 3.7 31.9 - - + +
217G LEU 3.0 14.3 + - - +
218G GLY 3.2 17.3 - - - +
220G PHE* 1.3 78.6 - - - +
222G GLN* 1.3 63.6 + - + +
223G HIS 3.4 3.0 - - - +
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Residues in contact with GLN 222 (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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218G GLY 3.3 16.4 + - - +
219G ILE* 3.3 6.0 + - - +
221G VAL* 1.3 83.0 - - + +
223G HIS* 1.3 85.7 + - + +
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Residues in contact with HIS 223 (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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203G ASN* 6.3 2.8 - - + +
205G ALA* 4.5 14.4 - - + +
219G ILE* 2.9 32.9 + - + +
220G PHE 2.7 27.3 - - - +
221G VAL 3.8 3.4 - - - +
222G GLN* 1.3 109.1 - - + +
224G ARG* 1.3 63.9 + - - +
225G VAL* 3.3 23.3 - - + +
403G AMP 5.6 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