Contacts of the helix formed by residues 209 - 223 (chain G) in PDB entry 1Q57
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 ASP 209 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207G ASP* 3.1 32.5 + - - +
208G MET* 1.3 77.5 - - - +
210G GLU* 1.3 73.9 + - + +
211G ALA* 3.4 8.3 + - - +
212G GLY* 2.9 28.6 + - - -
213G ARG* 2.8 22.9 + - - +
236G LYS* 4.0 19.9 + - + +
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Residues in contact with GLU 210 (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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115B ASN* 2.9 50.9 + - - +
209G ASP* 1.3 78.5 - - + +
211G ALA* 1.3 63.4 + - + +
212G GLY 3.1 0.2 + - - -
213G ARG* 3.3 4.2 + - - +
214G LYS* 3.3 17.5 + - - +
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Residues in contact with ALA 211 (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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182G ALA 5.0 2.1 - - - +
209G ASP* 3.4 6.6 + - - +
210G GLU* 1.3 79.6 - - + +
212G GLY* 1.3 56.5 + - - +
213G ARG 3.5 0.2 - - - -
214G LYS* 3.6 10.8 - - - +
215G ALA* 3.0 26.2 + - - +
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Residues in contact with GLY 212 (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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157G GLU* 4.6 3.1 - - - -
206G PHE* 3.7 2.6 - - - +
207G ASP* 3.4 30.1 - - - +
209G ASP* 2.9 17.5 + - - -
211G ALA* 1.3 76.6 - - - +
213G ARG* 1.3 63.1 + - - +
215G ALA* 3.5 7.8 + - - +
216G VAL* 3.3 25.3 + - - +
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Residues in contact with ARG 213 (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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204G LEU 5.1 0.2 + - - -
206G PHE* 3.4 18.0 + - - +
207G ASP 3.1 22.4 + - - -
208G MET* 3.2 35.3 - - - +
209G ASP 2.8 17.1 + - - +
210G GLU* 3.9 4.0 - - - +
212G GLY* 1.3 72.2 - - - +
214G LYS* 1.3 67.1 + - - +
216G VAL* 3.2 33.7 + - + +
217G GLU* 3.1 24.3 + - + +
230G VAL* 4.0 12.3 - - - +
231G ALA 3.4 17.6 + - - -
232G VAL* 4.2 3.2 - - - +
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Residues in contact with LYS 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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210G GLU 3.3 10.6 + - - +
211G ALA* 3.6 13.5 - - - +
212G GLY 3.3 0.2 - - - -
213G ARG* 1.3 79.2 - - - +
215G ALA* 1.3 63.9 + - - +
217G GLU* 3.1 12.3 + - + +
218G GLU* 3.0 57.9 + - - +
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Residues in contact with ALA 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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157G GLU* 5.1 4.5 - - - +
178G LEU* 5.8 0.4 - - + -
181G GLY 6.1 0.2 - - - -
182G ALA 3.8 21.1 - - - +
185G ALA* 3.7 12.1 - - + +
206G PHE* 3.5 22.4 - - + -
211G ALA 3.0 18.4 + - - +
212G GLY* 3.5 7.2 - - - +
213G ARG 3.2 0.2 - - - -
214G LYS* 1.3 75.7 - - - +
216G VAL* 1.3 63.8 + - - +
218G GLU* 3.4 2.5 + - - -
219G ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 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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204G LEU* 4.1 13.6 - - + +
206G PHE* 3.3 23.7 - - + +
212G GLY 3.3 15.7 - - - +
213G ARG* 3.2 33.2 - - + +
215G ALA* 1.3 74.9 - - - +
217G GLU* 1.3 62.1 + - + +
219G ALA* 3.1 3.7 + - - +
220G ALA* 2.9 28.2 + - - +
230G VAL* 2.8 35.7 - - + -
261G ILE* 4.9 7.6 - - + -
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Residues in contact with GLU 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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213G ARG* 3.1 12.5 + - + +
214G LYS* 3.1 13.8 + - + +
216G VAL* 1.3 82.5 - - + +
218G GLU* 1.3 68.1 + - - +
220G ALA* 3.6 1.6 + - - +
221G GLN* 2.9 41.2 + - - +
260G TRP* 5.9 1.7 - - - -
261G ILE* 4.0 28.0 - - - +
263G ASP* 4.1 22.0 - - - +
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Residues in contact with GLU 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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185G ALA* 5.0 1.1 - - + -
186G LYS* 3.1 73.0 + - + +
214G LYS* 3.0 46.1 + - + +
215G ALA* 3.9 5.2 - - - +
217G GLU* 1.3 79.3 - - - +
219G ALA* 1.3 63.4 + - - +
221G GLN* 3.5 12.0 - - - +
222G VAL 3.6 2.1 + - - -
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Residues in contact with ALA 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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185G ALA* 4.4 13.9 - - + +
186G LYS* 4.8 0.2 - - - +
189G CYS* 4.2 11.0 - - - +
204G LEU* 3.3 22.4 - - + -
206G PHE* 3.9 8.5 - - + -
215G ALA 2.9 17.8 + - - +
216G VAL 3.2 5.2 - - - +
218G GLU* 1.3 75.8 - - - +
220G ALA* 1.3 66.6 + - - +
222G VAL* 3.1 7.8 + - - +
223G LEU* 3.0 29.2 + - + +
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Residues in contact with ALA 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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204G LEU* 5.1 0.7 - - + -
216G VAL 2.9 12.1 + - - +
219G ALA* 1.3 76.1 - - - +
221G GLN* 1.3 64.2 + - - +
223G LEU* 3.0 31.2 + - - +
228G VAL* 3.9 9.2 - - + +
261G ILE* 2.6 58.7 - - + +
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Residues in contact with GLN 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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186G LYS* 4.9 7.0 - - + -
217G GLU* 2.9 34.7 + - - +
218G GLU* 3.5 14.3 - - - +
219G ALA 3.2 0.2 - - - -
220G ALA* 1.3 77.7 - - - +
222G VAL* 1.3 58.6 + - - +
223G LEU 3.7 2.8 + - - +
261G ILE* 3.9 15.8 + - - +
263G ASP* 6.1 4.0 - - - +
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Residues in contact with VAL 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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186G LYS* 4.2 17.7 - - + +
189G CYS 5.4 0.2 - - - -
190G ALA* 3.5 37.9 - - + +
193G TYR* 3.6 17.7 - - - -
218G GLU 3.6 6.3 + - - +
219G ALA 3.1 7.7 + - - +
221G GLN* 1.3 77.0 - - - +
223G LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 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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189G CYS* 3.7 23.3 - - + +
193G TYR* 3.8 2.3 - - - -
196G PHE* 3.6 23.3 - - + -
202G ILE* 3.3 37.9 - - + -
204G LEU* 3.8 14.1 - - + -
219G ALA 3.0 28.1 + - - +
220G ALA* 3.0 19.6 + - - +
221G GLN 4.3 2.1 - - - +
222G VAL* 1.3 81.6 - - - +
224G PRO* 1.3 73.7 - - + +
225G ALA 3.4 4.9 + - - +
228G VAL* 3.8 22.5 - - + +
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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