Contacts of the helix formed by residues 203 - 219 (chain G) in PDB entry 5JLH
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 203 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ASN* 4.8 0.4 - - - -
201G GLY* 3.2 7.4 + - - +
202G ALA* 1.3 80.0 - - - +
204G LYS* 1.3 57.1 + - - +
205G THR* 3.1 3.6 - - - -
206G GLU* 3.0 34.8 + - - +
207G ASN* 2.7 34.5 + - - +
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Residues in contact with LYS 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 3.3 32.4 + - + -
197G THR 3.1 19.2 + - - +
198G GLY* 3.4 2.6 - - - -
199G GLU* 3.3 34.3 - - + +
200G SER 5.0 2.2 - - - +
201G GLY 5.6 0.4 - - - +
202G ALA* 3.3 6.7 - - + -
203G GLY* 1.3 79.6 - - - +
205G THR* 1.3 53.8 + - - +
207G ASN* 3.4 8.0 + - - +
208G THR* 2.7 37.4 + - - +
478G ASP* 2.5 34.3 + - - +
479G ILE 3.2 21.2 + - - -
695G CYS* 3.8 20.4 - - - -
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Residues in contact with THR 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G GLY* 4.1 1.1 - - - -
204G LYS* 1.3 80.0 - - - +
206G GLU* 1.3 53.4 + - - +
208G THR* 2.9 10.4 + - - -
209G LYS* 2.7 37.6 + - + +
238G LEU 5.5 0.9 - - - +
242G ASN* 3.2 40.2 + - - +
264G LYS* 4.2 10.6 + - - +
266G ILE* 5.7 7.6 - - + -
478G ASP* 4.0 17.5 + - - +
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Residues in contact with GLU 206 (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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146G ASN* 5.5 2.3 + - - -
202G ALA 5.0 0.2 - - - +
203G GLY* 3.0 26.3 + - - +
205G THR* 1.3 79.8 - - + +
207G ASN* 1.3 60.7 + - - +
209G LYS* 3.1 46.3 + - + +
210G LYS* 3.3 18.4 + - - +
242G ASN* 6.0 2.2 - - - +
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Residues in contact with ASN 207 (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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134G ILE* 5.8 0.4 - - - +
135G TYR* 3.7 10.7 + - - -
144G VAL* 4.1 23.4 - - - +
154G TYR* 5.1 3.7 + - - -
174G VAL* 3.3 38.1 - - - +
203G GLY 2.7 15.3 + - - +
204G LYS* 3.5 12.1 - - - +
206G GLU* 1.3 71.6 - - - +
208G THR* 1.3 54.6 + - - +
210G LYS* 2.7 34.3 + - - +
211G VAL* 2.9 10.4 + - - +
693G VAL* 5.6 2.6 - - - +
695G CYS* 5.7 2.7 - - - -
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Residues in contact with THR 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 4.4 12.3 - - - -
204G LYS 2.7 19.5 + - - -
205G THR* 2.9 16.4 + - + -
207G ASN* 1.3 75.2 - - - +
209G LYS* 1.3 55.7 + - - +
211G VAL* 3.1 13.6 + - + +
212G ILE* 3.0 34.9 + - + +
266G ILE* 4.7 11.4 - - + -
476G ILE* 3.8 43.9 - - + +
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Residues in contact with LYS 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G THR* 2.7 25.1 + - + +
206G GLU* 3.2 33.5 - - + +
207G ASN 3.1 0.2 - - - -
208G THR* 1.3 76.4 - - - +
210G LYS* 1.3 62.2 + - + +
212G ILE* 3.2 17.7 + - + +
213G GLN* 2.8 28.1 + - - +
234G LEU* 5.5 0.3 - - - +
238G LEU* 6.0 4.3 - - + +
239G LEU* 3.2 42.6 - - + +
242G ASN* 4.8 11.3 - - - +
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Residues in contact with LYS 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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150G GLN* 6.3 1.0 - - - +
151G LEU 5.5 4.6 + - - +
154G TYR* 3.5 52.2 - - + +
175G TYR* 3.1 25.3 - - + +
206G GLU* 3.6 18.1 - - - +
207G ASN* 2.7 17.9 + - - +
209G LYS* 1.3 78.9 - - + +
211G VAL* 1.3 61.0 + - - -
213G GLN* 3.2 18.5 + - - +
214G TYR 3.0 18.7 + - - -
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Residues in contact with VAL 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G VAL* 3.3 31.2 - - + -
175G TYR* 4.5 6.3 - - - -
178G THR* 3.5 26.2 - - - +
194G ILE* 5.8 6.5 - - + -
207G ASN* 2.9 19.2 + - - +
208G THR* 3.1 19.5 + - + +
210G LYS* 1.3 74.6 - - - +
212G ILE* 1.3 59.3 + - - +
214G TYR* 3.2 7.3 + - - +
215G LEU* 2.9 31.2 + - + +
474G LEU* 5.4 1.3 - - + -
476G ILE* 4.5 18.8 - - + -
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Residues in contact with ILE 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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208G THR* 3.0 26.0 + - + +
209G LYS* 3.2 17.7 + - + +
211G VAL* 1.3 76.8 - - + +
213G GLN* 1.3 57.4 + - - +
215G LEU* 2.9 11.4 + - + +
216G ALA* 2.9 26.9 + - - +
234G LEU* 3.6 29.8 - - + +
235G GLU 5.9 0.2 - - - +
238G LEU* 3.7 34.1 - - + -
266G ILE* 5.7 7.9 - - + -
268G ILE* 4.1 23.8 - - + -
476G ILE* 5.1 1.8 - - + -
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Residues in contact with GLN 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G TYR* 3.2 26.6 + - - +
155G THR 5.0 1.2 + - - -
156G GLU* 4.3 12.9 + - - -
175G TYR* 4.0 12.8 + - - +
209G LYS 2.8 12.3 + - - +
210G LYS* 3.2 22.9 + - - +
212G ILE* 1.3 75.2 - - - +
214G TYR* 1.3 62.1 + - - +
216G ALA* 3.2 2.6 + - - +
217G HIS* 3.1 43.5 + - + +
234G LEU* 3.9 16.1 - - + +
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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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159G VAL* 3.4 37.2 - - + -
162G TYR* 4.7 4.7 - - + -
163G ARG* 5.1 4.3 - - + -
175G TYR* 3.3 55.3 - + + -
178G THR* 3.6 24.7 - - + -
179G GLU* 3.0 34.9 - - + +
182G TYR* 4.9 10.1 - + + +
183G ARG* 5.8 0.2 + - - -
210G LYS 3.0 6.1 + - - -
211G VAL* 3.3 8.7 - - - +
213G GLN* 1.3 75.1 - - - +
215G LEU* 1.3 66.2 + - + +
217G HIS* 3.1 3.3 + - - +
218G VAL* 2.9 63.6 + - + +
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Residues in contact with LEU 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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178G THR* 4.8 6.1 - - - +
182G TYR* 4.9 15.3 - - + -
211G VAL* 2.9 17.0 + - + +
212G ILE* 2.9 13.0 + - + +
214G TYR* 1.3 85.9 - - + +
216G ALA* 1.3 57.9 + - - +
218G VAL* 4.0 2.4 - - - +
219G ALA* 3.0 37.2 + - + +
234G LEU* 6.2 0.2 - - + -
268G ILE* 3.9 18.4 - - + -
270G PHE* 3.1 38.1 - - + -
276G ILE* 3.6 14.8 - - + +
474G LEU* 3.7 30.1 - - + -
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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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212G ILE 2.9 4.8 + - - -
213G GLN 3.5 4.5 - - - +
215G LEU* 1.3 75.1 - - - +
217G HIS* 1.3 67.6 + - + +
219G ALA* 2.7 26.0 - - - +
220G SER* 3.1 5.4 + - - -
234G LEU* 3.5 45.5 - - + +
276G ILE* 5.6 6.3 - - - -
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Residues in contact with HIS 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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156G GLU* 2.8 42.4 + - - +
159G VAL* 4.6 19.1 - - + -
160G GLU* 5.5 6.2 - - - +
163G ARG* 4.6 2.7 + - - -
213G GLN* 3.1 42.7 + - + +
214G TYR 3.9 2.7 - - - +
216G ALA* 1.3 83.6 - - + +
218G VAL* 1.3 63.1 + - - +
220G SER* 3.3 13.1 + - - -
234G LEU* 6.1 0.8 - - - +
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Residues in contact with VAL 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G VAL* 4.7 4.0 - - + -
163G ARG* 3.5 37.9 + - + +
182G TYR* 3.5 43.7 + - + +
183G ARG* 5.4 3.4 - - - +
214G TYR* 2.9 56.9 + - + +
215G LEU* 4.0 3.8 - - - +
217G HIS* 1.3 79.2 - - - +
219G ALA* 1.3 58.8 + - - +
220G SER* 3.5 4.7 + - - +
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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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182G TYR* 4.4 13.5 - - + +
215G LEU* 3.0 24.5 + - + +
216G ALA* 2.7 18.7 - - - +
218G VAL* 1.3 75.1 - - - +
220G SER* 1.3 58.3 + - - +
221G SER 3.7 8.4 - - - +
270G PHE* 5.8 0.2 - - + -
274G GLY 3.2 26.0 - - - +
275G TYR* 4.3 6.7 - - - -
276G ILE* 4.9 11.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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