Contacts of the helix formed by residues 225 - 238 (chain G) in PDB entry 3TDD
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 SER 225 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223G THR 4.0 0.4 + - - -
224G LEU* 1.3 73.9 - - - +
226G ALA* 1.3 65.7 + - - +
227G GLU* 3.6 6.3 + - - +
228G ASN* 2.6 41.1 + - - -
229G ILE* 2.9 27.0 + - - +
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Residues in contact with ALA 226 (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 LYS* 3.5 26.7 - - + +
208G ASN* 4.0 19.5 - - - +
225G SER* 1.3 74.3 - - - +
227G GLU* 1.3 63.1 + - + +
229G ILE* 3.4 6.0 + - - +
230G GLU* 2.8 28.1 + - - +
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Residues in contact with GLU 227 (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 LYS* 2.8 38.7 + - - +
225G SER* 3.1 7.2 + - - +
226G ALA* 1.3 78.4 - - + +
228G ASN* 1.3 67.7 + - - +
229G ILE 3.1 1.8 - - - -
230G GLU* 3.8 16.2 - - - +
231G GLU* 3.2 23.6 + - - +
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Residues in contact with ASN 228 (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 TRP* 5.9 1.6 - - + -
223G THR 4.8 1.4 - - - +
224G LEU* 3.6 26.9 - - + +
225G SER* 2.6 45.5 + - - +
227G GLU* 1.3 81.5 - - - +
229G ILE* 1.3 60.7 + - - +
231G GLU* 3.6 8.6 + - - +
232G ARG* 3.6 31.3 + - - +
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Residues in contact with ILE 229 (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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194G ILE* 4.7 6.5 - - + -
207G LYS* 4.1 15.9 - - - +
210G LEU* 3.8 34.8 - - + +
211G GLU* 4.4 0.9 - - - -
212G VAL* 4.0 29.6 - - + +
224G LEU* 4.1 14.1 - - + +
225G SER 2.9 22.6 + - - +
226G ALA* 3.5 4.7 - - - +
228G ASN* 1.3 75.1 - - - +
230G GLU* 1.3 57.7 + - - +
231G GLU 3.0 1.3 - - - -
232G ARG* 2.6 29.6 + - - +
233G LEU* 2.8 36.2 + - + -
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Residues in contact with GLU 230 (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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206G SER* 5.5 0.2 - - - -
207G LYS* 3.3 37.2 + - + +
226G ALA 2.8 20.6 + - - +
227G GLU* 3.5 19.9 + - - +
229G ILE* 1.3 73.5 - - - +
231G GLU* 1.3 58.6 + - - +
233G LEU* 3.3 12.0 + - - +
234G VAL* 2.9 50.3 + - + +
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Residues in contact with GLU 231 (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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227G GLU 3.2 11.4 + - - +
228G ASN* 3.6 14.3 + - - +
229G ILE 3.0 0.2 - - - -
230G GLU* 1.3 80.1 - - - +
232G ARG* 1.3 91.5 + - - +
234G VAL* 3.6 7.1 + - - +
235G ALA* 3.2 22.0 + - - +
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Residues in contact with ARG 232 (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 TRP* 4.9 4.7 - - - -
187G GLU* 3.8 37.1 + - - +
190G VAL* 3.5 31.0 - - + -
191G GLU* 3.1 39.3 + - + +
194G ILE* 4.3 12.1 - - + -
224G LEU* 4.7 7.4 - - + -
228G ASN* 3.6 16.0 + - - +
229G ILE* 2.6 22.8 + - - +
231G GLU* 1.3 118.2 + - - +
233G LEU* 1.3 59.8 + - - +
235G ALA* 3.2 7.1 + - - +
236G ILE* 3.1 27.4 + - - +
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Residues in contact with LEU 233 (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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194G ILE* 3.8 40.2 - - + -
198G ILE* 5.8 1.3 - - + -
205G PHE* 3.6 16.4 - - + +
206G SER* 3.3 37.9 - - - +
207G LYS* 3.5 10.8 - - - +
210G LEU* 4.5 4.7 - - + -
229G ILE* 2.8 16.7 + - + +
230G GLU* 3.6 17.3 - - - +
232G ARG* 1.3 74.1 - - - +
234G VAL* 1.3 62.0 + - - +
236G ILE* 2.9 34.0 - - + +
237G ALA* 3.2 7.1 + - - +
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Residues in contact with VAL 234 (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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230G GLU* 2.9 40.8 + - + +
231G GLU* 3.7 7.9 - - - +
233G LEU* 1.3 75.1 - - - +
235G ALA* 1.3 67.1 + - - +
237G ALA* 3.0 18.0 + - - +
238G GLU* 3.1 33.8 + - + +
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Residues in contact with ALA 235 (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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188G LYS* 5.5 2.5 - - - -
191G GLU* 3.4 31.2 - - - +
231G GLU 3.2 10.4 + - - +
232G ARG* 3.2 8.5 + - - +
234G VAL* 1.3 82.3 - - - +
236G ILE* 1.3 61.7 + - - +
238G GLU* 3.2 28.0 + - - +
239G GLN* 4.3 4.9 - - - +
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Residues in contact with ILE 236 (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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191G GLU* 3.6 33.9 - - + +
194G ILE* 5.3 6.7 - - + -
195G THR* 3.7 23.8 - - - +
198G ILE* 4.9 16.6 - - + -
204G GLU* 5.4 6.7 - - - +
232G ARG 3.1 11.0 + - - +
233G LEU* 2.9 37.5 - - + +
235G ALA* 1.3 75.9 - - - +
237G ALA* 1.3 84.0 + - + +
238G GLU 3.5 0.3 + - - -
239G GLN* 3.6 21.6 - - - +
240G ASP* 3.8 16.4 - - - +
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Residues in contact with ALA 237 (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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233G LEU 3.4 10.5 - - - +
234G VAL* 3.0 13.6 + - - +
236G ILE* 1.3 90.0 - - + +
238G GLU* 1.3 53.4 + - + +
239G GLN 2.8 13.7 + - - -
240G ASP* 3.1 21.3 + - - +
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Residues in contact with GLU 238 (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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234G VAL* 3.1 31.3 + - + +
235G ALA* 3.2 14.4 + - - +
237G ALA* 1.3 72.7 - - + +
239G GLN* 1.3 64.0 + - - +
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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