Contacts of the helix formed by residues 225 - 238 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224U LEU* 1.3 73.9 - - - +
226U ALA* 1.3 66.0 + - - +
227U GLU* 3.5 6.5 + - - +
228U ASN* 2.6 41.1 + - - -
229U ILE* 2.9 28.4 + - - +
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Residues in contact with ALA 226 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207U LYS* 3.5 25.0 - - + +
208U ASN* 4.0 20.2 - - - +
225U SER* 1.3 74.9 - - - +
227U GLU* 1.3 63.2 + - + +
229U ILE* 3.4 5.5 + - - +
230U GLU* 2.8 28.6 + - - +
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Residues in contact with GLU 227 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207U LYS* 2.8 38.3 + - - +
225U SER* 3.1 7.2 + - - +
226U ALA* 1.3 77.8 - - + +
228U ASN* 1.3 67.9 + - - +
229U ILE 3.1 1.8 - - - -
230U GLU* 3.7 15.9 - - - +
231U GLU* 3.2 23.3 + - - +
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Residues in contact with ASN 228 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186U TRP* 5.9 1.3 - - + -
223U THR 4.8 0.9 - - - +
224U LEU* 3.7 25.8 - - + +
225U SER* 2.6 46.6 + - - +
227U GLU* 1.3 81.8 - - - +
229U ILE* 1.3 61.1 + - - +
231U GLU* 3.6 8.8 + - - +
232U ARG* 3.5 32.3 + - - +
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Residues in contact with ILE 229 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194U ILE* 4.7 5.8 - - + -
207U LYS* 4.1 16.6 - - - +
210U LEU* 3.8 33.4 - - + +
211U GLU* 4.4 0.7 - - - -
212U VAL* 4.1 31.0 - - + +
224U LEU* 4.1 13.9 - - + +
225U SER 2.9 24.3 + - - +
226U ALA* 3.4 4.9 - - - +
228U ASN* 1.3 74.4 - - - +
230U GLU* 1.3 59.7 + - - +
231U GLU 3.0 1.6 - - - -
232U ARG* 2.6 28.4 + - - +
233U LEU* 2.8 37.0 + - + +
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Residues in contact with GLU 230 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207U LYS* 3.4 37.3 + - + +
226U ALA 2.8 16.9 + - - +
227U GLU* 3.7 19.5 - - - +
229U ILE* 1.3 75.4 - - - +
231U GLU* 1.3 56.7 + - - +
233U LEU* 3.3 11.2 + - - +
234U VAL* 2.9 50.4 + - + +
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Residues in contact with GLU 231 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227U GLU 3.2 11.3 + - - +
228U ASN* 3.6 14.2 + - - +
229U ILE 3.0 0.4 - - - -
230U GLU* 1.3 80.2 - - - +
232U ARG* 1.3 89.9 + - - +
234U VAL* 3.7 7.4 - - - +
235U ALA* 3.2 22.0 + - - +
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Residues in contact with ARG 232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186U TRP* 4.9 4.8 - - - -
187U GLU* 3.8 37.8 - - - +
190U VAL* 3.6 30.1 - - + -
191U GLU* 3.1 38.0 + - + +
194U ILE* 4.3 12.1 - - + -
224U LEU* 4.7 7.0 - - + -
228U ASN* 3.5 15.8 + - - +
229U ILE* 2.6 22.6 + - - +
231U GLU* 1.3 116.2 + - - +
233U LEU* 1.3 62.8 + - - +
235U ALA* 3.2 7.1 + - - +
236U ILE* 3.1 27.5 + - - +
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Residues in contact with LEU 233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194U ILE* 3.8 40.2 - - + -
198U ILE* 5.8 1.3 - - + -
205U PHE* 3.6 16.6 - - + +
206U SER* 3.3 38.4 - - - +
207U LYS* 3.5 10.8 - - - +
210U LEU* 4.5 4.5 - - + -
229U ILE* 2.8 17.3 + - + +
230U GLU* 3.6 16.6 - - - +
232U ARG* 1.3 74.3 - - - +
234U VAL* 1.3 62.7 + - - +
236U ILE* 3.0 34.3 - - + +
237U ALA* 3.2 6.8 + - - +
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Residues in contact with VAL 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230U GLU* 2.9 39.6 + - + +
231U GLU* 3.7 8.3 - - - +
233U LEU* 1.3 75.0 - - + +
235U ALA* 1.3 67.9 + - - +
237U ALA* 3.0 17.6 + - + +
238U GLU* 3.1 33.7 + - + +
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Residues in contact with ALA 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188U LYS* 5.5 2.2 - - - -
191U GLU* 3.4 31.2 - - - +
231U GLU 3.2 10.0 + - - +
232U ARG* 3.2 8.5 + - - +
234U VAL* 1.3 81.4 - - - +
236U ILE* 1.3 62.7 + - - +
238U GLU* 3.2 27.2 + - - +
239U GLN* 4.3 4.6 - - - +
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Residues in contact with ILE 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191U GLU* 3.6 34.1 - - + +
194U ILE* 5.3 6.7 - - + -
195U THR* 3.7 23.3 - - - +
198U ILE* 4.9 15.7 - - + -
204U GLU* 5.4 6.3 - - - +
232U ARG 3.1 13.9 + - - +
233U LEU* 3.0 34.1 - - + +
235U ALA* 1.3 76.1 - - - +
237U ALA* 1.3 84.3 + - + +
238U GLU 3.5 0.2 + - - -
239U GLN* 3.6 20.6 - - - +
240U ASP* 3.8 16.7 - - - +
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Residues in contact with ALA 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233U LEU 3.4 10.3 - - - +
234U VAL* 3.0 13.8 + - + +
236U ILE* 1.3 89.6 - - + +
238U GLU* 1.3 58.5 + - + +
239U GLN 2.8 8.4 + - - -
240U ASP* 3.1 21.0 + - - +
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Residues in contact with GLU 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234U VAL* 3.1 31.2 + - + +
235U ALA* 3.2 13.9 + - - +
237U ALA* 1.3 73.9 - - + +
239U GLN* 1.3 63.5 + - - +
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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