Contacts of the helix formed by residues 225 - 242 (chain Q) in PDB entry 3SDI
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224Q LEU* 1.3 73.8 - - - +
226Q SER* 1.3 65.9 + - - +
227Q GLU* 3.8 16.0 + - - +
228Q GLU* 3.0 47.0 + - - +
229Q ILE* 3.1 18.1 + - - +
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Residues in contact with SER 226 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q ARG* 5.5 4.8 + - - -
207Q ALA* 4.3 22.5 - - - +
208Q LYS* 5.7 2.4 - - - -
225Q SER* 1.3 72.8 - - - +
227Q GLU* 1.3 72.2 + - - +
229Q ILE* 3.7 9.4 + - - +
230Q ASN* 3.0 30.2 + - - +
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Residues in contact with GLU 227 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225Q SER* 3.1 14.6 + - - +
226Q SER* 1.3 92.0 + - - +
228Q GLU* 1.3 65.4 + - + +
230Q ASN* 3.1 20.6 + - - +
231Q GLN* 3.1 21.4 + - - +
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Residues in contact with GLU 228 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223Q ALA 4.6 2.1 - - - +
224Q LEU* 3.8 24.6 - - + +
225Q SER* 3.0 38.2 + - - +
227Q GLU* 1.3 78.0 - - + +
229Q ILE* 1.3 59.2 + - - +
231Q GLN* 3.5 21.8 - - - +
232Q TYR* 3.4 21.3 - - - -
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Residues in contact with ILE 229 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q ARG* 6.2 0.7 - - - +
190Q VAL* 6.2 0.9 - - + -
194Q VAL* 4.6 9.4 - - + -
207Q ALA* 5.0 4.0 - - - +
210Q ILE* 3.4 43.5 - - + +
211Q GLU* 4.0 2.9 - - + -
212Q ILE* 3.9 30.1 - - + +
224Q LEU* 3.9 22.2 - - + +
225Q SER 3.1 21.9 + - - +
226Q SER* 3.9 8.1 - - - +
228Q GLU* 1.3 71.0 - - - +
230Q ASN* 1.3 55.1 + - - +
231Q GLN 3.0 4.9 - - - -
232Q TYR* 2.8 31.9 + - - +
233Q VAL* 3.0 21.3 + - + -
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Residues in contact with ASN 230 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Q ALA* 3.6 29.3 - - - +
226Q SER* 3.0 16.5 + - - +
227Q GLU* 3.1 16.3 + - - +
229Q ILE* 1.3 75.7 - - - +
231Q GLN* 1.3 55.9 + - - +
232Q TYR 3.4 0.2 - - - -
233Q VAL* 3.7 19.7 - - - +
234Q THR* 2.8 33.7 + - - -
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Residues in contact with GLN 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227Q GLU* 3.1 18.0 + - - +
228Q GLU* 3.5 20.1 - - - +
229Q ILE 3.0 0.4 - - - -
230Q ASN* 1.3 77.4 - - - +
232Q TYR* 1.3 65.2 + - + +
234Q THR* 3.6 6.4 + - - -
235Q GLN* 3.4 22.0 + - - +
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Residues in contact with TYR 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q GLU* 3.2 60.6 + - + +
190Q VAL* 4.0 24.2 - - + +
191Q LYS* 4.0 25.6 - - + -
194Q VAL* 4.2 16.2 - - + -
224Q LEU* 5.0 6.3 - - + -
228Q GLU* 3.4 19.5 - - + -
229Q ILE* 2.8 14.3 + - - +
231Q GLN* 1.3 75.2 - - + +
233Q VAL* 1.3 65.4 + - - +
234Q THR 3.2 0.2 - - - -
235Q GLN* 3.5 7.6 + - + +
236Q ILE* 3.2 35.1 + - + +
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Residues in contact with VAL 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q VAL* 4.6 13.7 - - + -
198Q LEU* 5.0 12.5 - - + +
203Q THR* 5.4 9.0 - - + -
206Q GLY 4.9 15.9 - - - +
207Q ALA* 5.3 2.2 - - - -
210Q ILE* 5.2 5.2 - - + -
229Q ILE* 3.0 26.6 + - + +
230Q ASN* 3.5 25.8 - - - +
232Q TYR* 1.3 77.0 - - - +
234Q THR* 1.3 60.7 + - - +
236Q ILE* 4.2 2.7 - - - +
237Q GLU* 3.3 42.4 + - - +
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Residues in contact with THR 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230Q ASN* 2.8 19.5 + - - -
231Q GLN* 3.9 7.2 - - - -
232Q TYR 3.2 0.4 - - - -
233Q VAL* 1.3 77.0 - - - +
235Q GLN* 1.3 59.0 + - - +
237Q GLU* 3.5 5.2 + - - +
238Q GLN* 3.1 49.7 + - + +
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Residues in contact with GLN 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Q GLU* 5.4 6.5 + - - -
191Q LYS* 3.3 22.3 + - - +
231Q GLN 3.4 15.8 + - - +
232Q TYR* 3.5 7.7 + - + +
234Q THR* 1.3 77.2 - - - +
236Q ILE* 1.3 58.6 + - + +
238Q GLN* 3.9 14.5 - - + +
239Q GLU* 2.9 52.0 + - + +
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Residues in contact with ILE 236 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q LYS* 3.7 48.2 - - + +
194Q VAL* 3.8 23.6 - - + -
195Q ARG* 3.7 27.1 - - + -
198Q LEU* 3.8 15.9 - - + -
232Q TYR* 3.2 21.9 + - + +
233Q VAL 4.2 2.7 - - - +
235Q GLN* 1.3 77.0 - - + +
237Q GLU* 1.3 64.4 - - + +
238Q GLN 3.2 2.2 - - - -
239Q GLU* 3.5 4.1 + - - +
240Q LYS* 3.3 34.6 + - + +
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Residues in contact with GLU 237 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Q LEU* 5.0 15.4 - - + +
203Q THR* 3.4 28.6 + - - +
233Q VAL* 3.3 32.4 + - + +
234Q THR* 3.5 4.8 + - - +
236Q ILE* 1.3 76.1 - - + +
238Q GLN* 1.3 61.0 + - - +
240Q LYS* 4.2 6.5 - - - +
241Q GLN* 3.0 37.7 + - - +
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Residues in contact with GLN 238 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234Q THR* 3.1 40.5 + - + +
235Q GLN* 3.9 14.5 - - + +
236Q ILE 3.2 0.2 - - - -
237Q GLU* 1.3 75.6 - - - +
239Q GLU* 1.3 54.0 + - + +
240Q LYS 3.2 4.3 - - - -
241Q GLN* 3.2 6.8 + - - +
242Q GLU* 2.8 47.0 + - + +
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Residues in contact with GLU 239 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q LYS* 3.5 21.7 + - - -
235Q GLN* 2.9 41.8 + - + +
236Q ILE* 3.5 4.6 + - - +
238Q GLN* 1.3 79.7 - - + +
240Q LYS* 1.3 58.5 + - - +
242Q GLU* 3.6 29.3 - - - +
243Q GLN* 4.3 10.4 + - - +
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Residues in contact with LYS 240 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q PHE* 6.4 1.8 - - - -
195Q ARG* 6.4 2.0 - - + -
199Q GLU* 4.3 19.1 + - - -
236Q ILE* 3.3 26.7 + - + +
237Q GLU* 4.4 5.8 - - - +
238Q GLN 3.2 0.6 - - - -
239Q GLU* 1.3 78.9 - - - +
241Q GLN* 1.3 61.1 + - + +
242Q GLU 3.3 0.4 - - - -
243Q GLN* 3.4 27.9 + - - +
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Residues in contact with GLN 241 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237Q GLU* 3.0 25.5 + - - +
238Q GLN* 3.2 8.0 + - - +
240Q LYS* 1.3 73.2 - - + +
242Q GLU* 1.3 58.2 + - - +
243Q GLN 3.2 11.1 + - - +
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Residues in contact with GLU 242 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Q GLN* 2.8 27.6 + - + +
239Q GLU* 3.6 29.1 - - - +
240Q LYS 3.3 0.4 - - - -
241Q GLN* 1.3 76.2 - - - +
243Q GLN* 1.3 58.1 + - - +
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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