Contacts of the helix formed by residues 229 - 248 (chain I) in PDB entry 5T0G
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 LYS 229 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227I VAL 4.2 0.8 + - - -
228I LEU* 1.3 74.1 - - - +
230I GLN* 1.3 64.7 + - - +
231I LYS* 3.1 7.0 - - + +
232I GLU* 2.6 37.0 + - - +
233I VAL* 3.1 13.4 - - - +
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Residues in contact with GLN 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I ALA* 3.9 32.3 - - + +
209I GLU* 4.7 13.2 - - + +
228I LEU 4.2 0.6 + - - -
229I LYS* 1.3 71.7 - - - +
231I LYS* 1.3 58.8 + - - +
232I GLU 3.4 0.2 - - - -
233I VAL* 3.6 11.2 - - - +
234I GLU* 2.9 35.7 + - + +
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Residues in contact with LYS 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229I LYS* 3.1 6.3 - - + +
230I GLN* 1.3 79.4 - - - +
232I GLU* 1.3 66.8 + - - +
234I GLU* 3.6 18.3 + - - +
235I GLN* 3.9 8.5 + - - +
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Residues in contact with GLU 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I ARG* 3.6 16.9 + - - +
228I LEU* 3.4 14.4 - - + +
229I LYS* 2.6 48.4 + - - +
231I LYS* 1.3 75.3 - - - +
233I VAL* 1.3 67.1 + - + +
235I GLN* 3.4 34.4 + - - +
236I LEU* 3.6 11.3 + - - +
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Residues in contact with VAL 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206I LEU* 5.9 0.2 - - + -
208I ALA* 4.7 6.7 - - + +
211I VAL* 5.7 1.1 - - + -
213I ILE* 3.9 22.9 - - + -
228I LEU* 3.4 33.4 - - + -
229I LYS 3.1 18.6 - - - +
230I GLN* 3.1 14.0 + - - +
232I GLU* 1.3 79.5 - - + +
234I GLU* 1.3 58.5 + - - +
236I LEU* 3.0 13.0 + - + +
237I ILE* 2.8 51.9 + - + +
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Residues in contact with GLU 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I ALA* 3.6 14.8 - - + +
209I GLU* 3.3 24.6 - - - +
230I GLN* 2.9 22.7 + - - +
231I LYS* 3.8 9.6 - - - +
232I GLU 3.4 0.4 - - - -
233I VAL* 1.3 76.4 - - - +
235I GLN* 1.3 57.6 + - - +
237I ILE* 3.1 11.9 + - + +
238I LYS* 2.9 45.8 + - - +
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Residues in contact with GLN 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I LYS 3.9 5.4 + - - +
232I GLU* 3.4 37.9 + - - +
234I GLU* 1.3 78.2 - - - +
236I LEU* 1.3 56.8 + - + +
238I LYS* 3.5 18.8 + - - +
239I LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I LYS* 5.6 15.9 - - + +
190I LEU* 4.6 29.4 - - + -
191I ALA* 5.6 10.5 - - + +
232I GLU 3.6 12.1 - - - +
233I VAL* 3.0 18.7 + - + +
235I GLN* 1.3 81.3 - - + +
237I ILE* 1.3 59.2 + - + +
239I LYS* 3.2 13.8 + - + +
240I HIS* 2.9 26.2 + - - +
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Residues in contact with ILE 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I ILE* 5.6 4.7 - - + -
205I LYS 4.8 0.2 - - - +
206I LEU* 3.4 53.6 - - + +
208I ALA* 3.9 17.7 - - + -
211I VAL* 5.8 0.2 - - + -
233I VAL* 2.8 38.6 + - + +
234I GLU* 3.4 9.4 - - + +
236I LEU* 1.3 77.8 - - + +
238I LYS* 1.3 59.4 + - + +
240I HIS* 3.1 10.5 + - + +
241I GLU* 2.8 50.6 + - + +
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Residues in contact with LYS 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I GLU* 2.9 44.5 + - - +
235I GLN* 3.5 14.2 - - - +
237I ILE* 1.3 74.3 - - + +
239I LYS* 1.3 60.4 + - - +
241I GLU* 3.8 20.0 - - - +
242I GLU* 2.9 27.2 + - - +
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Residues in contact with LYS 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235I GLN 2.9 16.5 + - - +
236I LEU* 3.4 22.0 - - + +
237I ILE 3.2 0.4 - - - -
238I LYS* 1.3 77.8 - - - +
240I HIS* 1.3 57.1 + - - +
242I GLU* 3.2 19.6 + - + +
243I GLU* 2.5 64.7 + - + +
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Residues in contact with HIS 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I ALA* 3.5 28.7 + - + +
194I ILE* 4.2 12.3 - - + -
195I LYS* 3.3 55.4 - - + +
198I ASN* 3.7 25.0 + - + -
206I LEU* 5.2 3.1 - - + -
236I LEU* 2.9 14.0 + - - +
237I ILE* 3.1 14.6 + - + +
239I LYS* 1.3 76.0 - - - +
241I GLU* 1.3 58.4 + - + +
243I GLU* 3.0 17.0 + - + +
244I GLU* 2.9 28.8 + - + +
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Residues in contact with GLU 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I ASN* 5.3 9.2 - - - +
205I LYS* 3.9 16.5 - - - +
206I LEU* 5.4 0.5 - - - +
237I ILE* 2.8 40.1 + - + +
238I LYS* 3.9 20.4 - - - +
240I HIS* 1.3 75.1 - - + +
242I GLU* 1.3 60.5 + - - +
244I GLU* 3.3 13.2 + - + +
245I ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I LYS 2.9 19.8 + - - +
239I LYS* 3.3 22.3 + - + +
241I GLU* 1.3 77.4 - - - +
243I GLU* 1.3 82.7 + - - +
245I ALA* 3.4 7.6 + - + +
246I LYS* 2.9 35.4 + - - +
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Residues in contact with GLU 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239I LYS* 2.5 48.2 + - + +
240I HIS* 3.0 19.5 + - + +
242I GLU* 1.3 82.2 - - - +
244I GLU* 1.3 58.7 + - - +
246I LYS* 3.3 11.0 + - - +
247I ALA* 2.9 28.8 + - - +
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Residues in contact with GLU 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I ASN* 4.9 15.0 - - - +
240I HIS* 2.9 16.7 + - + +
241I GLU* 3.5 14.8 - - - +
242I GLU 3.3 0.2 - - - -
243I GLU* 1.3 73.7 - - - +
245I ALA* 1.3 70.6 + - - +
247I ALA* 3.0 17.8 + - + +
248I GLU* 3.0 30.0 + - - +
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I GLU 2.9 18.5 + - - +
242I GLU* 3.7 9.0 - - + +
244I GLU* 1.3 79.3 + - - +
246I LYS* 1.3 56.9 + - - +
248I GLU* 3.2 22.8 - - - +
249I ARG* 3.1 41.0 + - - +
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Residues in contact with LYS 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I GLU* 2.9 30.0 + - - +
243I GLU* 3.7 14.1 - - - +
244I GLU 3.1 0.2 - - - -
245I ALA* 1.3 78.3 - - - +
247I ALA* 1.3 63.7 + - - +
248I GLU 3.3 0.2 - - - -
249I ARG* 3.2 32.6 + - + +
250I GLU* 4.3 1.6 + - - +
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Residues in contact with ALA 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243I GLU 2.9 17.0 + - - +
244I GLU* 3.0 8.5 + - + +
246I LYS* 1.3 73.4 - - - +
248I GLU* 1.3 59.8 + - - +
249I ARG 3.1 5.8 + - - -
250I GLU* 3.5 17.5 + - - +
251I LYS 5.1 0.2 + - - -
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Residues in contact with GLU 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244I GLU* 3.0 24.3 + - - +
245I ALA* 3.2 34.0 - - - +
247I ALA* 1.3 75.8 - - - +
249I ARG* 1.3 76.8 + - - +
250I GLU 3.2 3.1 + - - -
251I LYS* 4.0 13.8 + - - +
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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