Contacts of the helix formed by residues 217 - 233 (chain I) in PDB entry 6MZL
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 217 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218I VAL* 1.3 59.2 + - - +
219I GLU* 2.9 14.0 + - - +
220I GLN* 2.5 64.7 + - - +
221I GLN* 2.9 31.2 + - - +
255I MET* 5.0 2.2 - - - +
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Residues in contact with VAL 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I SER* 1.3 74.1 - - - +
219I GLU* 1.3 63.6 + - + +
221I GLN* 3.3 22.9 - - - +
222I LEU* 3.0 40.2 + - + +
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Residues in contact with GLU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I SER* 2.9 10.1 + - - +
218I VAL* 1.3 78.8 - - + +
220I GLN* 1.3 58.1 + - + +
222I LEU* 3.1 9.2 + - - +
223I TYR* 2.9 25.4 + - - +
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Residues in contact with GLN 220 (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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217I SER* 2.5 45.0 + - - +
219I GLU* 1.3 72.4 - - + +
221I GLN* 1.3 61.1 + - - +
223I TYR* 3.3 16.6 + - + +
224I TYR* 2.8 25.6 + - - +
252I LEU* 5.1 8.3 - - + +
254I GLN* 4.7 20.2 - - - +
255I MET* 3.4 38.8 + - + +
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Residues in contact with GLN 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I SER 2.9 17.9 + - - +
218I VAL* 3.3 35.3 - - - +
220I GLN* 1.3 79.8 - - + +
222I LEU* 1.3 62.1 + - + +
224I TYR* 3.2 14.2 + - + +
225I LYS* 2.9 41.1 + - + +
255I MET* 4.6 8.1 - - + -
258I ARG* 4.8 12.3 + - - +
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Residues in contact with LEU 222 (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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218I VAL* 3.0 36.6 + - + +
219I GLU* 3.6 6.1 - - - +
221I GLN* 1.3 79.0 - - + +
223I TYR* 1.3 60.3 + - - +
225I LYS* 3.1 35.3 + - + +
226I GLU* 2.9 33.3 + - - +
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Residues in contact with TYR 223 (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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219I GLU 2.9 13.4 + - - +
220I GLN* 3.3 18.6 - - + +
222I LEU* 1.3 77.4 - - - +
224I TYR* 1.3 55.4 + - - +
226I GLU* 3.2 24.2 + - + +
227I ILE* 2.9 50.7 + - + +
241I GLU* 6.0 1.8 - - - -
245I SER* 2.6 18.6 + - - -
249I ASP* 2.3 34.4 + - - -
252I LEU* 4.4 22.9 - - + -
255I MET* 5.4 2.5 - - + -
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Residues in contact with TYR 224 (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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220I GLN 2.8 14.1 + - - +
221I GLN* 3.2 17.9 - - + +
223I TYR* 1.3 77.4 - - - +
225I LYS* 1.3 63.6 + - + +
227I ILE* 3.1 14.5 + - + +
228I THR* 2.9 50.0 + - + +
255I MET* 4.2 20.2 - - + -
258I ARG* 5.4 8.1 - - + -
259I PHE* 3.4 60.1 + + + -
262I PHE* 3.8 30.7 - + - -
263I ILE* 5.5 1.9 + - - +
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Residues in contact with LYS 225 (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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221I GLN* 2.9 27.1 + - - +
222I LEU* 3.1 35.2 + - + +
224I TYR* 1.3 80.6 - - + +
226I GLU* 1.3 60.7 + - - +
228I THR* 2.6 22.4 + - - +
229I GLU* 2.9 25.1 + - - +
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Residues in contact with GLU 226 (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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222I LEU 2.9 17.3 + - - +
223I TYR* 3.2 25.6 + - + +
225I LYS* 1.3 76.6 - - - +
227I ILE* 1.3 57.2 + - + +
229I GLU* 3.8 3.0 - - - +
230I ALA* 2.9 32.7 + - - +
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Residues in contact with ILE 227 (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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223I TYR* 2.9 53.7 + - + +
224I TYR* 3.2 21.5 - - + +
226I GLU* 1.3 75.8 - - + +
228I THR* 1.3 57.9 + - + +
230I ALA* 3.4 5.1 + - - +
231I CYS* 2.9 26.2 + - - +
242I ALA* 4.7 8.5 - - + +
245I SER* 4.9 7.9 - - - +
246I ILE* 5.0 12.8 - - + -
252I LEU* 5.0 9.9 - - + -
255I MET* 5.7 2.5 - - + -
259I PHE* 3.9 28.5 - - + -
285I MET* 4.0 10.7 - - + +
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Residues in contact with THR 228 (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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224I TYR* 2.9 47.7 + - + +
225I LYS* 2.6 29.5 + - - +
227I ILE* 1.3 78.5 - - + +
229I GLU* 1.3 63.2 + - - +
231I CYS* 3.0 11.3 + - - +
232I VAL* 2.9 29.1 + - - +
259I PHE* 5.6 1.3 - - + -
263I ILE* 6.3 2.9 - - + -
285I MET* 5.4 3.4 - - + -
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Residues in contact with GLU 229 (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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225I LYS* 2.9 18.9 + - - +
226I GLU* 4.4 2.8 - - - +
228I THR* 1.3 85.8 + - - +
230I ALA* 1.3 57.8 + - - +
232I VAL* 3.4 16.5 - - + +
233I GLY* 3.0 20.3 + - - -
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Residues in contact with ALA 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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226I GLU 2.9 20.3 + - - +
227I ILE* 3.8 2.0 - - - +
229I GLU* 1.3 73.9 - - - +
231I CYS* 1.3 61.3 + - - +
232I VAL 3.2 0.2 - - - -
233I GLY* 2.9 18.4 + - - +
238I LYS* 3.9 17.0 - - + +
239I ARG* 3.4 20.6 + - - -
241I GLU* 4.5 7.6 - - - +
242I ALA* 3.7 24.4 - - + +
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Residues in contact with CYS 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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227I ILE 2.9 14.8 + - - +
228I THR* 3.2 12.8 - - - +
230I ALA* 1.3 75.9 - - - +
232I VAL* 1.3 56.1 + - - +
239I ARG* 2.5 27.2 + - - +
242I ALA* 4.7 3.7 - - + +
278I LEU* 5.7 0.2 - - - +
281I TYR* 3.2 28.3 - - - -
282I LEU* 4.3 12.3 - - - -
285I MET* 3.6 36.3 - - + -
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Residues in contact with VAL 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228I THR 2.9 15.1 + - - +
229I GLU* 3.4 19.3 - - + +
230I ALA 3.2 0.2 - - - -
231I CYS* 1.3 76.3 - - - +
233I GLY* 1.3 64.8 + - - +
234I SER* 3.6 2.5 + - - +
239I ARG* 3.0 6.6 + - - -
278I LEU* 5.7 9.9 - - + -
281I TYR* 3.6 12.5 - - - -
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Residues in contact with GLY 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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229I GLU 3.0 12.3 + - - -
230I ALA* 2.9 18.7 + - - -
232I VAL* 1.3 74.1 - - - +
234I SER* 1.3 65.4 + - - +
235I CYS 3.4 8.4 - - - +
236I GLU* 5.6 0.3 - - - +
238I LYS* 5.1 8.3 - - - -
239I ARG* 2.4 29.5 + - - -
281I TYR* 4.1 2.6 + - - -
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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