Contacts of the helix formed by residues 235 - 248 (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 CYS 235 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233I GLY* 3.4 2.9 - - - +
234I SER* 1.3 86.1 + - - +
236I GLU* 1.3 60.5 + - - +
237I ALA* 4.4 4.9 - - + +
238I LYS* 3.0 51.7 + - + +
239I ARG* 2.9 22.7 + - - +
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Residues in contact with GLU 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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233I GLY 5.6 0.2 - - - +
234I SER 3.2 7.6 + - - +
235I CYS* 1.3 69.4 - - - +
237I ALA* 1.3 60.2 + - - +
239I ARG* 3.3 33.5 + - - +
240I ALA* 2.8 35.1 + - + +
243I LEU* 4.9 3.8 - - - +
281I TYR* 5.4 3.6 - - - -
284I ARG* 4.9 11.5 + - - -
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Residues in contact with ALA 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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235I CYS* 3.2 4.6 - - + +
236I GLU* 1.3 76.9 - - - +
238I LYS* 1.3 60.3 + - + +
240I ALA* 3.4 4.9 + - - +
241I GLU* 2.9 30.2 + - - +
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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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230I ALA* 3.9 15.7 - - + +
233I GLY* 5.1 9.4 - - - -
235I CYS* 3.0 43.0 + - + +
237I ALA* 1.3 74.6 - - + +
239I ARG* 1.3 60.0 + - - +
241I GLU* 3.5 12.0 + - - +
242I ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 239 (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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230I ALA 3.4 11.6 + - - -
231I CYS* 2.5 42.4 + - - +
232I VAL 3.0 9.9 + - - -
233I GLY 2.4 29.8 + - - +
235I CYS 2.9 6.7 + - - +
236I GLU* 3.2 44.6 + - - +
238I LYS* 1.3 77.0 - - - +
240I ALA* 1.3 57.0 + - - +
242I ALA* 3.1 7.2 + - - +
243I LEU* 2.9 47.1 + - + +
281I TYR* 3.2 46.9 + - - +
284I ARG* 6.2 5.2 - - - +
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Residues in contact with ALA 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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236I GLU* 2.8 24.1 + - + +
237I ALA* 4.0 4.7 - - - +
239I ARG* 1.3 70.9 - - - +
241I GLU* 1.3 59.8 + - - +
243I LEU* 3.2 13.6 + - + +
244I GLN* 2.9 31.4 + - - +
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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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223I TYR* 6.0 1.7 - - - -
230I ALA* 4.5 7.3 - - - +
237I ALA 2.9 18.6 + - - +
238I LYS* 3.5 13.0 - - - +
239I ARG 3.2 0.2 - - - -
240I ALA* 1.3 76.0 - - - +
242I ALA* 1.3 66.4 + - - +
244I GLN* 3.8 5.0 - - - +
245I SER* 2.9 40.4 + - - -
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Residues in contact with ALA 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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227I ILE* 4.7 10.1 - - + +
230I ALA* 3.7 27.8 - - + -
231I CYS* 4.7 3.6 - - - +
238I LYS 2.9 14.6 + - - +
239I ARG* 3.3 10.1 - - - +
241I GLU* 1.3 80.7 + - - +
243I LEU* 1.3 58.7 + - + +
245I SER* 3.1 6.6 + - - -
246I ILE* 2.8 41.5 + - + +
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Residues in contact with LEU 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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236I GLU* 4.9 3.1 - - - +
239I ARG* 2.9 40.3 + - + +
240I ALA* 3.2 15.2 + - + +
242I ALA* 1.3 76.8 - - + +
244I GLN* 1.3 58.1 + - - +
246I ILE* 3.4 9.6 + - + -
247I ALA* 3.0 30.2 + - - +
281I TYR 5.6 0.7 - - - +
284I ARG* 3.7 46.4 - - + +
285I MET* 4.4 2.9 - - + +
288I ALA* 3.6 15.0 - - + +
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Residues in contact with GLN 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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240I ALA 2.9 16.3 + - - +
241I GLU* 3.9 4.5 - - - +
243I LEU* 1.3 73.2 - - - +
245I SER* 1.3 60.2 + - - +
247I ALA* 4.4 5.1 - - - +
248I THR* 2.6 65.7 + - - +
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Residues in contact with SER 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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223I TYR* 2.6 32.7 + - - -
227I ILE* 4.9 8.6 - - - +
241I GLU* 2.9 29.5 + - - -
242I ALA* 3.1 8.9 + - - -
244I GLN* 1.3 73.8 - - - +
246I ILE* 1.3 66.6 + - - +
248I THR 5.0 0.9 - - - -
249I ASP* 2.8 33.5 + - - +
252I LEU* 5.8 0.5 - - - +
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Residues in contact with ILE 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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227I ILE* 5.0 15.7 - - + -
242I ALA* 2.8 27.9 + - + +
243I LEU* 3.6 8.5 - - + +
245I SER* 1.3 77.7 - - - +
247I ALA* 1.3 52.2 + - - +
248I THR 3.1 0.5 + - - -
249I ASP* 4.5 0.3 - - - +
252I LEU* 6.5 0.9 - - - -
259I PHE* 5.1 5.4 - - + -
285I MET* 3.7 35.0 - - + -
288I ALA* 3.4 37.0 - - + +
289I LEU* 3.6 24.7 - - + +
292I ASN* 2.4 35.8 + - + -
295I LEU* 5.0 0.2 - - - +
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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 LEU 3.0 15.3 + - - +
244I GLN* 4.2 5.6 - - - +
246I ILE* 1.3 79.2 - - - +
248I THR* 1.3 65.2 + - - +
288I ALA* 3.4 24.2 - - + +
291I ASP* 3.7 15.1 - - + +
292I ASN* 3.0 23.5 - - - +
293I PRO* 4.1 3.1 - - - +
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Residues in contact with THR 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 GLN* 2.6 40.0 + - - +
245I SER* 3.9 2.7 - - - +
247I ALA* 1.3 83.5 + - - +
249I ASP* 1.3 67.1 + - - +
250I PRO* 3.4 13.3 - - + +
292I ASN* 3.8 3.1 - - - -
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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