Contacts of the helix formed by residues 235 - 248 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230H ALA* 6.5 1.1 - - - -
233H GLY* 3.3 7.9 + - - +
234H SER* 1.3 72.4 - - - +
236H GLU* 1.3 54.0 + - - +
237H ALA 3.4 2.2 - - - -
238H LYS* 3.0 40.0 + - + -
239H ARG* 2.5 35.9 + - - +
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Residues in contact with GLU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234H SER* 3.0 12.4 + - - +
235H CYS* 1.3 73.3 - - - +
237H ALA* 1.3 56.9 + - - +
239H ARG* 3.2 15.1 - - - +
240H ALA* 3.0 30.2 + - + +
281H TYR* 4.4 13.6 + - - -
284H ARG* 4.0 19.6 + - - -
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Residues in contact with ALA 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H CYS 3.4 0.4 - - - -
236H GLU* 1.3 78.5 - - - +
238H LYS* 1.3 61.9 + - + +
240H ALA* 3.4 4.4 + - - +
241H GLU* 2.8 31.4 + - - +
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Residues in contact with LYS 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ALA* 4.4 14.6 - - + +
235H CYS* 3.0 36.8 + - + +
237H ALA* 1.3 76.1 - - + +
239H ARG* 1.3 59.9 + - - +
241H GLU* 3.8 10.4 - - - +
242H ALA* 2.9 31.9 + - - +
193K PHE* 4.4 4.3 - - + -
196K LYS 5.9 0.2 - - - +
197K THR* 3.7 48.0 + - + +
198K GLY* 5.7 1.4 - - - -
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Residues in contact with ARG 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ALA 3.0 15.2 + - - -
231H CYS* 2.5 43.4 + - - +
232H VAL 3.4 0.2 - - - -
233H GLY 2.3 29.7 + - - -
234H SER* 4.8 0.8 - - - +
235H CYS 2.5 18.3 + - - +
236H GLU* 3.2 30.7 - - - +
238H LYS* 1.3 73.1 - - - +
240H ALA* 1.3 65.3 + - + +
242H ALA* 3.1 4.1 + - - +
243H LEU* 3.0 44.0 + - + +
281H TYR* 3.2 56.2 + - + +
284H ARG* 4.7 6.5 - - - +
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Residues in contact with ALA 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H GLU* 3.0 14.5 + - - +
237H ALA* 4.0 4.0 - - - +
239H ARG* 1.3 81.6 - - + +
241H GLU* 1.3 57.2 + - - +
243H LEU* 3.2 14.7 + - + +
244H GLN* 2.9 37.3 + - - +
284H ARG* 6.3 1.1 - - - +
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Residues in contact with GLU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H ALA 2.8 19.6 + - - +
238H LYS* 3.9 5.5 - - - +
240H ALA* 1.3 73.8 - - - +
242H ALA* 1.3 61.1 + - - +
244H GLN* 3.4 9.4 + - + +
245H SER* 2.8 31.4 + - - -
192K ARG 3.4 7.8 - - - +
193K PHE* 3.1 43.8 - - - +
196K LYS* 3.7 34.1 - - + +
197K THR* 3.0 22.9 + - - -
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Residues in contact with ALA 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H ILE* 4.2 22.0 - - + +
230H ALA* 4.4 12.1 - - + -
231H CYS* 5.6 1.1 - - - +
238H LYS 2.9 18.5 + - - +
239H ARG* 3.4 5.6 - - - +
241H GLU* 1.3 76.9 + - - +
243H LEU* 1.3 60.9 + - + +
245H SER* 3.2 7.2 + - - -
246H ILE* 2.9 38.4 + - + +
193K PHE* 4.3 13.9 - - + -
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Residues in contact with LEU 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H CYS* 6.3 2.5 - - - -
239H ARG* 3.0 33.3 + - + +
240H ALA* 3.5 14.4 - - + +
241H GLU 3.2 0.2 - - - -
242H ALA* 1.3 81.4 - - + +
244H GLN* 1.3 58.2 + - + +
246H ILE* 3.4 6.9 + - + -
247H ALA* 2.9 28.7 + - - +
281H TYR 5.1 1.6 - - - +
284H ARG* 3.7 58.1 - - + +
285H MET* 4.2 9.9 - - + +
288H ALA* 3.8 13.7 - - + +
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Residues in contact with GLN 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H ALA* 2.9 24.5 + - + +
241H GLU* 4.0 8.2 - - + +
243H LEU* 1.3 75.2 - - + +
245H SER* 1.3 60.8 + - - +
247H ALA* 3.5 7.5 + - + -
248H THR* 2.6 38.2 + - - +
196K LYS* 5.2 7.8 + - - +
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Residues in contact with SER 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H TYR* 3.3 20.8 + - - -
227H ILE* 4.5 3.3 - - - +
241H GLU* 2.8 23.4 + - - -
242H ALA* 3.2 13.7 - - - -
243H LEU 3.2 0.4 - - - -
244H GLN* 1.3 75.2 - - - +
246H ILE* 1.3 59.5 + - - +
248H THR* 2.8 21.6 + - - +
249H ASP* 2.9 20.8 + - - +
189K ALA* 4.8 7.8 + - - -
192K ARG* 6.0 2.3 - - - +
193K PHE* 4.8 8.3 + - - +
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Residues in contact with ILE 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H TYR* 4.8 0.4 - - - +
227H ILE* 3.6 29.2 - - + -
242H ALA* 2.9 20.0 + - + +
243H LEU* 4.7 8.1 - - + -
245H SER* 1.3 73.9 - - - +
247H ALA* 1.3 61.6 + - - +
248H THR 3.2 1.0 + - - -
249H ASP* 3.2 22.1 + - - +
252H LEU* 4.8 8.7 - - + +
259H PHE* 3.9 22.2 - - + -
285H MET* 4.9 6.7 - - + -
288H ALA* 3.8 34.9 - - + +
289H LEU* 4.2 18.4 - - + +
292H ASN* 4.7 8.7 + - - +
295H LEU* 5.6 4.1 - - + +
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Residues in contact with ALA 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H LEU 2.9 17.5 + - - +
244H GLN* 3.7 9.2 - - + +
245H SER 3.2 0.2 - - - -
246H ILE* 1.3 77.3 - - - +
248H THR* 1.3 61.4 + - - +
249H ASP 3.5 1.7 + - - -
288H ALA* 4.1 14.2 - - + +
291H ASP* 3.3 31.5 - - + +
292H ASN* 4.6 4.2 - - - +
293H PRO* 4.7 4.2 - - - +
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Residues in contact with THR 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H GLN* 2.6 24.5 + - - +
245H SER* 2.8 9.2 + - - +
247H ALA* 1.3 82.4 + - - +
249H ASP* 1.3 60.8 + - - +
250H PRO* 3.3 11.2 - - + +
192K ARG* 3.7 19.8 + - - +
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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