Contacts of the helix formed by residues 239 - 250 (chain M) in PDB entry 5MQF
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 ASN 239 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229M SER 6.1 1.0 - - - -
234M LYS* 5.1 16.2 - - + +
236M GLN* 5.8 0.2 - - - +
238M LEU* 1.3 76.0 - - - +
240M VAL* 1.3 60.1 + - - +
242M ALA* 3.8 10.9 - - + +
243M ILE* 2.9 30.5 + - - +
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Residues in contact with VAL 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229M SER 5.9 0.7 - - - -
230M GLN* 5.3 20.3 - - + +
234M LYS* 5.5 7.5 + - - +
237M SER* 5.0 8.1 - - - -
238M LEU 3.1 7.2 - - - +
239M ASN* 1.3 78.4 - - - +
241M ASP* 1.3 59.6 + - - +
243M ILE* 3.2 5.1 + - - +
244M ILE* 2.9 29.2 + - - +
264M ASP* 5.5 13.2 - - + +
268M ARG* 6.2 2.7 - - + -
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Residues in contact with ASP 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M SER 5.4 4.7 - - - +
238M LEU* 3.4 8.4 + - - +
240M VAL* 1.3 78.9 - - - +
242M ALA* 1.3 57.4 + - - +
244M ILE* 4.0 6.1 - - - +
245M ARG* 2.9 30.1 + - - +
261M SER 5.5 2.0 - - - +
264M ASP* 5.9 2.9 - - - +
265M TYR* 4.3 27.4 - - + +
268M ARG* 6.3 1.1 - - + -
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Residues in contact with ALA 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M LEU 3.3 14.8 + - - +
239M ASN* 4.0 9.0 - - + +
240M VAL 3.2 0.4 - - - -
241M ASP* 1.3 80.1 - - - +
243M ILE* 1.3 57.8 + - - +
245M ARG* 3.8 5.1 - - - +
246M GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M ASP* 4.0 38.0 - - + +
229M SER* 5.1 7.6 - - - -
230M GLN* 5.3 4.9 - - + +
239M ASN 2.9 19.7 + - - +
240M VAL* 3.8 4.7 - - - +
242M ALA* 1.3 76.1 - - - +
244M ILE* 1.3 59.9 + - - +
246M GLY* 3.8 1.2 - - - +
247M GLY* 2.9 25.6 + - - -
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Residues in contact with ILE 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M VAL 2.9 17.4 + - - +
241M ASP* 4.0 6.1 - - - +
243M ILE* 1.3 77.5 - - - +
245M ARG* 1.3 56.4 + - - +
247M GLY* 3.5 1.4 + - - +
248M LEU* 2.9 30.0 + - - +
261M SER* 3.8 33.0 - - - -
264M ASP* 6.1 2.5 - - + -
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Residues in contact with ARG 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ASP 2.9 20.5 + - - +
242M ALA* 4.0 5.4 - - - +
244M ILE* 1.3 74.5 - - - +
246M GLY* 1.3 60.9 + - - +
248M LEU* 3.8 6.9 - - - +
249M THR* 2.9 29.3 + - - -
261M SER* 5.4 1.1 - - - -
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Residues in contact with GLY 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M ALA 2.9 18.0 + - - -
243M ILE* 3.8 1.8 - - - -
244M ILE 3.3 0.4 - - - -
245M ARG* 1.3 75.4 - - - +
247M GLY* 1.3 59.4 + - - +
249M THR* 3.2 7.0 + - - -
250M ARG* 2.9 28.1 + - - +
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Residues in contact with GLY 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M GLU* 4.5 21.0 - - - +
226M ASP* 5.6 2.8 - - - +
243M ILE 2.9 16.8 + - - -
244M ILE* 3.8 1.6 - - - -
246M GLY* 1.3 75.4 - - - +
248M LEU* 1.3 60.4 + - - +
250M ARG* 3.5 13.3 + - - +
251M PHE* 3.6 13.5 + - - +
253M ASP* 4.8 2.4 - - - +
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Residues in contact with LEU 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M ILE 2.9 18.3 + - - +
245M ARG* 3.9 7.6 - - - +
247M GLY* 1.3 76.8 - - - +
249M THR* 1.3 56.6 + - - +
251M PHE 2.8 17.0 - - - +
252M THR* 4.9 0.5 - - - -
253M ASP* 3.8 25.2 + - + +
257M LYS* 6.1 1.3 - - + -
258M LEU* 6.6 0.4 - - - -
261M SER* 6.0 4.5 - - - -
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Residues in contact with THR 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M ARG 2.9 17.6 + - - -
246M GLY* 3.2 7.1 + - - -
248M LEU* 1.3 77.8 - - - +
250M ARG* 1.3 64.3 + - - +
251M PHE 4.5 0.4 - - - -
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Residues in contact with ARG 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219M GLN* 5.3 15.2 - - + +
223M GLU* 5.4 7.9 - - + -
246M GLY 2.9 16.6 + - - +
247M GLY* 3.9 8.7 - - - +
248M LEU 3.4 0.6 - - - -
249M THR* 1.3 79.6 - - - +
251M PHE* 1.3 61.1 + - + +
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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