Contacts of the helix formed by residues 294 - 300 (chain M) in PDB entry 5IYB
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 PRO 294 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290M ARG 3.7 15.5 - - - +
291M LEU 3.8 8.3 - - - +
292M ILE 3.4 4.7 - - - -
293M TYR* 1.3 97.4 - - + +
295M ARG* 1.3 65.2 + - + +
296M ALA 3.7 0.2 - - - -
297M PRO* 4.9 3.9 - - - +
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Residues in contact with ARG 295 (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 LEU* 4.1 27.1 - - - +
244M LEU* 4.2 36.0 - - + +
292M ILE 3.3 7.7 + - - +
293M TYR 3.1 0.4 - - - -
294M PRO* 1.3 85.8 - - + +
296M ALA* 1.3 65.5 + - - +
297M PRO* 3.3 5.6 - - - -
298M ASP* 3.1 47.4 + - + +
299M LEU* 3.7 9.1 - - + +
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Residues in contact with ALA 296 (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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260M MET* 3.9 24.2 - - + -
292M ILE 3.5 5.8 + - - -
293M TYR* 3.2 14.8 + - + +
295M ARG* 1.3 75.6 - - - +
297M PRO* 1.4 71.1 - - + +
299M LEU* 3.2 23.9 + - - +
300M PHE* 3.9 15.9 + - + -
310M VAL* 4.3 8.1 - - + -
313M LEU* 4.2 17.5 - - + -
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Residues in contact with PRO 297 (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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293M TYR 4.8 2.2 - - - +
294M PRO 4.9 2.2 - - - +
295M ARG* 3.3 8.1 - - - +
296M ALA* 1.4 93.7 - - + +
298M ASP* 1.3 65.1 + - - +
299M LEU 3.3 1.2 + - - -
300M PHE* 3.8 15.4 + - + +
306M PHE* 5.6 3.0 - - + -
310M VAL* 3.7 33.6 - - + -
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Residues in contact with ASP 298 (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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234M HIS* 5.1 1.4 - - - -
238M LYS* 4.2 14.3 - - - -
242M LEU* 5.3 3.6 - - + -
295M ARG* 3.1 46.3 + - - +
297M PRO* 1.3 80.9 - - - +
299M LEU* 1.3 67.1 + - + +
300M PHE 3.5 4.0 + - - +
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Residues in contact with LEU 299 (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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234M HIS* 2.9 24.3 + - - -
235M ILE* 3.9 36.4 - - + +
238M LYS* 3.7 32.5 - - + +
239M ALA* 5.2 5.2 - - + -
242M LEU* 4.2 22.0 - - + -
244M LEU* 4.7 13.5 - - + -
260M MET* 4.8 7.2 - - - -
292M ILE* 4.6 15.5 - - + +
295M ARG* 3.7 19.3 - - + +
296M ALA* 3.2 15.9 + - - +
298M ASP* 1.3 82.6 - - + +
300M PHE* 1.3 64.5 + - + +
301M PRO* 3.8 0.7 - - - +
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Residues in contact with PHE 300 (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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231M ALA* 5.6 2.7 - - + -
234M HIS* 3.7 4.3 - - - -
235M ILE* 3.3 33.0 - - + -
260M MET* 3.7 29.6 - - + -
261M ALA* 5.2 1.6 - - - -
264M ALA* 3.9 28.5 - - + -
296M ALA* 3.9 10.7 + - + -
297M PRO 3.8 10.3 + - - +
298M ASP 3.5 4.7 - - - +
299M LEU* 1.3 79.0 - - - +
301M PRO* 1.3 76.2 - - + +
302M THR* 3.8 3.1 + - - +
304M PHE* 4.1 12.3 - + + -
306M PHE* 3.4 36.3 - + + -
308M THR 5.6 0.4 - - - -
310M VAL* 4.7 11.4 - - + -
313M LEU* 5.5 7.9 - - + -
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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