Contacts of the helix formed by residues 284 - 292 (chain B) in PDB entry 3MY0
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 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLY* 1.3 75.9 - - - +
285B LEU* 1.3 61.8 + - - +
286B TYR* 3.6 6.7 - - - +
287B ASP* 2.6 36.1 + - - +
288B PHE* 2.9 27.5 + - - +
333B SER 3.7 5.6 - - - -
334B ARG* 3.7 24.4 + - - +
336B VAL 3.2 12.1 - - - -
337B LEU* 4.0 8.0 - - - +
338B VAL* 4.4 1.3 - - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER* 1.3 68.9 - - - +
286B TYR* 1.3 60.9 + - - +
288B PHE* 4.7 1.3 - - + -
289B LEU* 2.8 55.2 + - + +
302B LEU* 4.2 19.5 - - + -
333B SER* 3.4 19.9 + - - +
336B VAL* 2.6 32.0 + - + +
338B VAL* 3.8 23.5 - - + +
344B CYS* 4.4 8.7 - - - -
404B VAL* 3.8 28.9 - - + +
408B ILE* 4.2 17.0 - - + -
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER* 3.6 8.7 - - - +
285B LEU* 1.3 79.0 - - - +
287B ASP* 1.3 75.9 + - - +
289B LEU* 3.9 4.2 - - - +
290B GLN* 3.1 47.8 + - - +
333B SER* 3.3 17.8 + - - +
334B ARG* 3.2 58.8 + - + -
421B TYR* 3.2 43.1 - + - -
423B PRO* 5.4 4.8 - - + +
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B HIS 3.9 11.7 - - - +
283B GLY* 4.0 4.7 - - - -
284B SER* 2.6 33.1 + - - +
286B TYR* 1.3 92.4 - - - +
288B PHE* 1.3 60.3 + - - +
290B GLN* 3.1 17.1 - - - +
291B ARG* 2.9 27.4 - - - +
334B ARG* 5.4 2.8 + - - -
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B HIS* 4.1 33.2 - + + +
284B SER 2.9 15.7 + - - +
285B LEU* 3.7 4.0 - - + +
287B ASP* 1.3 74.4 - - - +
289B LEU* 1.3 63.3 + - + +
290B GLN 3.3 0.3 + - - -
291B ARG* 3.3 21.1 + - - +
292B GLN* 2.9 61.7 + - + +
294B LEU* 3.8 19.3 - - + -
298B LEU* 4.4 15.7 - - + -
302B LEU* 3.8 30.7 - - + -
338B VAL* 3.9 23.6 - - + -
342B LEU* 4.9 9.0 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 2.8 43.5 + - + +
286B TYR* 4.0 1.8 - - - +
288B PHE* 1.3 76.3 - - + +
290B GLN* 1.3 58.8 + - - +
292B GLN 3.5 4.5 - - - +
294B LEU* 3.8 35.9 - - + -
302B LEU* 5.0 0.2 - - + -
333B SER* 5.6 0.2 - - - -
407B GLU* 3.2 45.5 - - + +
408B ILE* 3.8 6.1 - - + +
411B ARG* 2.6 43.2 + - + +
421B TYR* 3.7 20.4 - - + +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B TYR* 3.1 48.0 + - - +
287B ASP* 3.1 14.1 + - - +
289B LEU* 1.3 76.3 - - - +
291B ARG* 1.3 61.7 + - + +
411B ARG* 3.1 20.6 + - - -
421B TYR* 3.9 29.3 + - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU 4.7 3.2 + - - -
282B HIS* 3.3 55.3 + - - +
287B ASP* 2.9 30.4 + - - +
288B PHE* 3.3 15.6 + - - +
290B GLN* 1.3 82.0 - - + +
292B GLN* 1.3 81.8 + - - +
293B THR* 4.2 2.1 + - - +
411B ARG* 4.2 4.6 + - - -
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B PHE* 2.9 53.4 + - + +
289B LEU* 3.5 7.3 - - - +
291B ARG* 1.3 112.3 + - - +
293B THR* 1.3 66.9 + - - +
294B LEU* 4.6 2.8 - - - +
411B ARG* 3.5 21.8 + - - +
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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