Contacts of the helix formed by residues 281 - 287 (chain A) in PDB entry 1MWR
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 LYS 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A LEU 3.4 2.1 - - - +
254A GLY* 3.4 17.7 - - - -
255A TYR* 3.5 35.6 + - + +
279A GLY 3.5 0.8 - - - -
280A LYS* 1.3 87.7 - - - +
282A GLY* 1.3 70.8 + - - +
284A GLU* 3.5 2.9 + - - +
285A LYS* 3.2 19.3 + - + -
366A TYR* 3.5 22.8 + - - -
371A PHE* 5.0 9.9 - - - -
391A LEU* 5.0 14.3 + - - +
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A HIS 4.0 9.8 + - - -
252A LEU 3.5 10.5 - - - -
253A LEU 3.8 3.1 - - - -
254A GLY* 3.9 5.1 - - - -
281A LYS* 1.3 80.7 - - - +
283A LEU* 1.3 58.2 + - - -
285A LYS* 3.1 1.3 + - - +
286A LEU* 2.9 28.3 + - - +
496A TYR* 5.6 6.7 - - - -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.6 10.1 - - + -
252A LEU* 2.8 43.1 + - + +
253A LEU* 3.2 11.1 + - + +
282A GLY* 1.3 69.3 - - - -
284A GLU* 1.3 66.5 + - - +
286A LEU* 4.1 13.2 - - + -
287A TYR* 2.9 56.9 + - + +
291A LEU* 4.3 3.2 - - - +
326A LEU* 3.7 39.0 - - + -
496A TYR* 4.4 3.3 - - + -
549A LEU* 3.8 19.3 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.0 39.3 + - - -
154A ILE* 3.8 9.4 - - + +
163A ALA* 4.0 0.2 - - - +
241A ARG* 2.5 41.2 + - - -
243A TYR* 2.6 29.0 + - + +
253A LEU 2.9 26.7 + - - +
255A TYR 3.8 14.6 - - - +
256A VAL* 3.7 6.7 - - + -
279A GLY* 3.3 7.3 - - - -
281A LYS 3.7 4.9 - - - +
283A LEU* 1.3 76.5 - - - +
285A LYS* 1.3 56.8 + - - +
288A ASP* 3.2 15.8 - - - +
291A LEU* 3.3 8.3 - - - +
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLU* 6.0 1.1 - - - -
266A GLN* 5.1 8.3 + - - -
269A TYR* 4.7 13.8 + - - +
279A GLY* 3.4 27.3 - - - +
280A LYS* 3.7 20.0 - - - +
281A LYS* 3.2 13.7 + - + +
282A GLY 3.1 8.8 + - - +
283A LEU 3.0 0.2 - - - -
284A GLU* 1.3 76.1 - - - +
286A LEU* 1.3 68.9 + - - +
287A TYR 3.1 2.9 + - - -
288A ASP* 3.2 15.4 + - + +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLY 2.9 16.0 + - - +
283A LEU* 3.9 15.7 - - + +
285A LYS* 1.3 79.8 - - - +
287A TYR* 1.3 92.3 + - + +
288A ASP 3.9 0.5 + - - -
495A ASP 3.9 9.6 - - - +
496A TYR* 4.1 5.4 - - + -
497A PRO* 3.8 32.5 - - + -
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU* 2.9 32.3 + - + +
286A LEU* 1.3 106.4 - - + +
288A ASP* 1.3 65.3 + - - +
289A LYS* 3.4 4.1 + - - -
290A LYS* 3.4 24.1 + - + +
291A LEU* 3.4 22.6 + - + +
324A ILE* 3.5 20.6 - - + -
495A ASP* 2.8 30.2 + - - +
550A LEU* 3.5 34.6 - - + +
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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