Contacts of the helix formed by residues 287 - 292 (chain B) in PDB entry 1MWT
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 TYR 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU* 2.8 32.8 + - + +
284B GLU 3.9 2.5 - - - -
286B LEU* 1.3 106.9 - - + +
288B ASP* 1.3 66.3 + - - +
289B LYS* 3.1 5.6 + - - +
290B LYS* 3.2 39.8 + - + +
291B LEU* 3.4 15.7 + - + +
324B ILE* 3.6 18.8 - - + -
495B ASP* 2.5 31.4 + - - +
549B LEU* 4.5 0.7 - - + -
550B LEU* 3.4 35.7 - - + +
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Residues in contact with ASP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.1 22.5 + - - +
269B TYR* 5.2 5.4 - - + +
272B TYR* 2.7 40.3 + - - +
278B ILE* 3.9 4.7 - - - -
279B GLY 2.8 27.1 + - - +
284B GLU 3.1 15.9 + - - +
285B LYS* 3.3 13.8 + - - +
286B LEU 3.5 0.4 + - - -
287B TYR* 1.3 76.4 - - - +
289B LYS* 1.3 56.6 + - - +
291B LEU* 3.1 2.9 + - - +
292B GLN* 2.8 40.8 + - - +
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.9 23.6 + - - +
272B TYR* 3.8 20.3 + - + +
287B TYR* 3.1 2.6 - - - -
288B ASP* 1.3 81.0 + - - +
290B LYS* 1.3 67.1 + - + +
291B LEU 3.3 0.7 + - - -
292B GLN* 3.4 16.7 + - - +
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Residues in contact with LYS 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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287B TYR* 3.2 31.1 + - + -
289B LYS* 1.3 81.6 - - + +
291B LEU* 1.3 59.0 + - - +
292B GLN 3.5 1.0 - - - +
322B LYS* 3.2 46.2 + - - +
324B ILE* 3.8 25.7 - - + +
550B LEU* 3.8 27.3 - - - +
552B ASP* 5.0 9.5 + - - -
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Residues in contact with LEU 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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151B ARG* 3.5 38.4 - - + +
152B GLY 2.9 43.3 + - - +
153B LYS 3.4 19.7 - - - +
154B ILE* 4.0 16.2 - - + -
283B LEU 4.8 1.8 - - - +
284B GLU* 3.6 17.3 - - - +
287B TYR* 3.7 9.0 - - + +
288B ASP 3.1 6.5 + - - +
290B LYS* 1.3 76.7 - - - +
292B GLN* 1.3 68.4 + - - +
321B GLY* 3.5 1.2 - - - -
322B LYS 3.4 13.9 - - - +
324B ILE* 3.7 25.6 - - + -
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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
----------------------------------------------------------
151B ARG* 3.5 4.5 - - - +
272B TYR* 3.8 17.9 - - + +
276B ALA* 5.4 3.7 - - - +
277B VAL 2.9 29.9 + - - +
278B ILE* 3.7 8.7 - - - +
288B ASP* 2.8 47.7 + - - +
289B LYS* 3.4 13.5 + - - +
290B LYS 4.9 0.5 - - - +
291B LEU* 1.3 81.5 - - - +
293B HIS* 1.3 86.9 + - - +
320B ASP 4.3 1.0 - - - +
321B GLY* 3.2 12.8 - - - -
322B LYS 4.6 0.5 + - - -
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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