Contacts of the helix formed by residues 289 - 295 (chain Z) in PDB entry 1MVW
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 ILE 289 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632 GLY* 5.4 1.6 - - - -
642 ILE* 5.4 4.0 - - + -
166Z TYR* 3.7 40.2 - - + -
171Z LEU* 3.6 32.5 - - + -
285Z CYS* 4.0 7.4 - - + -
286Z ASP* 3.1 42.2 + - + +
287Z ILE 3.2 0.8 - - - -
288Z ASP* 1.4 76.9 - - + +
290Z ARG* 1.3 65.1 + - - +
291Z LYS* 3.3 6.1 - - - +
292Z ASP* 3.0 16.5 + - - +
293Z LEU* 3.3 30.4 + - + +
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Residues in contact with ARG 290 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022 THR* 1.9 48.4 - - - +
282Z ILE* 3.4 36.3 + - + +
283Z MET* 3.9 42.5 + - - +
285Z CYS* 2.4 33.4 + - + -
286Z ASP 3.3 11.5 + - - +
287Z ILE* 3.8 16.8 - - - +
288Z ASP 3.4 1.8 - - - -
289Z ILE* 1.3 79.0 - - - +
291Z LYS* 1.4 61.3 + - - +
292Z ASP 3.3 0.3 + - - -
293Z LEU* 4.1 8.0 - - - +
294Z TYR* 3.1 33.0 + - + -
325Z MET* 4.7 5.2 - - + -
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Residues in contact with LYS 291 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602 SER* 4.9 11.6 + - - -
287Z ILE 4.7 2.5 + - - +
288Z ASP* 3.0 30.1 + - - +
289Z ILE* 3.2 1.2 + - - +
290Z ARG* 1.4 76.1 - - - +
292Z ASP* 1.4 96.0 + - - +
294Z TYR* 3.4 3.3 + - - +
295Z ALA* 3.2 23.0 + - - +
325Z MET* 3.7 25.5 - - + +
326Z LYS* 4.5 2.3 - - - +
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Residues in contact with ASP 292 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442 MET* 5.6 9.0 - - - +
149Z THR* 3.9 23.3 - - + +
150Z GLY* 5.2 0.2 - - - -
166Z TYR* 4.0 19.9 + - - -
289Z ILE* 3.0 9.7 + - - +
291Z LYS* 1.4 104.2 + - - +
293Z LEU* 1.3 68.4 + - - +
295Z ALA* 3.1 5.6 + - - -
296Z ASN* 2.9 30.6 + - - +
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Residues in contact with LEU 293 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149Z THR* 3.8 22.7 - - + -
150Z GLY* 3.8 19.5 - - - +
151Z ILE* 3.4 30.8 - - + +
164Z PRO* 4.4 7.0 - - + -
165Z ILE 4.3 5.2 - - - +
282Z ILE* 4.5 17.3 - - + -
285Z CYS* 4.0 21.8 - - + -
289Z ILE* 3.3 41.6 + - + +
290Z ARG* 4.1 7.2 - - - +
292Z ASP* 1.3 77.3 - - - +
294Z TYR* 1.3 63.1 + - - +
296Z ASN 3.0 21.1 + - - -
297Z ASN* 3.7 1.4 + - - +
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Residues in contact with TYR 294 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279Z TYR* 3.4 19.7 - + - -
282Z ILE* 3.6 37.2 - - + +
283Z MET* 3.4 33.2 - - + +
290Z ARG* 3.1 29.3 + - + +
291Z LYS 3.7 3.4 - - - +
292Z ASP 3.2 1.0 - - - -
293Z LEU* 1.3 78.9 - - - +
295Z ALA* 1.3 57.9 + - - +
296Z ASN 3.1 0.9 + - - -
297Z ASN* 4.6 1.5 + - - +
317Z ILE* 4.0 19.9 - - + +
321Z ALA* 3.6 21.6 - - + +
322Z PRO* 4.7 0.2 - - + -
325Z MET* 3.4 31.4 - - + -
326Z LYS 3.2 15.9 - - - +
327Z ILE* 3.4 16.5 - - + -
328Z LYS 2.8 22.7 + - - +
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Residues in contact with ALA 295 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291Z LYS 3.2 11.5 + - - +
292Z ASP* 3.1 4.1 + - - +
294Z TYR* 1.3 78.5 - - - +
296Z ASN* 1.3 74.3 + - - +
326Z LYS* 3.8 33.0 - - + +
328Z LYS* 3.2 34.1 - - - +
330Z ILE* 3.8 0.7 - - - +
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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