Contacts of the helix formed by residues 381 - 391 (chain J) 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 GLU 381 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379J GLY* 3.6 4.1 - - - -
380J THR* 1.3 78.5 - - - +
382J VAL* 1.3 74.5 + - + +
383J ALA 3.5 0.4 - - - -
384J ASP* 3.4 11.8 - - - +
385J MLY 2.9 56.2 - - - +
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Residues in contact with VAL 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360J HIS* 3.4 46.7 - - + +
363J ASN* 4.1 24.5 - - + +
364J LEU* 3.6 12.6 - - + -
379J GLY 5.2 0.4 + - - -
381J GLU* 1.3 91.2 - - + +
383J ALA* 1.3 68.9 + - - +
384J ASP 2.9 1.8 - - - -
385J MLY 3.0 11.3 + - + +
386J ALA* 2.9 20.3 + - - +
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Residues in contact with ALA 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J LEU* 3.9 17.1 - - + +
379J GLY 4.6 3.9 + - - +
380J THR* 4.5 8.5 - - - +
381J GLU 3.5 0.4 - - - +
382J VAL* 1.3 79.4 - - - +
384J ASP* 1.3 53.2 + - - +
386J ALA* 3.1 3.6 + - - +
387J ALA* 2.6 38.9 + - - +
394J SER* 3.6 9.2 - - - +
397J LEU* 4.6 2.8 - - + +
398J LEU* 3.6 42.4 - - + -
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Residues in contact with ASP 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380J THR* 2.4 33.6 + - - +
381J GLU* 3.4 12.1 - - - +
383J ALA* 1.3 81.9 - - - +
385J MLY 1.3 59.0 + - + +
387J ALA* 3.6 2.1 - - - +
388J TYR* 3.0 29.6 + - - +
394J SER* 2.3 38.5 + - - -
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Residues in contact with MLY 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304J LEU* 4.1 46.9 - - + -
360J HIS* 4.1 26.7 - - + +
381J GLU* 2.9 56.3 - - - +
382J VAL* 3.0 12.0 + - + +
384J ASP* 1.3 77.0 + - + -
386J ALA* 1.3 66.3 + - - +
388J TYR* 3.2 2.7 + - - +
389J LEU* 2.9 31.0 + - - +
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Residues in contact with ALA 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J ALA* 4.5 4.5 - - - +
360J HIS* 4.2 14.1 - - + +
361J TYR* 3.6 34.5 - - + -
364J LEU* 4.6 4.5 - - + -
382J VAL 2.9 14.4 + - - +
383J ALA* 3.6 6.3 - - - +
385J MLY 1.3 78.7 + - - +
387J ALA* 1.3 63.7 + - - +
389J LEU* 3.3 4.5 + - - +
390J MET* 3.1 28.1 + - - +
397J LEU* 5.1 4.7 - - + -
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Residues in contact with ALA 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J ALA 2.6 21.5 + - - +
384J ASP 3.6 5.2 - - - +
386J ALA* 1.3 74.4 - - - +
388J TYR* 1.3 57.8 + - - +
391J GLY 3.1 2.9 + - - -
392J LEU* 2.6 50.1 + - + +
393J ASN 3.9 2.2 - - - -
394J SER* 3.5 34.1 - - - +
397J LEU* 4.6 6.0 - - + +
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Residues in contact with TYR 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302J MET 4.8 4.2 + - - -
304J LEU* 3.9 19.5 - - + -
353J MLY 3.1 41.3 - - - -
384J ASP 3.0 18.9 + - - +
385J MLY 3.8 1.8 - - - +
387J ALA* 1.3 75.0 - - - +
389J LEU* 1.3 88.9 + - + +
391J GLY* 3.1 13.1 + - - +
392J LEU 4.6 4.0 - - - +
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Residues in contact with LEU 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302J MET 3.6 22.9 - - - +
303J LEU* 3.1 26.5 - - - +
304J LEU* 4.0 4.9 - - + -
353J MLY 3.4 65.1 - - + +
354J LEU* 4.4 4.3 - - - +
356J GLY 4.7 0.7 - - - -
357J ALA* 4.4 10.1 - - + +
360J HIS* 3.9 17.7 - - + +
385J MLY 2.9 19.2 + - - +
386J ALA 3.7 3.4 - - - +
388J TYR* 1.3 98.2 - - + +
390J MET* 1.3 58.9 + - - +
391J GLY 3.5 0.2 - - - -
616J VAL* 4.4 2.4 - - - +
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Residues in contact with MET 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J LEU* 4.1 16.8 - - + +
357J ALA* 3.7 24.7 - - + -
358J VAL* 5.3 3.6 - - + -
361J TYR* 2.8 43.3 - - + +
386J ALA 3.1 14.3 + - - +
388J TYR 3.1 0.8 - - - -
389J LEU* 1.3 78.3 - - - +
391J GLY* 1.3 50.2 + - - +
392J LEU* 4.1 13.9 - - + +
433J VAL* 4.2 25.8 - - + -
611J TYR* 4.2 19.7 - - + +
614J SER* 2.4 28.4 + - - -
616J VAL* 3.4 11.6 - - - +
619J LEU* 3.6 19.1 - - + +
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Residues in contact with GLY 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353J MLY 4.9 0.9 - - - -
387J ALA 3.7 0.7 - - - -
388J TYR* 3.1 14.2 + - - -
389J LEU 3.5 0.2 - - - -
390J MET* 1.3 80.2 - - - +
392J LEU* 1.3 58.9 + - - +
613J MLY 4.9 0.5 - - - +
614J SER* 3.2 7.7 + - - -
615J SER* 2.7 39.7 + - - -
616J VAL* 3.6 11.6 - - - +
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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