Contacts of the helix formed by residues 381 - 391 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379G GLY* 3.6 4.1 - - - -
380G THR* 1.3 78.1 - - - +
382G VAL* 1.3 73.8 + - + +
383G ALA 3.5 0.2 - - - -
384G ASP* 3.4 11.4 - - - +
385G MLY 2.9 57.1 - - - +
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Residues in contact with VAL 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360G HIS* 3.4 46.0 - - + +
363G ASN* 4.1 23.8 - - + +
364G LEU* 3.6 13.7 - - + -
379G GLY 5.2 0.6 + - - -
381G GLU* 1.3 91.8 - - + +
383G ALA* 1.3 67.9 + - - +
384G ASP 2.9 1.8 - - - -
385G MLY 3.0 11.6 + - + +
386G ALA* 2.9 20.4 + - - +
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Residues in contact with ALA 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364G LEU* 3.9 18.0 - - + +
379G GLY 4.6 3.9 + - - +
380G THR* 4.5 8.5 - - - -
381G GLU 3.5 1.0 - - - +
382G VAL* 1.3 78.1 - - - +
384G ASP* 1.3 53.9 + - - +
386G ALA* 3.1 3.4 + - - +
387G ALA* 2.6 38.7 + - - +
394G SER* 3.6 8.7 - - - +
397G LEU* 4.6 3.2 - - + +
398G LEU* 3.6 42.2 - - + -
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Residues in contact with ASP 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380G THR* 2.4 33.6 + - - +
381G GLU* 3.4 11.7 - - - +
383G ALA* 1.3 81.0 - - - +
385G MLY 1.3 59.4 + - + +
387G ALA* 3.6 2.3 - - - +
388G TYR* 3.0 29.6 + - - +
394G SER* 2.3 38.3 + - - -
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Residues in contact with MLY 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G LEU* 4.1 47.8 - - + -
360G HIS* 4.1 26.7 - - + +
381G GLU* 2.9 56.3 - - - +
382G VAL* 3.0 14.0 + - + +
384G ASP* 1.3 77.0 + - + -
386G ALA* 1.3 67.5 + - - +
388G TYR* 3.8 2.4 - - - +
389G LEU* 2.9 31.1 + - - +
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Residues in contact with ALA 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G ALA* 4.5 4.9 - - - +
360G HIS* 4.2 14.3 - - + +
361G TYR* 3.6 34.8 - - + -
364G LEU* 4.6 4.9 - - + -
382G VAL 2.9 14.8 + - - +
383G ALA* 3.6 6.3 - - - +
385G MLY 1.3 77.5 + - - +
387G ALA* 1.3 64.3 + - - +
389G LEU* 3.7 4.3 - - - +
390G MET* 3.1 28.2 + - - +
397G LEU* 5.1 4.5 - - + -
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Residues in contact with ALA 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383G ALA 2.6 21.5 + - - +
384G ASP 3.6 5.4 - - - +
386G ALA* 1.3 74.5 - - - +
388G TYR* 1.3 58.9 + - - +
391G GLY 3.1 2.8 + - - -
392G LEU* 2.6 50.0 + - + +
393G ASN 3.9 2.7 - - - -
394G SER* 3.5 34.8 - - - +
397G LEU* 4.6 5.8 - - + +
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Residues in contact with TYR 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G MET 4.8 3.8 - - - -
304G LEU* 3.9 20.4 - - + -
353G MLY 3.1 41.4 - - - -
384G ASP 3.0 18.5 + - - +
385G MLY 3.8 2.0 - - - +
387G ALA* 1.3 75.1 - - - +
389G LEU* 1.3 88.9 + - + +
391G GLY* 3.1 12.6 + - - -
392G LEU 4.6 4.0 - - - +
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Residues in contact with LEU 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G MET 3.6 22.9 - - - +
303G LEU* 3.1 26.2 - - + +
304G LEU* 4.0 4.3 - - + -
353G MLY 3.4 65.3 - - + +
354G LEU* 4.4 4.2 - - - +
356G GLY 4.7 0.7 - - - -
357G ALA* 4.4 10.1 - - + +
360G HIS* 3.9 17.9 - - + +
385G MLY 2.9 20.1 + - - +
386G ALA 3.7 3.8 - - - +
388G TYR* 1.3 98.8 - - + +
390G MET* 1.3 58.6 + - - +
616G VAL* 4.4 2.4 - - - +
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Residues in contact with MET 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G LEU* 4.1 16.8 - - + +
357G ALA* 3.7 23.3 - - + -
358G VAL* 5.3 3.6 - - + -
361G TYR* 2.8 43.1 - - + +
386G ALA 3.1 15.2 + - - +
387G ALA 4.1 0.2 - - - +
388G TYR 3.1 0.6 - - - -
389G LEU* 1.3 78.6 - - - +
391G GLY* 1.3 50.1 + - - +
392G LEU* 4.1 14.0 - - + +
433G VAL* 4.2 25.8 - - + -
611G TYR* 4.2 19.3 - - + +
614G SER* 2.4 28.6 + - - -
616G VAL* 3.4 11.4 - - - +
619G LEU* 3.6 18.5 - - + +
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Residues in contact with GLY 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G MLY 4.9 0.9 - - - -
387G ALA 3.7 0.7 - - - -
388G TYR* 3.1 13.8 + - - -
389G LEU 3.5 0.2 - - - -
390G MET* 1.3 80.8 - - - +
392G LEU* 1.3 59.8 + - - +
613G MLY 4.9 0.5 - - - +
614G SER* 3.2 8.7 + - - -
615G SER* 2.7 39.1 + - - -
616G VAL* 3.6 11.8 - - - +
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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