Contacts of the helix formed by residues 381 - 391 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379P GLY* 3.6 4.3 - - - -
380P THR* 1.3 78.8 - - - +
382P VAL* 1.3 75.3 + - + +
384P ASP* 3.4 10.9 - - - +
385P MLY 2.9 55.8 - - - +
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Residues in contact with VAL 382 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360P HIS* 3.4 47.8 - - + +
363P ASN* 4.1 23.3 - - + +
364P LEU* 3.6 11.9 - - + -
379P GLY 5.2 0.6 + - - -
381P GLU* 1.3 90.1 - - + +
383P ALA* 1.3 69.0 + - - +
384P ASP 2.9 2.2 - - - -
385P MLY 3.0 12.9 + - + +
386P ALA* 2.9 20.8 + - - +
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Residues in contact with ALA 383 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364P LEU* 3.9 16.6 - - + +
379P GLY 4.6 3.3 + - - +
380P THR* 4.5 9.2 - - - -
381P GLU 3.5 1.0 - - - +
382P VAL* 1.3 79.3 - - - +
384P ASP* 1.3 54.0 + - - +
386P ALA* 3.1 4.0 + - - +
387P ALA* 2.6 38.4 + - - +
394P SER* 3.6 8.5 - - - +
397P LEU* 4.6 3.3 - - + +
398P LEU* 3.6 42.2 - - + -
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Residues in contact with ASP 384 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380P THR* 2.4 34.1 + - - +
381P GLU* 3.4 12.4 - - - +
383P ALA* 1.3 81.1 - - - +
385P MLY 1.3 58.4 + - + +
387P ALA* 3.5 2.3 + - - +
388P TYR* 3.0 29.5 + - - +
394P SER* 2.3 38.3 + - - -
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Residues in contact with MLY 385 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P LEU* 4.1 49.1 - - + -
360P HIS* 4.1 26.9 - - + +
381P GLU* 2.9 55.6 - - - +
382P VAL* 3.0 12.7 + - + +
384P ASP* 1.3 77.2 + - + -
386P ALA* 1.3 67.9 + - - +
388P TYR* 3.8 2.5 - - - +
389P LEU* 2.9 31.7 + - - +
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Residues in contact with ALA 386 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357P ALA* 4.5 4.3 - - - +
360P HIS* 4.2 14.9 - - + +
361P TYR* 3.6 35.2 - - + -
364P LEU* 4.6 4.3 - - + -
382P VAL 2.9 15.3 + - - +
383P ALA* 3.6 6.5 - - - +
385P MLY 1.3 79.1 + - - +
387P ALA* 1.3 63.9 + - - +
389P LEU* 3.3 4.5 + - - +
390P MET* 3.1 28.2 + - - +
397P LEU* 5.1 4.5 - - + -
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Residues in contact with ALA 387 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383P ALA 2.6 21.7 + - - +
384P ASP 3.6 4.9 - - - +
386P ALA* 1.3 74.5 - - - +
388P TYR* 1.3 58.9 + - - +
391P GLY 3.1 3.1 + - - -
392P LEU* 2.6 48.9 + - + +
393P ASN 3.9 2.9 - - - +
394P SER* 3.5 34.5 - - - +
397P LEU* 4.6 6.0 - - + +
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Residues in contact with TYR 388 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302P MET 4.8 4.0 - - - -
304P LEU* 3.9 19.7 - - + -
353P MLY 3.1 39.2 - - - -
384P ASP 3.0 18.3 + - - +
385P MLY 3.2 2.2 + - - +
387P ALA* 1.3 73.8 - - - +
389P LEU* 1.3 89.9 + - + +
391P GLY* 3.1 12.4 + - - -
392P LEU 4.6 4.0 - - - +
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Residues in contact with LEU 389 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302P MET 3.6 22.2 - - - +
303P LEU* 3.1 26.5 - - - +
304P LEU* 4.0 4.5 - - + -
353P MLY 3.4 64.2 - - + +
354P LEU* 4.4 4.2 - - - +
356P GLY 4.7 0.7 - - - -
357P ALA* 4.4 9.9 - - + +
360P HIS* 3.9 17.7 - - + +
385P MLY 2.9 19.7 + - - +
386P ALA 3.7 3.8 - - - +
388P TYR* 1.3 98.0 - - + +
390P MET* 1.3 59.1 + - - +
616P VAL* 4.4 2.6 - - - +
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Residues in contact with MET 390 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354P LEU* 4.1 17.5 - - + +
357P ALA* 3.7 23.6 - - + -
358P VAL* 5.3 3.6 - - + -
361P TYR* 2.8 43.3 - - + +
386P ALA 3.1 14.9 + - - +
387P ALA 4.1 0.2 - - - +
388P TYR 3.1 0.4 - - - -
389P LEU* 1.3 78.1 - - - +
391P GLY* 1.3 50.3 + - - +
392P LEU* 4.1 13.8 - - + +
433P VAL* 4.2 25.8 - - + -
611P TYR* 4.2 19.5 - - + +
614P SER* 2.4 28.4 + - - -
616P VAL* 3.4 12.3 - - - +
619P LEU* 3.6 19.0 - - + +
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Residues in contact with GLY 391 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353P MLY 4.9 0.9 - - - -
387P ALA 3.7 0.7 - - - -
388P TYR* 3.1 14.2 + - - -
389P LEU 3.5 0.4 - - - -
390P MET* 1.3 80.0 - - - +
392P LEU* 1.3 59.3 + - - +
613P MLY 4.9 0.5 - - - +
614P SER* 3.2 8.4 + - - -
615P SER* 2.7 40.4 + - - -
616P VAL* 3.6 10.9 - - - +
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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