Contacts of the helix formed by residues 381 - 391 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D GLY* 3.6 4.5 - - - -
380D THR* 1.3 77.5 - - - +
382D VAL* 1.3 73.2 - - + +
383D ALA 3.5 0.2 - - - -
384D ASP* 3.4 10.9 - - - +
385D MLY 2.9 56.5 - - - +
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Residues in contact with VAL 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D HIS* 3.4 46.9 - - + +
363D ASN* 4.1 23.6 - - + +
364D LEU* 3.6 13.0 - - + -
379D GLY 5.2 0.6 + - - -
381D GLU* 1.3 91.4 - - + +
383D ALA* 1.3 67.6 + - - +
384D ASP 2.9 1.8 - - - -
385D MLY 3.0 12.0 + - + +
386D ALA* 2.9 20.4 + - - +
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Residues in contact with ALA 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D LEU* 3.9 17.5 - - + +
379D GLY 4.6 3.5 + - - +
380D THR* 4.5 9.4 - - - -
381D GLU 3.5 0.8 - - - +
382D VAL* 1.3 78.7 - - - +
384D ASP* 1.3 54.3 + - - +
386D ALA* 3.1 3.4 + - - +
387D ALA* 2.6 37.9 + - - +
394D SER* 3.6 8.5 - - - +
397D LEU* 4.6 3.3 - - + +
398D LEU* 3.6 42.4 - - + -
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Residues in contact with ASP 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D THR* 2.4 32.9 + - - +
381D GLU* 3.4 11.9 - - - +
383D ALA* 1.3 80.8 - - - +
385D MLY 1.3 58.7 + - + +
387D ALA* 3.5 2.1 + - - +
388D TYR* 3.0 29.1 + - - +
394D SER* 2.3 38.4 + - - -
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Residues in contact with MLY 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D LEU* 4.1 48.7 - - + -
360D HIS* 4.1 26.5 - - + +
381D GLU* 2.9 57.4 - - - +
382D VAL* 3.0 13.5 + - + +
384D ASP* 1.3 76.6 + - + -
386D ALA* 1.3 66.6 + - - +
388D TYR* 3.2 2.2 + - - +
389D LEU* 2.9 31.5 + - - +
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Residues in contact with ALA 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ALA* 4.5 4.9 - - - +
360D HIS* 4.2 13.8 - - + +
361D TYR* 3.6 34.5 - - + -
364D LEU* 4.6 5.4 - - + -
382D VAL 2.9 15.3 + - - +
383D ALA* 3.6 6.1 - - - +
385D MLY 1.3 77.2 + - - +
387D ALA* 1.3 64.0 + - - +
389D LEU* 3.7 4.3 - - - +
390D MET* 3.1 28.6 + - - +
397D LEU* 5.1 4.0 - - + -
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Residues in contact with ALA 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D ALA 2.6 20.9 + - - +
384D ASP 3.6 4.7 - - - +
386D ALA* 1.3 76.0 - - - +
388D TYR* 1.3 58.1 + - - +
391D GLY 3.1 2.9 + - - -
392D LEU* 2.6 49.6 + - + +
393D ASN 4.0 2.7 - - - +
394D SER* 3.5 34.3 - - - +
397D LEU* 4.6 6.2 - - + +
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Residues in contact with TYR 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D MET 4.8 4.0 - - - -
304D LEU* 3.9 20.0 - - + -
353D MLY 3.1 40.7 - - - -
384D ASP 3.0 19.3 + - - +
385D MLY 3.8 2.0 - - - +
387D ALA* 1.3 75.5 - - - +
389D LEU* 1.3 88.0 + - + +
391D GLY* 3.1 13.0 + - - -
392D LEU 4.6 3.4 - - - +
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Residues in contact with LEU 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D MET 3.6 23.6 - - - +
303D LEU* 3.1 26.5 - - - +
304D LEU* 4.0 4.9 - - + -
353D MLY 3.4 65.2 - - + +
354D LEU* 4.4 4.3 - - - +
356D GLY 4.7 0.9 - - - -
357D ALA* 4.4 10.1 - - + +
360D HIS* 3.9 17.7 - - + +
385D MLY 2.9 19.2 + - - +
386D ALA 3.7 3.8 - - - +
388D TYR* 1.3 97.7 - - + +
390D MET* 1.3 59.4 + - - +
391D GLY 3.5 0.2 - - - -
616D VAL* 4.4 2.4 - - - +
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Residues in contact with MET 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D LEU* 4.1 15.9 - - + +
357D ALA* 3.7 23.6 - - + -
358D VAL* 5.3 3.8 - - + -
361D TYR* 2.8 42.8 - - + +
386D ALA 3.1 14.9 + - - +
387D ALA 4.1 0.2 - - - +
388D TYR 3.1 0.2 - - - -
389D LEU* 1.3 77.7 - - - +
391D GLY* 1.3 50.9 + - - +
392D LEU* 4.1 14.0 - - + +
433D VAL* 4.2 26.2 - - + -
611D TYR* 4.2 19.3 - - + +
614D SER* 2.4 28.2 + - - -
616D VAL* 3.4 11.8 - - - +
619D LEU* 3.6 18.7 - - + +
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Residues in contact with GLY 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D MLY 4.9 0.9 - - - -
387D ALA 3.7 1.1 - - - -
388D TYR* 3.1 14.6 + - - -
389D LEU 3.5 0.2 - - - -
390D MET* 1.3 78.3 - - - +
392D LEU* 1.3 60.1 + - - +
613D MLY 4.9 0.3 - - - +
614D SER* 3.2 7.5 + - - -
615D SER* 2.7 39.5 + - - -
616D 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