Contacts of the helix formed by residues 384 - 397 (chain D) in PDB entry 1MK9
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 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D PHE* 3.0 52.8 - - + +
314D LEU* 3.9 8.1 + - - +
382D THR* 2.9 12.0 + - - +
383D THR* 1.3 89.7 - - - +
385D GLY* 1.3 53.6 + - - +
386D GLU 3.1 3.4 - - - -
387D GLN* 2.7 41.4 + - + +
388D ILE* 3.0 13.6 + - + +
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Residues in contact with GLY 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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361D ALA* 3.2 22.1 - - - +
362D SER 4.5 5.1 + - - -
365D SER 4.1 6.1 - - - -
366D PHE* 4.0 8.9 - - - -
382D THR* 3.6 21.6 + - - +
383D THR 3.3 4.8 + - - -
384D GLU* 1.3 76.2 - - - +
386D GLU* 1.3 57.1 + - - +
388D ILE* 4.8 0.7 - - - -
389D ALA* 3.1 26.9 + - - +
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Residues in contact with GLU 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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361D ALA* 4.3 4.9 - - + +
362D SER 5.3 1.4 + - - -
383D THR 5.0 1.0 + - - +
384D GLU 2.9 3.0 + - - -
385D GLY* 1.3 73.2 - - - +
387D GLN* 1.3 80.0 + - - +
389D ALA* 3.9 7.1 - - + +
390D GLN* 3.0 44.4 + - + +
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Residues in contact with GLN 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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313D PHE* 4.5 17.6 - - + -
383D THR 3.8 5.2 - - - +
384D GLU* 2.7 45.7 + - + +
386D GLU* 1.3 98.4 + - - +
388D ILE* 1.3 59.2 + - - +
389D ALA 3.0 1.6 - - - -
390D GLN* 3.0 14.4 + - - +
391D LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 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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313D PHE* 3.5 55.4 - - + -
315D VAL* 4.8 1.3 - - + -
330D LEU* 4.2 19.3 - - + -
332D ILE* 4.6 6.5 - - + -
366D PHE* 3.6 33.2 - - + -
382D THR* 4.1 24.5 - - + +
384D GLU* 3.0 16.1 + - + +
387D GLN* 1.3 76.1 - - - +
389D ALA* 1.3 60.7 + - - +
391D LEU* 4.0 2.6 - - + +
392D ILE* 3.2 30.5 + - + +
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Residues in contact with ALA 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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740A ASP* 6.0 0.7 - - - +
359D TRP* 3.7 30.5 + - + +
361D ALA* 4.3 10.8 - - + -
366D PHE* 4.2 4.0 - - + -
385D GLY 3.1 21.2 + - - +
386D GLU* 3.9 9.4 - - + +
387D GLN 3.0 0.6 - - - -
388D ILE* 1.3 77.7 - - - +
390D GLN* 1.3 64.7 + - + +
392D ILE* 4.2 1.0 - - - +
393D ALA* 3.3 24.4 + - - +
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Residues in contact with GLN 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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386D GLU* 3.0 36.9 + - + +
387D GLN* 3.0 17.8 + - - +
389D ALA* 1.3 78.5 - - + +
391D LEU* 1.3 72.0 + - - +
393D ALA* 3.3 6.4 + - - +
394D GLY* 3.0 15.8 + - - -
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Residues in contact with LEU 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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311D SER* 4.1 22.4 - - - +
313D PHE* 4.4 14.1 - - + -
332D ILE* 3.8 30.3 - - + +
387D GLN 2.9 15.3 + - - +
388D ILE* 4.0 5.8 - - - +
389D ALA 3.4 0.2 - - - -
390D GLN* 1.3 81.7 - - - +
392D ILE* 1.3 67.7 + - + +
394D GLY* 2.6 10.9 + - - -
395D TYR* 3.0 49.0 + - + +
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Residues in contact with ILE 392 (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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332D ILE* 4.0 24.0 - - + -
337D VAL* 5.2 0.2 - - + -
353D LEU* 4.6 6.1 - - + -
356D ILE* 4.4 10.5 - - + -
359D TRP* 4.2 15.9 - - + -
366D PHE* 3.4 29.2 - - + -
368D LEU* 4.4 15.7 - - + -
388D ILE* 3.2 25.2 + - + +
389D ALA* 4.2 2.9 - - - +
391D LEU* 1.3 78.5 - - + +
393D ALA* 1.3 55.2 + - - +
395D TYR* 3.0 10.7 + - - +
396D ILE* 2.6 64.3 + - + +
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Residues in contact with ALA 393 (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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359D TRP* 3.7 28.0 - - + -
389D ALA 3.3 18.8 + - - +
390D GLN* 3.4 7.0 - - - +
391D LEU 3.1 0.4 - - - -
392D ILE* 1.3 78.9 - - - +
394D GLY* 1.3 64.0 + - - +
396D ILE* 3.8 0.6 - - - +
397D ASP* 3.1 32.7 + - - +
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Residues in contact with GLY 394 (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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390D GLN 3.0 8.4 + - - -
391D LEU 2.6 13.9 + - - -
393D ALA* 1.3 73.3 - - - +
395D TYR* 1.3 63.5 + - - -
397D ASP* 3.6 3.9 + - - +
398D ILE* 3.2 26.7 + - - +
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Residues in contact with TYR 395 (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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311D SER* 4.6 7.8 + - - -
332D ILE* 4.3 6.8 + - + -
333D THR* 3.0 44.7 - - - -
334D LYS* 3.3 16.3 - - + +
353D LEU* 3.4 14.4 - - + -
391D LEU* 3.0 49.1 + - + +
392D ILE* 3.0 8.6 + - - +
394D GLY* 1.3 75.5 - - - +
396D ILE* 1.3 68.9 + - - +
398D ILE* 2.9 26.7 + - + +
399D ILE* 3.1 15.4 + - - +
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Residues in contact with ILE 396 (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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742A ALA* 3.6 30.3 - - + +
744A ASN* 6.3 0.4 - - - +
353D LEU* 4.2 15.9 - - + +
356D ILE* 3.9 18.8 - - + -
359D TRP* 3.3 33.7 - - + -
392D ILE* 2.6 37.6 + - + +
393D ALA* 3.8 4.7 - - - +
395D TYR* 1.3 73.3 - - - +
397D ASP* 1.3 64.2 + - - +
399D ILE* 2.7 49.5 + - + +
400D LEU 3.6 5.3 + - - -
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Residues in contact with ASP 397 (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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742A ALA* 5.3 4.6 - - - +
359D TRP* 5.4 4.3 - - - -
393D ALA* 3.1 21.2 + - - +
394D GLY* 4.3 3.1 - - - +
395D TYR 3.3 0.2 + - - -
396D ILE* 1.3 83.3 - - - +
398D ILE* 1.3 59.2 + - - +
400D LEU* 4.4 9.0 + - - +
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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