Contacts of the helix formed by residues 384 - 398 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B PHE 5.3 0.3 - - - +
313B PHE* 3.6 31.1 - - + +
314B LEU* 3.6 29.7 + - - +
382B THR* 3.2 9.2 + - - +
383B THR* 1.3 92.4 - - - +
385B GLY* 1.3 67.7 + - - +
386B GLU 3.1 3.1 - - - -
387B GLN* 2.6 38.0 + - - +
388B ILE* 3.0 11.7 + - + -
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Residues in contact with GLY 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ALA* 3.8 11.4 - - - +
362B SER 4.9 3.8 + - - -
365B SER 4.1 14.1 - - - -
366B PHE* 4.1 5.8 - - - -
382B THR* 3.5 16.1 + - - +
383B THR 3.6 2.8 + - - -
384B GLU* 1.3 75.4 - - - +
386B GLU* 1.3 63.9 + - - +
388B ILE* 3.0 12.1 + - - +
389B ALA* 2.8 24.9 + - - +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ALA* 4.1 11.6 - - + +
362B SER 5.4 3.4 + - - -
383B THR 5.2 1.3 + - - +
384B GLU 2.8 3.0 + - - -
385B GLY* 1.3 72.7 - - - +
387B GLN* 1.3 76.1 + - + +
389B ALA* 3.4 4.3 + - - +
390B GLN* 3.1 32.8 + - - +
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Residues in contact with GLN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PHE* 4.3 16.7 - - + -
383B THR 4.2 6.1 + - - +
384B GLU* 2.6 51.5 + - - +
386B GLU* 1.3 87.0 - - + +
388B ILE* 1.3 63.8 + - - +
390B GLN* 3.2 8.7 + - - +
391B LEU* 3.1 22.5 + - - +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PHE* 3.7 38.4 - - + -
315B VAL* 4.7 0.9 - - + -
330B LEU* 4.4 15.0 - - + -
332B ILE* 4.6 10.1 - - + -
366B PHE* 3.4 37.5 - - + -
382B THR* 4.0 19.5 - - + +
384B GLU* 3.7 23.8 - - + +
385B GLY* 3.0 10.9 + - - +
387B GLN* 1.3 76.2 - - - +
389B ALA* 1.3 63.8 + - - +
391B LEU* 3.3 4.6 + - - +
392B ILE* 3.1 36.4 + - + +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TRP* 3.3 36.4 + - + +
361B ALA* 4.5 10.3 - - + -
366B PHE* 4.0 6.7 - - + -
385B GLY 2.8 16.4 + - - +
386B GLU* 3.6 5.8 - - - +
388B ILE* 1.3 79.2 - - - +
390B GLN* 1.3 56.5 - - - +
392B ILE* 3.5 1.9 + - - -
393B ALA* 2.9 30.2 + - - +
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Residues in contact with GLN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLU* 3.1 26.4 + - - +
387B GLN* 3.2 8.7 + - - +
389B ALA* 1.3 73.6 - - - +
391B LEU* 1.3 66.2 + - - +
393B ALA* 3.8 5.3 - - + +
394B GLY* 3.1 18.7 + - - -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B SER* 4.0 20.4 - - - +
313B PHE* 4.2 12.1 - - + -
332B ILE* 3.2 40.6 - - + -
387B GLN 3.1 12.5 + - - +
388B ILE* 3.7 7.6 - - - +
390B GLN* 1.3 76.9 - - - +
392B ILE* 1.3 58.2 + - - +
394B GLY* 3.2 2.8 + - - -
395B TYR* 3.0 65.0 + - + +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 4.3 29.2 - - + -
337B VAL* 4.9 1.6 - - + -
353B LEU* 4.2 7.4 - - + -
356B ILE* 4.2 7.2 - - + -
359B TRP* 4.0 16.4 - - + -
366B PHE* 3.7 30.5 - - + -
368B LEU* 4.4 14.1 - - + -
388B ILE* 3.1 20.0 + - + +
389B ALA* 3.9 4.7 - - - +
391B LEU* 1.3 74.5 - - - +
393B ALA* 1.3 66.4 + - - +
395B TYR* 3.9 5.1 - - - -
396B ILE* 3.0 55.1 + - + +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TRP* 3.4 28.2 - - + -
389B ALA 2.9 19.5 + - - +
390B GLN* 3.8 7.2 - - + +
391B LEU 3.3 0.2 - - - -
392B ILE* 1.3 76.5 - - - +
394B GLY* 1.3 64.4 + - - +
396B ILE* 4.0 1.6 - - - +
397B ASP* 3.2 21.7 + - - +
740C ASP* 5.7 1.1 - - - +
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Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLN 3.1 12.1 + - - -
391B LEU 3.6 3.4 - - - -
393B ALA* 1.3 79.3 - - - +
395B TYR* 1.3 63.9 + - - +
397B ASP* 3.1 17.3 + - - +
398B ILE* 3.4 13.4 + - - +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B SER* 4.1 9.9 + - - -
332B ILE* 3.9 9.3 + - + -
333B THR* 3.7 30.0 - - - -
334B LYS* 3.3 50.8 + - + +
353B LEU* 3.6 21.4 - - + +
391B LEU* 3.0 57.4 + - + +
392B ILE* 4.1 3.1 - - - +
394B GLY* 1.3 76.4 - - - +
396B ILE* 1.3 61.0 + - - +
398B ILE* 3.4 30.2 - - + +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.4 33.7 - - + +
356B ILE* 3.7 21.3 - - + +
359B TRP* 3.9 9.4 - - + -
392B ILE* 3.0 40.1 + - + +
393B ALA* 4.0 4.3 - - - +
394B GLY 3.2 0.2 - - - -
395B TYR* 1.3 76.4 - - - +
397B ASP* 1.3 64.5 + - - +
398B ILE* 4.5 2.5 - - - -
742C ALA* 3.9 29.3 - - + +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ALA 3.2 11.9 + - - +
394B GLY* 3.1 11.1 + - - +
396B ILE* 1.3 75.7 - - - +
398B ILE* 1.3 71.5 + - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B LYS* 4.8 17.0 - - + -
394B GLY 3.4 10.4 + - - +
395B TYR* 3.4 33.2 - - + +
396B ILE 3.3 2.9 - - - -
397B ASP* 1.3 85.4 - - - +
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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