Contacts of the helix formed by residues 384 - 399 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312H PHE 4.7 0.3 - - - +
313H PHE* 2.6 53.2 - - + +
314H LEU 4.4 3.8 + - - +
382H THR* 2.9 10.3 + - - +
383H THR* 1.3 86.2 - - - +
385H GLY* 1.3 57.6 + - - +
387H GLN* 3.1 23.0 - - + +
388H ILE* 2.7 32.4 + - + +
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Residues in contact with GLY 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361H ALA* 3.4 26.9 - - - +
362H SER 4.0 6.6 + - - -
365H SER 3.9 13.0 - - - -
366H PHE* 3.8 10.5 - - - -
382H THR* 4.1 3.3 + - - -
383H THR 3.2 8.1 + - - -
384H GLU* 1.3 75.2 - - - +
386H GLU* 1.3 70.0 + - - +
388H ILE* 3.6 2.8 - - - +
389H ALA* 3.1 13.7 + - - +
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Residues in contact with GLU 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H ALA* 4.0 6.9 - - - +
362H SER 4.8 2.0 + - - -
383H THR 5.0 0.2 + - - -
385H GLY* 1.3 70.8 - - - +
387H GLN* 1.3 89.0 + - - +
389H ALA* 2.6 20.6 + - - +
390H GLN* 2.8 22.1 + - + +
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Residues in contact with GLN 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313H PHE* 4.1 19.5 - - + -
383H THR 4.1 3.2 - - - +
384H GLU* 3.1 37.3 - - + +
385H GLY 3.7 0.2 + - - -
386H GLU* 1.3 93.0 + - - +
388H ILE* 1.3 59.0 + - - +
390H GLN* 2.8 43.2 + - - +
391H LEU* 3.0 8.5 + - - +
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Residues in contact with ILE 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H PHE* 3.4 47.3 - - + -
315H VAL* 4.8 0.7 - - + -
330H LEU* 4.4 17.5 - - + -
332H ILE* 5.1 8.4 - - + +
366H PHE* 3.4 35.4 - - + -
382H THR* 3.9 20.6 - - + +
384H GLU 2.7 28.4 + - - +
385H GLY 3.6 3.8 - - - +
386H GLU 2.9 2.0 + - - -
387H GLN* 1.3 74.7 - - - +
389H ALA* 1.3 59.9 + - - +
391H LEU* 3.8 3.4 + - - +
392H ILE* 3.4 26.2 + - + +
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Residues in contact with ALA 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H TRP* 3.3 36.3 + - + +
361H ALA* 4.7 6.5 - - + +
366H PHE* 4.0 5.2 - - + -
385H GLY 3.1 11.0 + - - +
386H GLU* 2.6 16.1 + - - +
388H ILE* 1.3 70.9 - - - +
390H GLN* 1.3 55.4 + - - +
391H LEU 3.2 0.2 + - - -
392H ILE* 3.3 3.6 + - - +
393H ALA* 2.7 37.5 + - - +
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Residues in contact with GLN 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H GLU* 2.8 21.0 + - + +
387H GLN* 2.8 32.4 + - - +
389H ALA* 1.3 75.9 - - - +
391H LEU* 1.3 65.1 + - + +
393H ALA* 3.0 9.4 - - - +
394H GLY* 3.0 16.3 + - - -
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Residues in contact with LEU 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H SER* 3.9 24.9 - - - +
313H PHE* 4.1 14.8 - - + -
332H ILE* 3.4 35.2 - - + +
387H GLN 3.0 10.1 + - - +
388H ILE* 3.9 7.9 - - - +
389H ALA 3.2 0.2 - - - -
390H GLN* 1.3 73.5 - - + +
392H ILE* 1.3 67.9 + - - +
393H ALA 2.6 5.4 + - - -
394H GLY* 2.8 15.0 + - - -
395H TYR* 2.9 35.9 + - + +
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Residues in contact with ILE 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H ILE* 4.2 28.0 - - + +
337H VAL* 4.8 0.4 - - + -
353H LEU* 4.5 7.0 - - + -
356H ILE* 4.7 8.5 - - + -
359H TRP* 4.1 23.1 - - + -
366H PHE* 3.5 32.3 - - + -
368H LEU* 3.9 21.8 - - + -
388H ILE* 3.4 9.4 + - + +
389H ALA* 3.3 8.7 + - - +
391H LEU* 1.3 78.8 - - - +
393H ALA* 1.3 61.6 + - - +
395H TYR* 3.9 6.5 - - - -
396H ILE* 2.6 49.1 + - + +
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Residues in contact with ALA 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740E ASP* 5.9 0.7 - - - +
359H TRP* 4.1 23.1 - - + -
389H ALA 2.7 16.0 + - - +
390H GLN* 3.0 14.6 - - - +
391H LEU 2.6 4.2 + - - -
392H ILE* 1.3 69.1 - - - +
394H GLY* 1.3 55.5 + - - +
396H ILE* 2.6 28.3 + - - +
397H ASP* 2.9 16.1 + - - +
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Residues in contact with GLY 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390H GLN 3.0 5.8 + - - -
391H LEU* 2.8 10.2 + - - -
393H ALA* 1.3 76.9 - - - +
395H TYR* 1.3 62.9 + - - -
396H ILE 3.4 0.2 + - - -
397H ASP* 3.4 15.4 + - - +
398H ILE* 3.6 23.5 - - - +
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Residues in contact with TYR 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311H SER* 6.2 0.2 - - - -
332H ILE* 3.9 19.7 - - + -
333H THR* 3.6 13.2 - - - -
334H LYS* 3.1 47.5 - - + +
353H LEU* 3.4 18.7 - - + +
391H LEU* 2.9 39.9 + - + +
392H ILE* 4.1 3.8 - - - +
394H GLY* 1.3 75.2 - - - +
396H ILE* 1.3 61.7 + - - +
398H ILE* 4.1 11.6 - - + +
399H ILE* 3.2 29.1 + - - +
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Residues in contact with ILE 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E ALA* 3.8 33.9 - - + +
353H LEU* 3.3 41.5 - - + +
356H ILE* 5.3 5.2 - - + +
359H TRP* 4.5 13.2 - - + -
392H ILE* 2.6 45.1 + - + +
393H ALA* 2.6 14.4 + - - +
395H TYR* 1.3 69.9 - - - +
397H ASP* 1.3 75.9 + - - +
399H ILE* 3.1 23.8 + - + +
400H LEU* 4.0 4.8 - - - +
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Residues in contact with ASP 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H ALA* 2.9 25.3 - - - +
394H GLY* 3.4 15.3 - - - +
396H ILE* 1.3 86.0 - - - +
398H ILE* 1.3 68.2 + - + +
399H ILE 3.0 0.2 + - - -
400H LEU 3.3 20.8 - - - +
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Residues in contact with ILE 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H LYS* 5.6 11.0 - - + -
394H GLY 3.6 18.6 - - - +
395H TYR* 4.1 14.6 - - + +
397H ASP* 1.3 82.3 - - + +
399H ILE* 1.3 66.0 + - + +
400H LEU* 2.9 7.8 + - - +
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Residues in contact with ILE 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744E ASN* 6.2 0.7 - - - +
334H LYS* 3.6 26.2 - - + +
353H LEU* 4.0 29.6 - - + +
354H THR* 4.2 23.8 - - + -
395H TYR 3.2 21.3 + - - +
396H ILE* 3.3 12.4 - - + +
397H ASP 3.0 3.4 + - - -
398H ILE* 1.3 81.9 - - + +
400H LEU* 1.3 74.9 + - - +
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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