Contacts of the helix formed by residues 324 - 337 (chain H) in PDB entry 1MKD
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 SER 324 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H ASN* 4.3 3.5 - - - +
322H ASP 3.9 3.0 + - - -
323H SER* 1.3 72.8 - - - +
325H VAL* 1.3 65.7 + - - +
326H LEU 3.3 2.6 + - - -
327H GLU* 3.3 23.4 + - - -
328H ASN* 2.8 30.5 + - - -
366H LEU* 4.3 8.1 + - - +
369H ASP* 2.7 27.4 + - - +
372H LYS* 3.7 19.1 + - - -
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Residues in contact with VAL 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ASN* 3.4 12.8 + - + +
309H LEU* 4.1 13.5 - - + -
310H ILE* 4.3 10.5 - - + -
316H LEU* 3.5 42.0 - - + +
317H ALA* 3.7 16.6 - - + +
320H TYR* 3.7 14.8 - - + -
322H ASP* 3.7 33.4 - - - +
323H SER 3.1 3.5 - - - +
324H SER* 1.3 77.5 - - - +
326H LEU* 1.3 63.3 + - - +
328H ASN 3.5 0.2 + - - -
329H HIS* 3.1 20.1 + - - +
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Residues in contact with LEU 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H HIS* 3.5 17.9 - - + +
302H PRO* 3.4 30.1 - - + -
304H VAL 3.4 24.0 - - - +
305H SER* 4.5 1.1 - - - -
306H ASN* 2.8 36.9 + - - +
309H LEU* 3.7 16.8 - - + -
316H LEU* 4.7 7.9 - - + -
324H SER 3.4 0.2 - - - -
325H VAL* 1.3 70.3 - - - +
327H GLU* 1.3 68.2 + - - +
329H HIS* 2.9 9.1 + - + +
330H HIS* 2.8 51.9 + - + +
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Residues in contact with GLU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ASN* 2.9 27.7 + - - -
324H SER* 3.5 16.1 - - - +
326H LEU* 1.3 76.6 - - - +
328H ASN* 1.3 62.5 + - - +
330H HIS* 3.4 13.8 + - + +
331H LEU* 3.2 26.2 + - - +
365H VAL* 3.8 12.6 - - - +
366H LEU* 4.2 14.6 - - + -
368H THR* 3.6 22.9 - - - +
369H ASP* 3.5 30.6 - - + +
370H MET 4.7 0.7 + - - -
2016H MG 3.7 15.0 - - - -
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Residues in contact with ASN 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E TYR* 4.7 4.3 - - - +
321E ASN* 2.8 32.4 + - - +
320H TYR* 3.5 33.5 + - + +
323H SER* 3.0 27.9 + - - -
324H SER* 2.8 25.1 + - - +
325H VAL 3.8 1.8 - - - +
327H GLU* 1.3 72.0 - - - +
329H HIS* 1.3 64.2 + - - +
331H LEU* 3.3 4.5 + - - +
332H ALA* 3.0 21.5 + - - +
366H LEU* 3.9 14.3 - - - +
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Residues in contact with HIS 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E MET* 5.4 2.8 - - + +
299H VAL 4.6 2.5 - - - -
300H ASP* 2.7 42.2 + - + -
316H LEU* 3.7 36.3 - - + +
320H TYR* 4.0 17.2 + - + -
325H VAL 3.1 11.2 + - - +
326H LEU* 2.9 14.1 + - + +
328H ASN* 1.3 77.8 - - - +
330H HIS* 1.3 67.6 + - - +
332H ALA* 3.1 4.3 + - + +
333H VAL* 3.0 43.8 + - + +
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Residues in contact with HIS 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H ILE* 3.6 14.0 - - - +
297H HIS 2.9 27.1 - - - +
298H ASP* 3.2 32.9 + - - -
299H VAL* 2.7 35.2 + - - +
300H ASP 4.7 0.4 - - - -
301H HIS* 3.8 22.1 - + + -
326H LEU* 2.8 49.5 + - + +
327H GLU* 3.5 13.2 - - + +
329H HIS* 1.3 74.1 - + - +
331H LEU* 1.3 58.4 + - - +
334H GLY* 2.9 27.0 + - - -
365H VAL* 4.5 3.1 - - + -
2016H MG 4.2 3.7 - - - -
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E ASN* 3.3 23.6 - - - +
296H ILE* 4.1 5.6 - - + -
327H GLU 3.2 10.2 + - - +
328H ASN 3.5 4.3 - - - +
329H HIS 3.2 0.4 - - - -
330H HIS* 1.3 79.7 - - - +
332H ALA* 1.3 64.2 + - - +
334H GLY* 3.3 0.7 + - - -
335H PHE* 3.0 54.5 + - + -
361H VAL* 3.7 14.8 - - + +
362H ILE* 3.7 25.6 - - - +
365H VAL* 3.5 34.5 - - + -
366H LEU* 3.7 20.4 - - + -
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E LEU* 3.5 30.4 - - + +
319E MET* 4.1 13.7 - - + +
321E ASN* 4.1 0.6 + - - -
320H TYR* 3.7 16.8 - - - +
328H ASN 3.0 14.6 + - - +
329H HIS* 3.5 10.1 - - - +
331H LEU* 1.3 76.6 - - - +
333H VAL* 1.3 59.4 + - + +
335H PHE* 4.9 0.2 - - - -
336H LYS* 2.9 32.8 + - - +
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Residues in contact with VAL 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H HIS* 4.5 13.9 - - + -
299H VAL* 4.0 24.9 - - + -
300H ASP* 4.3 9.9 - - + +
329H HIS* 3.0 47.6 + - + +
330H HIS 3.8 2.9 - - - +
332H ALA* 1.3 76.5 - - + +
334H GLY* 1.3 63.7 + - - +
336H LYS* 3.2 6.1 + - - +
337H LEU* 3.0 37.1 + - + +
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Residues in contact with GLY 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H TYR* 2.8 32.1 + - - -
246H LEU* 4.6 4.9 - - - -
292H PHE* 4.2 0.6 - - - -
296H ILE* 4.2 21.8 - - - -
299H VAL* 4.0 4.0 - - - +
330H HIS 2.9 16.8 + - - -
331H LEU 3.8 1.1 - - - -
333H VAL* 1.3 77.6 - - - +
335H PHE* 1.3 61.8 + - - +
337H LEU* 3.8 4.3 + - - +
338H LEU* 3.9 3.5 - - - +
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Residues in contact with PHE 335 (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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318E LEU* 4.2 10.8 - - + -
321E ASN* 4.5 2.2 - - - -
292H PHE* 4.2 14.1 - + - -
296H ILE* 4.9 1.6 - - + -
331H LEU* 3.0 50.7 + - + +
332H ALA* 3.9 2.2 - - - +
334H GLY* 1.3 73.6 - - - +
336H LYS* 1.3 66.8 + - - +
338H LEU* 3.0 38.5 + - + +
339H GLN* 4.0 6.1 + - - +
357H LEU* 5.2 5.2 - - + -
358H ARG* 3.2 54.7 - - + +
361H VAL* 3.5 27.4 - - + -
362H ILE* 3.7 8.7 - - + -
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Residues in contact with LYS 336 (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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315E GLU* 3.2 29.0 + - - +
318E LEU* 3.9 18.3 - - + +
332H ALA 2.9 20.9 + - - +
333H VAL* 3.2 8.0 + - - +
335H PHE* 1.3 77.9 - - - +
337H LEU* 1.3 65.9 + - + +
339H GLN* 3.0 48.8 + - - +
340H GLU* 4.2 4.0 + - - +
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Residues in contact with LEU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H TYR* 3.7 14.6 - - + -
245H THR* 3.7 11.2 - - + -
246H LEU* 3.7 44.6 - - + +
249H HIS* 3.5 42.2 - - + +
333H VAL* 3.0 28.0 + - + +
334H GLY* 4.0 1.6 - - - +
335H PHE 3.3 0.4 - - - -
336H LYS* 1.3 79.8 - - + +
338H LEU* 1.3 61.4 + - - +
339H GLN 3.3 0.3 + - - -
340H GLU* 3.4 24.0 + - - +
343H CYS* 3.2 19.6 - - - +
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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