Contacts of the helix formed by residues 283 - 297 (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 THR 283 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H VAL 5.3 1.8 - - - +
282H PHE* 1.3 77.4 - - - +
284H ASP* 1.3 64.2 + - - +
285H LEU* 3.3 9.6 + - - +
286H GLU* 2.7 46.2 + - - +
287H ILE* 3.0 22.4 + - - +
403H ARG* 5.2 5.8 - - - +
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Residues in contact with ASP 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H ARG 5.6 1.4 - - - +
228H LEU* 4.4 8.2 - - + +
231H THR* 3.9 21.4 + - + +
232H PHE* 3.5 23.0 - - + -
283H THR* 1.3 74.7 - - - +
285H LEU* 1.3 58.0 + - - +
287H ILE* 3.4 16.4 + - - +
288H LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 3.6 25.6 - - + -
283H THR* 3.1 8.3 + - - +
284H ASP* 1.3 80.5 - - - +
286H GLU* 1.3 57.0 + - + +
288H LEU* 3.3 3.8 + - + +
289H ALA* 2.9 28.4 + - - +
349H LEU* 4.1 15.7 - - + -
353H GLN* 3.8 41.5 - - + +
356H SER* 3.9 16.8 - - - +
357H LEU* 3.9 18.4 - - + -
360H MET* 4.0 11.4 - - + -
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Residues in contact with GLU 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H PHE* 3.2 21.5 - - + +
283H THR* 2.7 47.6 + - - +
285H LEU* 1.3 73.1 - - - +
287H ILE* 1.3 65.7 + - - +
289H ALA* 3.3 2.3 + - - +
290H ALA* 3.0 24.8 + - - +
360H MET* 3.9 28.2 - - + +
400H TYR* 5.1 5.4 - - - -
403H ARG* 2.8 40.7 + - - +
407H LEU* 4.0 17.4 - - + +
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Residues in contact with ILE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H ARG* 3.9 28.9 - - - +
228H LEU* 4.8 7.4 - - + -
273H LEU* 3.9 29.8 - - + -
282H PHE* 3.9 24.7 - - + +
283H THR 3.0 20.7 + - - +
284H ASP* 3.6 17.5 - - - +
286H GLU* 1.3 77.8 - - - +
288H LEU* 1.3 62.9 + - - +
290H ALA* 3.4 2.1 + - - +
291H ILE* 3.1 34.6 + - + +
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Residues in contact with LEU 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H PHE* 3.8 34.8 - - + -
228H LEU* 4.0 14.1 - - + +
232H PHE* 3.8 36.8 - - + -
234H ILE* 4.9 2.9 - - + -
284H ASP 2.9 17.9 + - - +
285H LEU* 3.4 7.9 - - + +
287H ILE* 1.3 79.9 - - - +
289H ALA* 1.3 58.5 + - - +
291H ILE* 3.3 1.7 + - - +
292H PHE* 2.9 32.1 + - + +
346H PHE* 3.7 26.7 - - + -
349H LEU* 4.3 2.0 - - + -
357H LEU* 3.6 21.3 - - + -
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Residues in contact with ALA 289 (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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285H LEU 2.9 17.2 + - - +
286H GLU* 3.6 5.4 - - - +
287H ILE 3.3 0.2 - - - -
288H LEU* 1.3 76.7 - - - +
290H ALA* 1.3 57.3 + - - +
292H PHE* 4.5 0.4 - - - -
293H ALA* 2.8 34.8 + - - +
357H LEU* 3.8 18.2 - - + -
360H MET* 3.9 32.1 - - + -
361H VAL* 3.7 12.6 - - + +
364H ILE* 4.5 3.6 - - + -
407H LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H THR* 4.2 15.7 - - + -
273H LEU* 4.4 7.2 - - + -
286H GLU 3.0 16.8 + - - +
287H ILE 3.8 4.0 - - - +
289H ALA* 1.3 75.9 - - - +
291H ILE* 1.3 58.7 + - - +
293H ALA* 3.5 2.4 + - - +
294H SER* 2.9 32.3 + - - -
364H ILE* 3.9 16.1 - - + +
407H LEU* 4.0 21.8 - - + -
410H MET* 5.4 0.4 - - - -
411H VAL* 4.1 7.5 - - + +
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Residues in contact with ILE 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H MET* 3.8 22.5 - - - +
222H ILE* 4.0 14.6 - - + -
223H PHE* 4.1 14.6 - - + -
226H ARG* 3.6 37.0 - - - +
228H LEU* 4.5 6.7 - - + -
266H VAL* 4.1 11.0 - - + +
269H THR* 4.6 6.5 - - + -
270H HIS* 4.6 6.5 - - + +
273H LEU* 3.8 13.5 - - + -
287H ILE* 3.1 23.3 + - + +
288H LEU* 3.8 3.8 - - - +
290H ALA* 1.3 74.2 - - - +
292H PHE* 1.3 66.5 + - - +
294H SER* 3.3 7.9 + - - -
295H ALA* 3.0 21.5 + - - +
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Residues in contact with PHE 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H MET* 4.6 12.1 - - + -
223H PHE* 5.8 2.0 - + + -
242H TYR* 3.4 43.1 - + - -
288H LEU* 2.9 25.5 + - + +
289H ALA* 3.8 3.8 - - - +
291H ILE* 1.3 73.9 - - - +
293H ALA* 1.3 62.3 - - - +
295H ALA* 3.2 8.3 + - + +
296H ILE* 3.1 46.1 + - + +
334H GLY 4.2 2.9 - - - -
335H PHE* 4.2 17.5 - + - -
338H LEU* 4.1 8.3 - - + -
345H ILE* 4.1 8.3 - - + -
346H PHE* 3.7 42.2 - + + -
357H LEU* 4.6 0.2 - - + -
361H VAL* 3.8 20.2 - - + -
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Residues in contact with ALA 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ALA 2.8 19.3 + - - +
290H ALA 3.6 4.5 - - - +
292H PHE* 1.3 77.6 - - - +
294H SER* 1.3 57.8 + - - +
296H ILE* 3.3 6.9 + - - +
297H HIS* 2.9 32.4 + - - +
361H VAL* 4.2 12.3 - - + -
364H ILE* 3.9 30.1 - - + -
365H VAL* 3.7 16.8 - - + +
411H VAL* 5.2 0.9 - - - -
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Residues in contact with SER 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H TYR* 4.5 0.3 + - - -
262H ALA* 4.3 3.1 - - - +
265H VAL* 4.0 6.7 - - - +
266H VAL* 3.8 28.5 - - - +
269H THR* 2.8 25.4 + - - +
290H ALA 2.9 15.4 + - - -
291H ILE 3.5 9.0 - - - -
292H PHE 3.2 0.2 - - - -
293H ALA* 1.3 75.8 - - - +
295H ALA* 1.3 65.1 + - - +
297H HIS* 3.0 31.6 + - - -
411H VAL* 3.8 11.5 - - - +
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Residues in contact with ALA 295 (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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215H LEU* 4.1 4.0 - - + +
219H MET* 3.6 38.6 - - + -
246H LEU* 3.8 16.9 - - + +
250H TYR* 2.7 31.4 + - - -
262H ALA* 3.9 4.4 - - - +
266H VAL* 3.4 11.4 - - + +
291H ILE 3.0 7.6 + - - +
292H PHE* 3.2 10.9 + - + +
294H SER* 1.3 77.4 - - - +
296H ILE* 1.3 52.4 + - + +
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Residues in contact with ILE 296 (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 23.1 - - - +
246H LEU* 3.8 21.8 - - + -
250H TYR* 3.5 3.6 - - - -
292H PHE* 3.1 36.7 + - + +
293H ALA* 3.6 10.3 - - - +
295H ALA* 1.3 78.0 - - - +
297H HIS* 1.3 61.7 + - - +
298H ASP 2.9 10.9 + - - -
299H VAL* 3.2 16.8 + - + +
330H HIS* 3.6 5.0 - - - +
331H LEU* 4.1 22.0 - - + +
334H GLY* 4.2 19.5 - - - -
335H PHE* 4.9 2.0 - - + +
361H VAL* 4.0 15.5 - - + -
365H VAL* 4.4 3.4 - - + -
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Residues in contact with HIS 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H TYR* 4.7 1.4 + - - -
261H HIS* 3.2 20.9 - + - -
262H ALA* 4.5 6.0 - - - -
265H VAL* 3.4 25.6 - - + +
293H ALA 2.9 17.5 + - - +
294H SER* 3.0 23.8 + - - +
296H ILE* 1.3 75.1 - - - +
298H ASP* 1.3 80.3 + - + +
330H HIS* 2.9 21.0 - - - +
365H VAL* 4.1 20.7 - - + +
368H THR* 4.3 19.7 + - + -
411H VAL* 5.3 2.0 - - + -
415H ASP* 2.8 13.1 + - + -
2015H ZN 2.3 29.0 - - - -
2016H MG 4.2 3.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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