Contacts of the helix formed by residues 283 - 297 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J VAL 5.3 1.6 - - - +
282J PHE* 1.3 77.4 - - - +
284J ASP* 1.3 63.7 + - - +
285J LEU* 3.3 9.5 + - - +
286J GLU* 2.7 46.6 + - - +
287J ILE* 3.0 22.4 + - - +
403J ARG* 5.2 5.2 - - - +
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Residues in contact with ASP 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J ARG 5.6 1.7 - - - +
228J LEU* 4.4 7.8 - - + +
231J THR* 3.9 21.0 + - + +
232J PHE* 3.5 23.6 - - + -
283J THR* 1.3 74.3 - - - +
285J LEU* 1.3 57.4 + - - +
287J ILE* 3.3 15.5 + - - +
288J LEU* 2.8 29.8 + - - +
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Residues in contact with LEU 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232J PHE* 3.6 25.8 - - + -
283J THR* 3.2 8.8 + - - +
284J ASP* 1.3 80.5 - - - +
286J GLU* 1.3 57.2 + - + +
288J LEU* 3.2 2.8 + - + +
289J ALA* 2.9 29.1 + - - +
349J LEU* 4.1 15.9 - - + -
353J GLN* 3.7 39.5 - - + +
356J SER* 3.9 18.8 - - - +
357J LEU* 3.9 21.1 - - + -
360J MET* 3.9 11.0 - - + -
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Residues in contact with GLU 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282J PHE* 3.2 18.9 - - + -
283J THR* 2.7 46.5 + - - +
285J LEU* 1.3 74.6 - - + +
287J ILE* 1.3 65.0 + - - +
289J ALA* 3.3 2.3 + - - +
290J ALA* 3.0 24.6 + - - +
360J MET* 3.9 28.2 - - + +
400J TYR* 5.1 5.0 - - - -
403J ARG* 2.8 43.0 + - - +
407J LEU* 4.0 20.1 - - + +
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Residues in contact with ILE 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J ARG* 3.9 29.2 - - - +
228J LEU* 4.8 7.6 - - + -
273J LEU* 3.8 31.1 - - + +
282J PHE* 3.9 24.9 - - + +
283J THR 3.0 21.2 + - - +
284J ASP* 3.6 18.2 - - - +
286J GLU* 1.3 76.3 - - - +
288J LEU* 1.3 64.3 + - - +
290J ALA* 3.4 2.0 + - - +
291J ILE* 3.1 33.3 + - + +
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Residues in contact with LEU 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J PHE* 3.7 35.4 - - + -
228J LEU* 4.1 14.1 - - + -
232J PHE* 3.8 35.4 - - + -
234J ILE* 4.9 2.5 - - + -
284J ASP 2.8 17.8 + - - +
285J LEU* 3.4 7.2 - - + +
287J ILE* 1.3 78.9 - - - +
289J ALA* 1.3 57.5 + - - +
291J ILE* 3.3 2.1 + - + +
292J PHE* 2.8 31.8 + - + +
346J PHE* 3.7 26.2 - - + -
349J LEU* 4.4 2.0 - - + -
357J LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285J LEU 2.9 17.4 + - - +
286J GLU* 3.6 4.9 - - - +
287J ILE 3.3 0.2 - - - -
288J LEU* 1.3 76.7 - - - +
290J ALA* 1.3 57.2 + - - +
292J PHE* 4.5 0.7 - - - -
293J ALA* 2.8 34.5 + - - +
357J LEU* 3.8 16.8 - - + -
360J MET* 3.9 32.3 - - + -
361J VAL* 3.7 13.5 - - + +
364J ILE* 4.4 3.6 - - + -
407J LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J THR* 4.2 15.7 - - + -
273J LEU* 4.4 6.5 - - + -
286J GLU 3.0 17.4 + - - +
287J ILE 3.8 4.0 - - - +
289J ALA* 1.3 76.3 - - - +
291J ILE* 1.3 58.6 + - - +
293J ALA* 3.5 2.1 + - - +
294J SER* 2.9 32.6 + - - -
364J ILE* 3.9 15.6 - - + +
407J LEU* 4.0 22.9 - - + -
410J MET* 5.4 0.2 - - - -
411J VAL* 4.0 7.5 - - + +
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Residues in contact with ILE 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J MET* 3.8 22.9 - - - +
222J ILE* 4.0 14.6 - - + -
223J PHE* 4.1 14.1 - - + -
226J ARG* 3.6 36.8 - - - +
228J LEU* 4.5 6.7 - - + -
266J VAL* 4.1 12.1 - - + +
269J THR* 4.5 7.2 - - + -
270J HIS* 4.6 6.7 - - + +
273J LEU* 3.8 13.5 - - + -
287J ILE* 3.1 23.1 + - + +
288J LEU* 3.8 4.5 - - - +
290J ALA* 1.3 74.3 - - - +
292J PHE* 1.3 65.2 + - - +
294J SER* 3.3 7.6 + - - -
295J ALA* 3.1 21.1 + - - +
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Residues in contact with PHE 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J MET* 4.6 12.6 - - + -
223J PHE* 5.7 2.0 - + + -
242J TYR* 3.4 42.4 - + - -
288J LEU* 2.8 22.3 + - + +
289J ALA* 3.8 4.5 - - - +
291J ILE* 1.3 76.2 - - - +
293J ALA* 1.3 61.9 + - - +
295J ALA* 3.1 14.9 + - + +
296J ILE* 3.2 38.8 + - + +
334J GLY 4.3 3.1 - - - -
335J PHE* 4.2 17.3 - + - -
338J LEU* 4.1 8.3 - - + -
345J ILE* 4.1 9.2 - - + -
346J PHE* 3.7 41.1 - + + -
357J LEU* 4.7 0.2 - - + -
361J VAL* 3.8 20.2 - - + -
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Residues in contact with ALA 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289J ALA 2.8 19.5 + - - +
290J ALA 3.6 4.9 - - - +
292J PHE* 1.3 79.1 - - - +
294J SER* 1.3 57.3 + - - +
296J ILE* 3.4 6.1 + - - +
297J HIS* 2.9 32.7 + - - +
361J VAL* 4.2 12.6 - - + -
364J ILE* 3.9 30.1 - - + -
365J VAL* 3.7 17.0 - - + +
411J VAL* 5.2 0.9 - - - -
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Residues in contact with SER 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J TYR* 4.5 0.2 + - - -
262J ALA 4.3 3.9 - - - +
265J VAL* 4.0 10.0 - - - +
266J VAL* 3.8 26.3 - - - +
269J THR* 2.8 24.9 + - - -
290J ALA 2.9 15.0 + - - -
291J ILE 3.6 8.7 - - - -
292J PHE 3.2 0.2 - - - -
293J ALA* 1.3 77.1 - - - +
295J ALA* 1.3 62.6 + - - +
297J HIS* 2.9 29.8 + - - -
411J VAL* 3.7 12.1 - - - +
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Residues in contact with ALA 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LEU* 4.0 4.0 - - + +
219J MET* 3.6 28.0 - - + -
246J LEU* 3.8 16.9 - - + +
250J TYR* 2.7 30.8 + - - -
262J ALA* 3.9 4.7 - - - +
266J VAL* 3.4 16.5 - - + +
291J ILE 3.1 9.9 + - - +
292J PHE* 3.1 10.5 + - + +
294J SER* 1.3 80.6 - - - +
296J ILE* 1.3 54.1 + - + +
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Residues in contact with ILE 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J TYR* 3.7 22.9 - - - +
246J LEU* 3.8 23.1 - - + -
250J TYR* 3.5 3.4 - - - -
292J PHE* 3.2 37.6 + - + +
293J ALA* 3.6 10.3 - - - +
295J ALA* 1.3 77.1 - - + +
297J HIS* 1.3 60.7 + - - +
298J ASP 2.8 11.5 + - - -
299J VAL* 3.1 17.0 + - + +
330J HIS* 3.6 5.4 - - - +
331J LEU* 4.2 21.5 - - + +
334J GLY* 4.2 19.1 - - - -
335J PHE* 5.0 1.3 - - + -
361J VAL* 4.0 16.6 - - + -
365J VAL* 4.4 3.4 - - + -
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Residues in contact with HIS 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250J TYR* 4.7 1.4 + - - -
261J HIS* 3.3 20.9 - + - -
262J ALA* 4.5 5.8 - - - -
265J VAL* 3.3 26.9 - - + +
293J ALA 2.9 19.0 + - - +
294J SER* 2.9 23.4 + - - +
296J ILE* 1.3 73.6 - - - +
298J ASP* 1.3 75.5 + - + +
330J HIS* 3.0 20.7 - - - +
365J VAL* 4.1 17.3 - - + +
368J THR* 4.3 21.8 + - + -
411J VAL* 5.2 1.6 - - + -
415J ASP* 2.7 14.4 + - - -
2019J ZN 2.2 32.2 - - - -
2020J MG 4.2 3.3 - - - -
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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
------------------------------------------------------------
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