Contacts of the helix formed by residues 283 - 297 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F VAL 5.3 1.6 - - - +
282F PHE* 1.3 78.3 - - - +
284F ASP* 1.3 63.4 + - - +
285F LEU* 3.3 9.3 + - - +
286F GLU* 2.7 46.0 + - - +
287F ILE* 3.0 21.5 + - - +
403F ARG* 5.3 5.2 - - - +
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Residues in contact with ASP 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ARG 5.6 1.6 - - - +
228F LEU* 4.4 7.9 - - + +
231F THR* 3.8 22.6 + - + +
232F PHE* 3.5 22.0 - - + -
283F THR* 1.3 75.6 - - - +
285F LEU* 1.3 58.6 + - - +
287F ILE* 3.3 15.3 + - - +
288F LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F PHE* 3.5 27.2 - - + -
283F THR* 3.2 8.4 + - - +
284F ASP* 1.3 78.5 - - - +
286F GLU* 1.3 57.4 + - + +
288F LEU* 3.2 3.6 + - + +
289F ALA* 2.8 28.1 + - - +
349F LEU* 4.0 15.5 - - + -
353F GLN* 3.7 41.5 - - + +
356F SER* 3.9 17.5 - - - +
357F LEU* 3.9 20.9 - - + -
360F MET* 4.0 10.8 - - + -
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Residues in contact with GLU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F PHE* 3.2 19.0 - - + +
283F THR* 2.7 47.6 + - - +
285F LEU* 1.3 73.6 - - + +
287F ILE* 1.3 65.1 + - - +
289F ALA* 3.4 1.7 + - - +
290F ALA* 3.0 25.1 + - - +
360F MET* 3.8 28.4 - - + +
400F TYR* 5.1 5.0 - - - -
403F ARG* 2.8 42.6 + - - +
407F LEU* 4.0 19.9 - - + +
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Residues in contact with ILE 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ARG* 3.9 28.9 - - - +
228F LEU* 4.8 7.6 - - + -
273F LEU* 3.8 30.7 - - + -
282F PHE* 3.9 24.7 - - + +
283F THR 3.0 21.4 + - - +
284F ASP* 3.6 17.9 - - - +
285F LEU 3.2 0.2 - - - -
286F GLU* 1.3 75.3 - - - +
288F LEU* 1.3 63.9 + - - +
290F ALA* 3.4 2.6 + - - +
291F ILE* 3.1 33.9 + - + +
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Residues in contact with LEU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F PHE* 3.8 34.3 - - + -
228F LEU* 4.1 14.6 - - + +
232F PHE* 3.7 35.4 - - + -
234F ILE* 4.9 2.7 - - + -
284F ASP 2.9 14.5 + - - +
285F LEU* 3.4 12.1 - - + +
287F ILE* 1.3 79.6 - - - +
289F ALA* 1.3 56.1 + - - +
291F ILE* 3.3 1.7 + - - +
292F PHE* 2.9 32.5 + - + +
346F PHE* 3.7 26.5 - - + -
349F LEU* 4.4 2.5 - - + -
357F LEU* 3.6 21.3 - - + -
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Residues in contact with ALA 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F LEU 2.8 16.3 + - - +
286F GLU* 3.7 5.2 - - - +
288F LEU* 1.3 76.6 - - - +
290F ALA* 1.3 53.9 + - - +
292F PHE* 4.5 0.9 - - - -
293F ALA* 2.7 37.6 + - - +
357F LEU* 3.7 17.2 - - + +
360F MET* 3.9 33.7 - - + -
361F VAL* 3.7 13.4 - - + +
364F ILE* 4.5 3.4 - - + -
407F LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F THR* 4.2 15.5 - - + -
273F LEU* 4.4 6.7 - - + -
286F GLU 3.0 17.0 + - - +
287F ILE 3.7 3.8 - - - +
288F LEU 3.3 0.2 - - - -
289F ALA* 1.3 76.3 - - - +
291F ILE* 1.3 57.9 + - - +
293F ALA* 3.6 2.3 - - - +
294F SER* 2.9 32.2 + - - -
364F ILE* 3.9 16.3 - - + +
407F LEU* 4.1 22.7 - - + -
410F MET* 5.4 0.2 - - - -
411F VAL* 4.0 6.8 - - + +
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Residues in contact with ILE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F MET* 3.8 22.7 - - - -
222F ILE* 4.0 14.1 - - + -
223F PHE* 4.1 13.9 - - + -
226F ARG* 3.5 36.8 - - - +
228F LEU* 4.5 7.4 - - + -
266F VAL* 4.1 11.6 - - + +
269F THR* 4.6 6.7 - - + -
270F HIS* 4.6 6.5 - - + +
273F LEU* 3.8 13.9 - - + -
287F ILE* 3.1 22.5 + - + +
288F LEU* 3.9 3.8 - - - +
290F ALA* 1.3 74.6 - - - +
292F PHE* 1.3 64.8 + - - +
294F SER* 3.3 7.9 + - - -
295F ALA* 3.1 21.3 + - - +
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Residues in contact with PHE 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F MET* 4.6 12.3 - - + -
223F PHE* 5.8 2.0 - + + -
242F TYR* 3.5 42.8 - + - -
288F LEU* 2.9 26.5 + - + +
289F ALA* 3.8 3.8 - - - +
291F ILE* 1.3 72.9 - - - +
293F ALA* 1.3 62.2 - - - +
295F ALA* 3.2 15.9 + - + +
296F ILE* 3.2 38.7 + - + +
334F GLY 4.3 3.4 - - - -
335F PHE* 4.2 17.5 - + - -
338F LEU* 4.1 8.5 - - + -
345F ILE* 4.1 8.5 - - + -
346F PHE* 3.7 41.7 - + + -
361F VAL* 3.8 20.4 - - + -
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Residues in contact with ALA 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F ALA 2.7 19.7 + - - +
290F ALA 3.6 4.7 - - - +
292F PHE* 1.3 77.9 - - - +
294F SER* 1.3 56.3 + - - +
296F ILE* 3.3 4.0 + - - +
297F HIS* 2.8 32.9 + - - +
361F VAL* 4.2 15.7 - - + -
364F ILE* 3.9 30.1 - - + -
365F VAL* 3.7 16.9 - - + +
411F VAL* 5.2 0.9 - - - -
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Residues in contact with SER 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F TYR* 4.5 0.3 + - - -
262F ALA* 4.4 3.3 - - - +
265F VAL* 4.0 4.9 - - - -
266F VAL* 3.8 28.8 - - - +
269F THR* 2.8 25.6 + - - +
290F ALA 2.9 15.3 + - - -
291F ILE 3.5 8.7 - - - -
292F PHE 3.2 0.2 - - - -
293F ALA* 1.3 76.7 - - - +
295F ALA* 1.3 63.5 + - - +
297F HIS* 2.9 33.5 + - - -
411F VAL* 3.7 13.0 - - - +
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Residues in contact with ALA 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F LEU* 4.0 3.8 - - + +
219F MET* 3.6 38.1 - - + -
246F LEU* 3.7 17.8 - - + +
250F TYR* 2.7 25.6 + - - -
262F ALA* 3.9 4.3 - - - +
266F VAL* 3.4 11.8 - - + +
291F ILE 3.1 5.7 + - - +
292F PHE* 3.2 10.5 + - + +
294F SER* 1.3 79.5 - - - +
296F ILE* 1.3 58.6 + - + +
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Residues in contact with ILE 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F TYR* 3.7 23.6 - - - +
246F LEU* 3.7 23.1 - - + -
250F TYR* 3.6 4.0 - - - -
292F PHE* 3.2 37.8 + - + +
293F ALA* 3.6 9.6 - - - +
295F ALA* 1.3 78.7 - - + +
297F HIS* 1.3 61.9 + - - +
298F ASP 2.9 10.5 + - - -
299F VAL* 3.2 16.3 + - + +
330F HIS* 3.6 5.7 - - - +
331F LEU* 4.2 22.4 - - + +
334F GLY* 4.1 19.3 - - - -
335F PHE* 4.8 1.3 - - + +
361F VAL* 4.1 15.5 - - + -
365F VAL* 4.4 2.5 - - + -
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Residues in contact with HIS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F TYR* 4.7 1.4 + - - -
261F HIS* 3.2 21.3 - + - -
262F ALA* 4.6 5.6 - - - -
265F VAL* 3.4 24.0 - - + +
293F ALA 2.8 18.1 + - - +
294F SER* 2.9 24.2 + - - +
296F ILE* 1.3 74.7 - - - +
298F ASP* 1.3 78.4 + - + +
330F HIS* 3.0 21.6 - - - +
365F VAL* 4.1 19.3 - - + +
368F THR* 4.3 18.4 + - + -
411F VAL* 5.2 2.0 - - + -
415F ASP* 2.8 13.1 + - + -
2011F ZN 2.3 28.6 - - - -
2012F MG 3.9 5.9 - - - -
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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