Contacts of the helix formed by residues 283 - 297 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L VAL 5.3 1.8 - - - +
282L PHE* 1.3 76.6 - - - +
284L ASP* 1.3 62.4 + - - +
285L LEU* 3.3 9.7 + - - +
286L GLU* 2.8 44.7 + - - +
287L ILE* 3.0 22.8 + - - +
403L ARG* 5.2 4.9 - - - +
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Residues in contact with ASP 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L ARG 5.5 2.1 - - - +
228L LEU* 4.4 8.1 - - + +
231L THR* 3.8 21.8 + - + +
232L PHE* 3.5 22.9 - - + -
283L THR* 1.3 74.5 - - - +
285L LEU* 1.3 57.6 + - - +
287L ILE* 3.4 16.2 + - - +
288L LEU* 2.8 29.6 + - - +
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Residues in contact with LEU 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232L PHE* 3.6 27.6 - - + -
283L THR* 3.2 8.4 + - - +
284L ASP* 1.3 79.4 - - - +
286L GLU* 1.3 57.4 + - + +
288L LEU* 3.2 4.1 + - + +
289L ALA* 2.8 28.9 + - - +
349L LEU* 4.0 16.6 - - + -
353L GLN* 3.7 38.1 - - + +
356L SER* 3.8 20.0 - - - +
357L LEU* 3.9 20.8 - - + +
360L MET* 3.9 11.4 - - + -
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Residues in contact with GLU 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282L PHE* 3.2 20.1 - - + -
283L THR* 2.8 45.8 + - - +
285L LEU* 1.3 72.5 - - + +
287L ILE* 1.3 66.3 + - - +
289L ALA* 3.3 2.4 + - - +
290L ALA* 3.0 25.1 + - - +
360L MET* 3.9 28.1 - - + +
400L TYR* 5.1 5.0 - - - -
403L ARG* 2.8 41.7 + - - +
407L LEU* 4.0 20.4 - - + +
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Residues in contact with ILE 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L ARG* 3.9 29.4 - - + +
228L LEU* 4.8 7.6 - - + -
273L LEU* 3.8 31.0 - - + -
282L PHE* 3.9 24.7 - - + +
283L THR 3.0 21.6 + - - +
284L ASP* 3.6 18.2 - - - +
286L GLU* 1.3 78.1 - - - +
288L LEU* 1.3 63.5 + - - +
290L ALA* 3.4 2.1 + - - +
291L ILE* 3.1 34.5 + - + +
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Residues in contact with LEU 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L PHE* 3.7 35.4 - - + -
228L LEU* 4.1 14.8 - - + +
232L PHE* 3.8 36.3 - - + -
234L ILE* 4.9 2.5 - - + -
284L ASP 2.8 17.9 + - - +
285L LEU* 3.4 9.0 - - + +
287L ILE* 1.3 78.6 - - - +
289L ALA* 1.3 57.3 + - - +
291L ILE* 3.3 2.5 + - - +
292L PHE* 2.8 32.6 + - + +
346L PHE* 3.7 26.7 - - + -
349L LEU* 4.3 2.2 - - + -
357L LEU* 3.6 21.1 - - + -
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Residues in contact with ALA 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285L LEU 2.8 19.5 + - - +
286L GLU* 3.3 5.4 + - - +
288L LEU* 1.3 72.7 - - - +
290L ALA* 1.3 53.9 + - - +
292L PHE* 4.5 0.9 - - - -
293L ALA* 2.7 38.1 + - - +
357L LEU* 3.7 17.6 - - + +
360L MET* 3.9 33.4 - - + -
361L VAL* 3.7 13.1 - - + +
364L ILE* 4.4 3.1 - - + -
407L LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269L THR* 4.2 16.2 - - + -
273L LEU* 4.3 7.0 - - + -
286L GLU 3.0 17.1 + - - +
287L ILE 3.7 4.5 - - - +
289L ALA* 1.3 75.5 - - - +
291L ILE* 1.3 58.0 + - - +
293L ALA* 3.6 2.4 - - - +
294L SER* 2.9 32.1 + - - -
364L ILE* 3.9 15.8 - - + +
407L LEU* 4.0 22.0 - - + -
410L MET* 5.3 0.4 - - - -
411L VAL* 4.0 7.1 - - + +
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Residues in contact with ILE 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219L MET* 3.8 23.4 - - - +
222L ILE* 4.0 13.9 - - + -
223L PHE* 4.1 14.4 - - + -
226L ARG* 3.5 37.2 - - - +
228L LEU* 4.5 7.2 - - + -
266L VAL* 4.1 12.0 - - + +
269L THR* 4.6 6.7 - - + -
270L HIS* 4.6 6.3 - - + +
273L LEU* 3.8 13.7 - - + -
287L ILE* 3.1 21.6 + - + +
288L LEU* 3.8 3.8 - - - +
290L ALA* 1.3 73.4 - - - +
292L PHE* 1.3 66.8 + - - +
294L SER* 3.3 7.5 + - - -
295L ALA* 3.0 21.1 + - - +
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Residues in contact with PHE 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L MET* 4.6 12.6 - - + -
223L PHE* 5.7 1.8 - + + -
242L TYR* 3.4 43.3 - + - -
288L LEU* 2.8 25.5 + - + +
289L ALA* 3.8 3.6 - - - +
291L ILE* 1.3 72.8 - - - +
293L ALA* 1.3 63.5 + - - +
295L ALA* 3.1 15.9 + - + +
296L ILE* 3.1 38.9 + - + +
334L GLY 4.3 2.9 - - - -
335L PHE* 4.2 17.0 - + - -
338L LEU* 4.1 8.3 - - + -
345L ILE* 4.1 9.0 - - + -
346L PHE* 3.7 42.2 - + + -
357L LEU* 4.6 0.2 - - + -
361L VAL* 3.8 20.9 - - + -
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Residues in contact with ALA 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289L ALA 2.7 22.2 + - - +
290L ALA 3.6 5.2 - - - +
292L PHE* 1.3 75.4 - - - +
294L SER* 1.3 63.0 + - - +
296L ILE* 3.2 3.7 + - - +
297L HIS* 2.9 26.9 + - - +
361L VAL* 4.2 15.7 - - + -
364L ILE* 3.9 30.5 - - + -
365L VAL* 3.8 16.9 - - + +
411L VAL* 5.2 1.1 - - - -
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Residues in contact with SER 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L TYR* 4.5 0.2 + - - -
262L ALA 4.4 3.2 - - - +
265L VAL* 4.0 5.6 - - - -
266L VAL* 3.8 29.0 - - - +
269L THR* 2.8 25.4 + - - +
290L ALA 2.9 19.3 + - - -
291L ILE* 3.5 8.5 - - - -
292L PHE 3.2 0.2 - - - -
293L ALA* 1.3 75.5 - - - +
295L ALA* 1.3 64.0 + - - +
296L ILE 3.2 0.2 + - - -
297L HIS* 2.9 30.6 + - - -
411L VAL* 3.7 13.1 - - - +
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Residues in contact with ALA 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L LEU* 4.0 3.7 - - + +
219L MET* 3.6 34.5 - - + -
246L LEU* 3.8 17.2 - - + +
250L TYR* 2.7 30.7 + - - -
262L ALA* 3.9 4.6 - - - +
266L VAL* 3.4 15.9 - - + +
291L ILE 3.0 7.6 + - - +
292L PHE* 3.1 10.9 + - + +
294L SER* 1.3 77.3 - - - +
296L ILE* 1.3 54.2 + - + +
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Residues in contact with ILE 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L TYR* 3.6 23.8 - - - +
246L LEU* 3.8 19.7 - - + -
250L TYR* 3.5 4.0 - - - -
292L PHE* 3.1 36.5 + - + +
293L ALA* 3.6 10.1 - - - +
295L ALA* 1.3 77.4 - - - +
297L HIS* 1.3 60.4 + - - +
298L ASP 2.8 11.6 + - - -
299L VAL* 3.1 17.1 + - + +
330L HIS* 3.6 5.2 - - - +
331L LEU* 4.2 22.0 - - + +
334L GLY* 4.1 22.2 - - - -
335L PHE* 4.8 1.8 - - + +
361L VAL* 4.1 15.7 - - + -
365L VAL* 4.4 3.4 - - + -
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Residues in contact with HIS 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L TYR* 4.7 2.0 + - - -
261L HIS* 3.2 20.4 - + - -
262L ALA* 4.5 5.4 - - - -
265L VAL* 3.3 26.6 - - + +
293L ALA 2.9 17.1 + - - +
294L SER* 2.9 23.2 + - - +
296L ILE* 1.3 74.7 - - - +
298L ASP* 1.3 78.8 + - + +
330L HIS* 3.0 21.4 - - - +
365L VAL* 4.1 18.8 - - + +
368L THR* 4.3 21.5 + - + -
411L VAL* 5.2 1.6 - - + -
415L ASP* 2.7 14.4 + - + -
2023L ZN 2.2 28.6 - - - -
2024L MG 3.8 4.9 - - - -
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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