Contacts of the helix formed by residues 283 - 297 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C VAL 5.3 1.6 - - - +
282C PHE* 1.3 77.1 - - - +
284C ASP* 1.3 63.5 + - - +
285C LEU* 3.3 9.1 + - - +
286C GLU* 2.7 45.1 + - - +
287C ILE* 3.0 22.2 + - - +
403C ARG* 5.3 5.4 - - - +
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ARG 5.6 1.4 - - - +
228C LEU* 4.4 8.2 - - + +
231C THR* 3.9 21.0 - - + +
232C PHE* 3.5 22.9 - - + -
283C THR* 1.3 74.7 - - - +
285C LEU* 1.3 58.3 + - - +
287C ILE* 3.4 16.0 + - - +
288C LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 3.6 25.6 - - + -
283C THR* 3.2 8.1 + - - +
284C ASP* 1.3 79.8 - - - +
286C GLU* 1.3 57.3 + - + +
288C LEU* 3.3 3.3 + - + +
289C ALA* 2.8 28.6 + - - +
349C LEU* 4.0 16.2 - - + -
353C GLN* 3.8 40.6 - - + +
356C SER* 3.9 17.7 - - - +
357C LEU* 3.8 21.8 - - + -
360C MET* 4.0 10.5 - - + -
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C PHE* 3.2 20.2 - - + +
283C THR* 2.7 46.3 + - - +
285C LEU* 1.3 72.7 - - + +
287C ILE* 1.3 66.4 + - - +
289C ALA* 3.3 2.3 + - - +
290C ALA* 3.0 25.0 + - - +
360C MET* 3.9 28.2 - - + +
400C TYR* 5.2 5.0 - - - -
403C ARG* 2.8 41.2 + - - +
407C LEU* 4.1 19.7 - - + +
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ARG* 3.9 28.3 - - - +
228C LEU* 4.8 7.4 - - + -
273C LEU* 3.8 31.0 - - + -
282C PHE* 3.9 24.5 - - + +
283C THR 3.0 17.5 + - - +
284C ASP* 3.6 17.9 - - - +
286C GLU* 1.3 77.5 - - - +
288C LEU* 1.3 63.0 + - - +
290C ALA* 3.4 2.4 + - - +
291C ILE* 3.1 33.3 + - + +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.8 35.2 - - + -
228C LEU* 4.0 14.3 - - + +
232C PHE* 3.8 36.1 - - + -
234C ILE* 4.9 2.5 - - + -
284C ASP 2.9 17.2 + - - +
285C LEU* 3.4 8.5 - - + +
286C GLU 3.2 0.2 - - - -
287C ILE* 1.3 78.6 - - - +
289C ALA* 1.3 57.1 + - - +
291C ILE* 3.3 2.5 + - + +
292C PHE* 2.9 32.8 + - + +
346C PHE* 3.7 25.6 - - + -
349C LEU* 4.4 1.6 - - + -
357C LEU* 3.6 22.0 - - + -
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LEU 2.8 16.9 + - - +
286C GLU* 3.3 5.1 + - - +
288C LEU* 1.3 75.8 - - - +
290C ALA* 1.3 57.9 + - - +
292C PHE* 4.5 0.9 - - - -
293C ALA* 2.8 33.9 + - - +
357C LEU* 3.7 17.0 - - + +
360C MET* 3.9 33.7 - - + -
361C VAL* 3.7 13.8 - - + +
364C ILE* 4.5 3.1 - - + -
407C LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C THR* 4.2 16.4 - - + -
273C LEU* 4.4 7.0 - - + -
286C GLU 3.0 16.1 + - - +
287C ILE 3.8 3.8 - - - +
289C ALA* 1.3 75.3 - - - +
291C ILE* 1.3 59.3 + - - +
293C ALA* 3.5 1.9 + - - +
294C SER* 2.9 32.7 + - - -
364C ILE* 3.9 16.0 - - + +
407C LEU* 4.0 22.4 - - + -
410C MET* 5.3 0.2 - - - -
411C VAL* 4.0 7.6 - - + +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C MET* 3.9 21.5 - - - -
222C ILE* 4.0 14.1 - - + -
223C PHE* 4.1 15.0 - - + -
226C ARG* 3.6 35.9 - - - +
228C LEU* 4.5 6.5 - - + -
266C VAL* 4.1 12.7 - - + +
269C THR* 4.6 6.3 - - + -
270C HIS* 4.6 5.8 - - + +
273C LEU* 3.8 13.7 - - + -
287C ILE* 3.1 22.9 + - + +
288C LEU* 3.9 4.3 - - - +
290C ALA* 1.3 74.3 - - - +
292C PHE* 1.3 65.3 + - - +
294C SER* 3.2 8.5 + - - -
295C ALA* 3.0 21.0 + - - +
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Residues in contact with PHE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C MET* 4.6 11.4 - - + -
223C PHE* 5.7 2.0 - + + -
242C TYR* 3.5 42.8 - + - -
288C LEU* 2.9 21.9 + - + +
289C ALA* 3.8 3.4 - - - +
291C ILE* 1.3 76.4 - - - +
293C ALA* 1.3 63.7 + - - +
295C ALA* 3.1 15.6 + - + +
296C ILE* 3.1 38.8 + - + +
334C GLY 4.2 3.4 - - - -
335C PHE* 4.2 17.3 - + - -
338C LEU* 4.1 8.5 - - + -
345C ILE* 4.1 9.4 - - + -
346C PHE* 3.7 41.7 - + + -
357C LEU* 4.7 0.2 - - + -
361C VAL* 3.8 19.5 - - + -
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ALA 2.8 22.8 + - - +
290C ALA 3.6 4.7 - - - +
292C PHE* 1.3 72.5 - - - +
294C SER* 1.3 64.3 + - - +
296C ILE* 3.3 3.5 + - - +
297C HIS* 2.8 26.7 + - - +
361C VAL* 4.2 14.8 - - + -
364C ILE* 3.8 30.7 - - + -
365C VAL* 3.8 17.9 - - + +
411C VAL* 5.3 0.9 - - - -
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C TYR* 4.5 0.2 + - - -
262C ALA* 4.3 3.5 - - - +
265C VAL* 4.0 6.2 - - - +
266C VAL* 3.8 28.1 - - - +
269C THR* 2.8 25.6 + - - -
290C ALA 2.9 15.4 + - - -
291C ILE 3.2 8.9 + - - -
293C ALA* 1.3 77.0 - - - +
295C ALA* 1.3 62.8 + - - +
297C HIS* 2.9 30.7 + - - -
411C VAL* 3.7 11.2 - - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 4.0 4.0 - - + +
219C MET* 3.6 38.1 - - + -
246C LEU* 3.7 17.4 - - + +
250C TYR* 2.8 25.3 + - - -
262C ALA* 3.9 4.9 - - - +
266C VAL* 3.4 12.2 - - + +
291C ILE 3.0 7.0 + - - +
292C PHE* 3.1 11.0 + - + +
294C SER* 1.3 77.7 - - - +
296C ILE* 1.3 59.3 + - + +
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C TYR* 3.6 23.6 - - - +
246C LEU* 3.8 19.7 - - + -
250C TYR* 3.5 3.1 - - - -
292C PHE* 3.1 36.7 + - + +
293C ALA* 3.6 9.9 - - - +
295C ALA* 1.3 76.9 - - + +
297C HIS* 1.3 61.9 + - - +
298C ASP 2.9 10.4 + - - -
299C VAL* 3.2 16.4 + - + +
330C HIS* 3.6 5.4 - - - +
331C LEU* 4.2 22.9 - - + +
334C GLY* 4.1 21.8 - - - -
335C PHE* 4.8 1.8 - - + +
361C VAL* 4.1 15.5 - - + -
365C VAL* 4.4 3.6 - - + -
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Residues in contact with HIS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C TYR* 4.7 1.4 + - - -
261C HIS* 3.3 20.6 - + - -
262C ALA* 4.5 5.6 - - - -
265C VAL* 3.3 25.8 - - + +
293C ALA 2.8 17.7 + - - +
294C SER* 2.9 24.7 + - - +
295C ALA 3.5 0.2 - - - -
296C ILE* 1.3 75.8 - - - +
298C ASP* 1.3 74.6 + - + +
330C HIS* 3.0 20.7 - - - +
365C VAL* 4.2 19.3 - - + +
368C THR* 4.3 18.9 + - + -
411C VAL* 5.2 2.0 - - + -
415C ASP* 2.8 13.9 + - + -
2005C ZN 2.2 32.7 - - - -
2006C MG 3.9 3.9 - - - -
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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
------------------------------------------------------------
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