Contacts of the helix formed by residues 283 - 297 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E VAL 5.3 1.3 - - - +
282E PHE* 1.3 76.7 - - - +
284E ASP* 1.3 64.9 + - - +
285E LEU* 3.3 9.2 + - - +
286E GLU* 2.7 45.7 + - - +
287E ILE* 3.0 22.2 + - - +
403E ARG* 5.2 5.4 - - - +
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Residues in contact with ASP 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ARG 5.6 1.4 - - - +
228E LEU* 4.5 7.8 - - + +
231E THR* 3.9 21.6 + - + +
232E PHE* 3.5 22.7 - - + -
283E THR* 1.3 74.0 - - - +
285E LEU* 1.3 57.0 + - - +
287E ILE* 3.3 17.0 + - - +
288E LEU* 2.8 29.6 + - - +
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Residues in contact with LEU 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E PHE* 3.6 27.4 - - + -
283E THR* 3.2 7.9 + - - +
284E ASP* 1.3 79.6 - - - +
286E GLU* 1.3 56.4 + - - +
288E LEU* 3.2 4.1 + - + +
289E ALA* 2.9 28.4 + - - +
349E LEU* 4.1 15.7 - - + -
353E GLN* 3.7 39.5 - - + +
356E SER* 3.9 19.5 - - - +
357E LEU* 3.9 18.8 - - + -
360E MET* 3.9 10.8 - - + -
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Residues in contact with GLU 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E PHE* 3.1 18.9 - - + +
283E THR* 2.7 47.2 + - - +
285E LEU* 1.3 73.2 - - + +
287E ILE* 1.3 66.6 + - - +
289E ALA* 3.3 2.6 + - - +
290E ALA* 3.0 24.1 + - - +
360E MET* 3.8 27.3 - - + +
400E TYR* 5.1 5.4 - - - -
403E ARG* 2.8 40.8 + - - +
407E LEU* 4.0 20.3 - - + +
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Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ARG* 3.9 29.6 - - - +
228E LEU* 4.8 7.6 - - + -
273E LEU* 3.8 30.7 - - + +
282E PHE* 3.9 24.5 - - + +
283E THR 3.0 21.2 + - - +
284E ASP* 3.5 17.5 - - - +
286E GLU* 1.3 76.3 - - - +
288E LEU* 1.3 63.9 + - - +
290E ALA* 3.4 2.4 + - - +
291E ILE* 3.1 34.0 + - + +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E PHE* 3.8 35.0 - - + -
228E LEU* 4.1 14.3 - - + +
232E PHE* 3.8 36.1 - - + -
234E ILE* 4.9 2.9 - - + -
284E ASP 2.8 17.3 + - - +
285E LEU* 3.4 8.3 - - + +
287E ILE* 1.3 80.1 - - - +
289E ALA* 1.3 57.6 + - - +
291E ILE* 3.3 1.9 + - - +
292E PHE* 2.8 32.7 + - + +
346E PHE* 3.7 25.8 - - + -
349E LEU* 4.4 1.8 - - + -
357E LEU* 3.5 22.2 - - + -
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Residues in contact with ALA 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E LEU 2.9 16.1 + - - +
286E GLU* 3.5 5.8 - - - +
288E LEU* 1.3 77.8 - - - +
290E ALA* 1.3 54.0 + - - +
292E PHE* 4.5 0.2 - - - -
293E ALA* 2.8 37.9 + - - +
357E LEU* 3.7 17.7 - - + +
360E MET* 3.9 32.5 - - + -
361E VAL* 3.8 12.5 - - + +
364E ILE* 4.4 3.6 - - + -
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E THR* 4.2 16.4 - - + -
273E LEU* 4.4 7.6 - - + -
286E GLU 3.0 16.8 + - - +
287E ILE* 3.7 4.0 - - - +
288E LEU 3.3 0.2 - - - -
289E ALA* 1.3 76.7 - - - +
291E ILE* 1.3 59.4 + - - +
293E ALA* 3.6 2.1 - - - +
294E SER* 2.9 31.9 + - - -
364E ILE* 4.0 16.1 - - + +
407E LEU* 4.1 21.8 - - + -
411E VAL* 4.0 7.3 - - + +
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Residues in contact with ILE 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E MET* 3.8 22.0 - - - -
222E ILE* 4.0 13.9 - - + -
223E PHE* 4.1 14.6 - - + -
226E ARG* 3.6 36.3 - - - +
228E LEU* 4.5 6.5 - - + -
266E VAL* 4.1 12.3 - - + +
269E THR* 4.5 6.3 - - + -
270E HIS* 4.7 6.7 - - + +
273E LEU* 3.8 13.7 - - + -
287E ILE* 3.1 22.5 + - + +
288E LEU* 3.8 3.6 - - - +
290E ALA* 1.3 73.7 - - - +
292E PHE* 1.3 65.1 + - - +
294E SER* 3.3 8.6 + - - -
295E ALA* 3.1 21.1 + - - +
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Residues in contact with PHE 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E MET* 4.6 11.9 - - + -
223E PHE* 5.7 2.0 - + + -
242E TYR* 3.4 42.6 - + - -
288E LEU* 2.8 26.1 + - + +
289E ALA* 3.8 3.4 - - - +
291E ILE* 1.3 70.4 - - - +
293E ALA* 1.3 65.4 + - - +
295E ALA* 3.1 15.2 + - + +
296E ILE* 3.2 39.0 + - + +
334E GLY 4.3 2.7 - - - -
335E PHE* 4.2 17.0 - + - -
338E LEU* 4.1 8.3 - - + -
345E ILE* 4.1 8.7 - - + -
346E PHE* 3.7 42.4 - + + -
361E VAL* 3.8 20.9 - - + -
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Residues in contact with ALA 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E ALA 2.8 23.7 + - - +
290E ALA 3.6 4.9 - - - +
292E PHE* 1.3 73.5 - - - +
294E SER* 1.3 62.2 + - - +
296E ILE* 3.3 3.8 + - - +
297E HIS* 2.9 26.7 + - - +
361E VAL* 4.2 14.6 - - + -
364E ILE* 3.9 30.1 - - + -
365E VAL* 3.8 17.0 - - + +
411E VAL* 5.2 0.9 - - - -
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Residues in contact with SER 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E TYR* 4.5 0.2 + - - -
262E ALA* 4.4 3.6 - - - +
265E VAL* 4.0 9.8 - - - +
266E VAL* 3.8 27.0 - - - +
269E THR* 2.8 25.4 + - - +
290E ALA 2.9 14.9 + - - -
291E ILE 3.5 8.7 - - - -
292E PHE 3.3 0.2 - - - -
293E ALA* 1.3 75.3 - - - +
295E ALA* 1.3 63.4 + - - +
297E HIS* 3.0 30.4 + - - -
411E VAL* 3.7 11.5 - - - +
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Residues in contact with ALA 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.0 4.0 - - + +
219E MET* 3.6 38.8 - - + -
246E LEU* 3.7 17.7 - - + +
250E TYR* 2.7 30.8 + - - -
262E ALA* 3.9 4.6 - - - +
266E VAL* 3.4 11.8 - - + +
291E ILE 3.1 8.1 + - - +
292E PHE* 3.1 11.4 + - + +
294E SER* 1.3 76.5 - - - +
296E ILE* 1.3 53.0 + - + +
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Residues in contact with ILE 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E TYR* 3.7 23.3 - - - +
246E LEU* 3.8 19.7 - - + -
250E TYR* 3.5 3.4 - - - -
292E PHE* 3.2 37.8 + - + +
293E ALA* 3.6 9.6 - - - +
295E ALA* 1.3 77.8 - - - +
297E HIS* 1.3 61.3 - - - +
298E ASP 2.8 11.1 + - - -
299E VAL* 3.1 16.4 + - + +
330E HIS* 3.6 5.6 - - - +
331E LEU* 4.1 21.3 - - + +
334E GLY* 4.1 22.2 - - - -
335E PHE* 4.8 2.0 - - + +
361E VAL* 4.0 15.7 - - + -
365E VAL* 4.4 3.6 - - + -
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Residues in contact with HIS 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E TYR* 4.7 1.4 + - - -
261E HIS* 3.2 16.8 - + - -
262E ALA* 4.5 6.0 - - - -
265E VAL* 3.3 26.8 - - + +
293E ALA 2.9 18.1 + - - +
294E SER* 3.0 23.3 + - - +
296E ILE* 1.3 74.5 - - - +
298E ASP* 1.3 74.5 + - + +
330E HIS* 3.0 20.9 - - - +
365E VAL* 4.1 16.8 - - + +
368E THR* 4.3 20.0 + - + -
411E VAL* 5.3 2.0 - - + -
415E ASP* 2.8 12.7 + - + -
2009E ZN 2.1 37.7 - - - -
2010E MG 3.6 6.7 - - - -
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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
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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