Contacts of the helix formed by residues 283 - 297 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K VAL 5.3 1.8 - - - +
282K PHE* 1.3 75.5 - - - +
284K ASP* 1.3 64.5 + - - +
285K LEU* 3.3 9.9 + - - +
286K GLU* 2.7 45.9 + - - +
287K ILE* 3.0 22.3 + - - +
403K ARG* 5.3 5.4 - - - +
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Residues in contact with ASP 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ARG 5.5 2.1 - - - +
228K LEU* 4.4 8.5 - - + +
231K THR* 3.8 21.0 + - + +
232K PHE* 3.5 22.9 - - + -
283K THR* 1.3 74.1 - - - +
285K LEU* 1.3 57.4 + - - +
287K ILE* 3.3 16.6 + - - +
288K LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K PHE* 3.6 25.9 - - + -
283K THR* 3.2 8.4 + - - +
284K ASP* 1.3 79.5 - - - +
286K GLU* 1.3 56.5 + - + +
288K LEU* 3.2 3.3 + - + +
289K ALA* 2.8 29.3 + - - +
349K LEU* 4.0 15.5 - - + -
353K GLN* 3.7 40.8 - - + +
356K SER* 3.9 17.3 - - - -
357K LEU* 3.8 22.6 - - + +
360K MET* 3.9 10.3 - - + -
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Residues in contact with GLU 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282K PHE* 3.2 19.6 - - + +
283K THR* 2.7 47.2 + - - +
285K LEU* 1.3 72.8 - - + +
287K ILE* 1.3 67.1 + - - +
289K ALA* 3.2 2.6 + - - +
290K ALA* 3.0 24.8 + - - +
360K MET* 3.9 26.8 - - + +
400K TYR* 5.1 5.0 - - - -
403K ARG* 2.8 40.2 + - - +
407K LEU* 4.1 19.5 - - + +
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Residues in contact with ILE 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ARG* 3.9 29.2 - - - +
228K LEU* 4.8 7.6 - - + -
273K LEU* 3.8 30.1 - - + -
282K PHE* 3.9 24.5 - - + +
283K THR 3.0 21.0 + - - +
284K ASP* 3.6 18.8 - - - +
286K GLU* 1.3 77.3 - - - +
288K LEU* 1.3 62.7 + - - +
290K ALA* 3.4 2.1 + - - +
291K ILE* 3.1 33.7 + - + +
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Residues in contact with LEU 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K PHE* 3.7 35.4 - - + -
228K LEU* 4.0 13.7 - - + -
232K PHE* 3.8 35.7 - - + -
234K ILE* 4.9 2.2 - - + -
284K ASP 2.8 18.1 + - - +
285K LEU* 3.2 8.9 + - + +
287K ILE* 1.3 78.2 - - - +
289K ALA* 1.3 55.8 + - - +
291K ILE* 3.3 2.1 + - - +
292K PHE* 2.9 33.2 + - + +
346K PHE* 3.7 26.2 - - + -
349K LEU* 4.3 2.2 - - + -
357K LEU* 3.5 22.7 - - + -
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Residues in contact with ALA 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285K LEU 2.8 16.5 + - - +
286K GLU 3.2 4.7 + - - +
288K LEU* 1.3 76.9 - - - +
290K ALA* 1.3 57.1 + - - +
292K PHE* 4.5 0.9 - - - -
293K ALA* 2.8 35.0 + - - +
357K LEU* 3.8 16.1 - - + +
360K MET* 3.9 34.1 - - + -
361K VAL* 3.8 12.9 - - + +
364K ILE* 4.4 4.0 - - + -
407K LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K THR* 4.2 16.2 - - + -
273K LEU* 4.4 7.0 - - + -
286K GLU 3.0 15.9 + - - +
287K ILE 3.8 4.3 - - - +
288K LEU 3.3 0.2 - - - -
289K ALA* 1.3 76.7 - - - +
291K ILE* 1.3 57.7 + - - +
293K ALA* 3.6 1.7 - - - +
294K SER* 2.9 32.4 + - - -
364K ILE* 3.9 15.8 - - + +
407K LEU* 4.0 22.4 - - + -
410K MET* 5.4 0.4 - - - -
411K VAL* 4.0 8.0 - - + +
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Residues in contact with ILE 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K MET* 3.8 22.7 - - - -
222K ILE* 4.0 15.0 - - + -
223K PHE* 4.1 13.9 - - + -
226K ARG* 3.5 37.5 - - - +
228K LEU* 4.5 6.7 - - + -
266K VAL* 4.1 12.0 - - + +
269K THR* 4.5 7.2 - - + -
270K HIS* 4.6 6.3 - - + +
273K LEU* 3.8 13.0 - - + -
287K ILE* 3.1 22.6 + - + +
288K LEU* 3.9 4.0 - - - +
290K ALA* 1.3 74.4 - - - +
292K PHE* 1.3 63.9 + - - +
294K SER* 3.3 7.7 + - - -
295K ALA* 3.1 21.5 + - - +
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Residues in contact with PHE 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K MET* 4.6 12.3 - - + -
223K PHE* 5.7 2.0 - + + -
242K TYR* 3.4 42.8 - + - -
288K LEU* 2.9 21.7 + - + +
289K ALA* 3.8 3.6 - - - +
291K ILE* 1.3 73.8 - - - +
293K ALA* 1.3 66.7 + - - +
295K ALA* 3.1 16.1 + - + +
296K ILE* 3.2 37.7 + - + +
334K GLY 4.2 3.4 - - - -
335K PHE* 4.2 17.5 - + - -
338K LEU* 4.1 8.5 - - + -
345K ILE* 4.1 8.7 - - + -
346K PHE* 3.7 42.0 - + + -
361K VAL* 3.8 20.4 - - + -
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Residues in contact with ALA 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289K ALA 2.8 18.2 + - - +
290K ALA 3.6 5.2 - - - +
292K PHE* 1.3 78.5 - - - +
294K SER* 1.3 56.9 + - - +
296K ILE* 3.3 3.7 + - - +
297K HIS* 2.8 32.4 + - - +
361K VAL* 4.2 15.0 - - + +
364K ILE* 3.9 29.4 - - + -
365K VAL* 3.7 18.4 - - + +
411K VAL* 5.3 0.9 - - - -
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Residues in contact with SER 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K TYR* 4.5 0.2 + - - -
262K ALA* 4.3 3.5 - - - +
265K VAL* 4.0 10.0 - - - +
266K VAL* 3.8 26.2 - - - +
269K THR* 2.8 24.4 + - - -
290K ALA 2.9 16.2 + - - -
291K ILE 3.5 9.0 - - - -
292K PHE 3.2 0.2 - - - -
293K ALA* 1.3 75.9 - - - +
295K ALA* 1.3 61.6 + - - +
297K HIS* 2.9 31.6 + - - -
411K VAL* 3.7 11.8 - - - +
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Residues in contact with ALA 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K LEU* 4.0 4.6 - - + +
219K MET* 3.6 34.5 - - + -
246K LEU* 3.7 18.0 - - + +
250K TYR* 2.6 31.2 + - - -
262K ALA* 3.9 4.6 - - - +
266K VAL* 3.4 17.4 - - + +
291K ILE 3.1 7.0 + - - +
292K PHE* 3.1 10.1 + - + +
294K SER* 1.3 76.9 - - - +
296K ILE* 1.3 53.7 + - + +
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Residues in contact with ILE 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242K TYR* 3.7 22.9 - - - +
246K LEU* 3.7 20.0 - - + -
250K TYR* 3.5 3.6 - - - -
292K PHE* 3.2 36.5 + - + +
293K ALA* 3.6 10.1 - - - +
295K ALA* 1.3 78.5 - - + +
297K HIS* 1.3 62.4 + - - +
298K ASP 2.8 11.6 + - - -
299K VAL* 3.1 17.2 + - + +
330K HIS* 3.6 5.0 - - - +
331K LEU* 4.2 20.6 - - + +
334K GLY* 4.1 22.9 - - - -
335K PHE* 4.8 1.6 - - + +
361K VAL* 4.1 15.5 - - + -
365K VAL* 4.4 3.1 - - + -
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Residues in contact with HIS 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K TYR* 4.7 1.6 + - - -
261K HIS* 3.2 21.8 - + - -
262K ALA* 4.5 5.6 - - - -
265K VAL* 3.3 25.9 - - + +
293K ALA 2.8 17.7 + - - +
294K SER* 2.9 24.3 + - - +
296K ILE* 1.3 75.5 - - - +
298K ASP* 1.3 79.4 + - + +
330K HIS* 3.0 20.2 - - - +
365K VAL* 4.1 19.7 - - + +
368K THR* 4.3 16.7 + - + -
411K VAL* 5.2 2.2 - - + -
415K ASP* 2.7 12.2 + - + -
2021K ZN 2.5 27.6 - - - -
2022K MG 3.3 9.0 - - - -
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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