Contacts of the helix formed by residues 283 - 297 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G VAL 5.3 1.6 - - - +
282G PHE* 1.3 75.8 - - - +
284G ASP* 1.3 64.8 + - - +
285G LEU* 3.3 9.9 + - - +
286G GLU* 2.7 45.4 + - - +
287G ILE* 3.0 22.3 + - - +
403G ARG* 5.2 5.2 - - - +
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Residues in contact with ASP 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ARG 5.6 1.7 - - - +
228G LEU* 4.4 8.9 - - + +
231G THR* 3.9 21.1 + - + +
232G PHE* 3.5 22.7 - - + -
283G THR* 1.3 73.6 - - - +
285G LEU* 1.3 57.6 + - - +
287G ILE* 3.3 16.1 + - - +
288G LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 3.6 24.6 - - + -
283G THR* 3.2 8.6 + - - +
284G ASP* 1.3 82.1 - - - +
286G GLU* 1.3 56.7 + - + +
288G LEU* 3.2 4.3 + - + +
289G ALA* 2.9 28.2 + - - +
349G LEU* 4.1 15.9 - - + -
353G GLN* 3.8 40.4 - - + +
356G SER* 3.9 19.1 - - - -
357G LEU* 3.8 20.9 - - + -
360G MET* 3.9 11.0 - - + -
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Residues in contact with GLU 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G PHE* 3.2 19.4 - - + -
283G THR* 2.7 46.1 + - - +
285G LEU* 1.3 73.6 - - + +
287G ILE* 1.3 66.0 + - - +
289G ALA* 3.3 2.8 + - - +
290G ALA* 3.0 24.4 + - - +
360G MET* 3.9 28.3 - - + +
400G TYR* 5.2 5.2 - - - -
403G ARG* 2.8 40.5 + - - +
407G LEU* 4.0 20.2 - - + +
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Residues in contact with ILE 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ARG* 3.9 27.4 - - - +
228G LEU* 4.8 8.1 - - + -
273G LEU* 3.8 31.8 - - + +
282G PHE* 3.9 24.7 - - + +
283G THR 3.0 21.1 + - - +
284G ASP* 3.6 17.5 - - - +
285G LEU 3.2 0.2 - - - -
286G GLU* 1.3 75.7 - - - +
288G LEU* 1.3 63.8 + - - +
290G ALA* 3.4 2.3 + - - +
291G ILE* 3.1 35.0 + - + +
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Residues in contact with LEU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G PHE* 3.7 35.7 - - + -
228G LEU* 4.1 14.1 - - + -
232G PHE* 3.8 35.0 - - + -
234G ILE* 4.9 3.4 - - + -
284G ASP 2.8 18.5 + - - +
285G LEU* 3.2 8.3 + - + +
287G ILE* 1.3 80.5 - - - +
289G ALA* 1.3 57.4 + - - +
291G ILE* 3.8 1.7 - - + +
292G PHE* 2.8 32.9 + - + +
346G PHE* 3.6 27.4 - - + -
349G LEU* 4.4 2.0 - - + -
357G LEU* 3.5 21.8 - - + -
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Residues in contact with ALA 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285G LEU 2.9 16.9 + - - +
286G GLU* 3.6 5.4 - - - +
287G ILE 3.3 0.2 - - - -
288G LEU* 1.3 76.5 - - - +
290G ALA* 1.3 53.7 + - - +
292G PHE* 4.5 0.4 - - - -
293G ALA* 2.7 38.6 + - - +
357G LEU* 3.8 17.9 - - + +
360G MET* 3.9 32.5 - - + -
361G VAL* 3.7 13.2 - - + +
364G ILE* 4.5 3.6 - - + -
407G LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G THR* 4.2 16.2 - - + -
273G LEU* 4.4 7.0 - - + -
286G GLU 3.0 16.8 + - - +
287G ILE 3.7 4.3 - - - +
289G ALA* 1.3 75.1 - - - +
291G ILE* 1.3 59.2 + - - +
293G ALA* 3.5 2.3 + - - +
294G SER* 2.9 32.6 + - - -
364G ILE* 3.9 15.6 - - + +
407G LEU* 4.0 22.7 - - + -
411G VAL* 4.0 7.5 - - + +
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Residues in contact with ILE 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G MET* 3.8 23.0 - - - +
222G ILE* 4.0 14.8 - - + -
223G PHE* 4.1 13.9 - - + -
226G ARG* 3.6 36.3 - - - +
228G LEU* 4.5 7.0 - - + -
266G VAL* 4.1 11.3 - - + +
269G THR* 4.6 7.0 - - + -
270G HIS* 4.7 6.7 - - + +
273G LEU* 3.8 13.0 - - + -
287G ILE* 3.1 22.7 + - + +
288G LEU* 3.9 3.6 - - - +
290G ALA* 1.3 73.0 - - - +
292G PHE* 1.3 66.4 + - - +
294G SER* 3.3 7.6 + - - -
295G ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G MET* 4.6 11.9 - - + -
223G PHE* 5.7 1.8 - + + -
242G TYR* 3.4 44.0 - + - -
288G LEU* 2.8 25.9 + - + +
289G ALA* 3.8 3.4 - - - +
291G ILE* 1.3 71.4 - - - +
293G ALA* 1.3 65.8 + - - +
295G ALA* 3.1 15.9 + - + +
296G ILE* 3.2 38.7 + - + +
334G GLY 4.3 2.7 - - - -
335G PHE* 4.2 17.5 - + - -
338G LEU* 4.2 8.1 - - + -
345G ILE* 4.1 9.0 - - + -
346G PHE* 3.7 42.2 - + + -
357G LEU* 4.6 0.2 - - + -
361G VAL* 3.8 19.3 - - + -
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Residues in contact with ALA 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G ALA 2.7 23.1 + - - +
290G ALA 3.6 5.2 - - - +
292G PHE* 1.3 73.9 - - - +
294G SER* 1.3 56.8 + - - +
296G ILE* 3.3 4.6 + - - +
297G HIS* 2.8 32.9 + - - +
361G VAL* 4.2 14.6 - - + -
364G ILE* 3.9 29.8 - - + -
365G VAL* 3.8 17.4 - - + +
411G VAL* 5.3 0.9 - - - -
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Residues in contact with SER 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G TYR* 4.5 0.3 + - - -
262G ALA* 4.3 3.3 - - - +
265G VAL* 4.0 6.2 - - - +
266G VAL* 3.8 29.4 - - - +
269G THR* 2.8 25.3 + - - +
290G ALA 2.9 18.6 + - - -
291G ILE* 3.5 8.7 - - - -
292G PHE 3.2 0.2 - - - -
293G ALA* 1.3 74.9 - - - +
295G ALA* 1.3 63.1 + - - +
297G HIS* 2.9 31.8 + - - -
411G VAL* 3.7 11.2 - - - +
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Residues in contact with ALA 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G LEU* 4.1 6.3 - - + +
219G MET* 3.6 36.1 - - + -
246G LEU* 3.8 16.8 - - + +
250G TYR* 2.6 31.2 + - - -
262G ALA* 3.9 4.4 - - - +
266G VAL* 3.4 12.7 - - + +
291G ILE 3.1 4.6 + - - +
292G PHE* 3.4 10.5 - - + +
294G SER* 1.3 79.9 - - - +
296G ILE* 1.3 53.5 + - + +
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Residues in contact with ILE 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G TYR* 3.6 23.1 - - - +
246G LEU* 3.7 22.9 - - + -
250G TYR* 3.5 3.6 - - - -
292G PHE* 3.2 36.7 + - + +
293G ALA* 3.6 10.1 - - - +
295G ALA* 1.3 78.2 - - + +
297G HIS* 1.3 60.9 + - - +
298G ASP 2.8 10.9 + - - -
299G VAL* 3.1 17.1 + - + +
330G HIS* 3.6 5.2 - - - +
331G LEU* 4.2 22.7 - - + +
334G GLY* 4.1 19.7 - - - -
335G PHE* 4.8 1.8 - - + +
361G VAL* 4.1 15.5 - - + -
365G VAL* 4.4 2.9 - - + -
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Residues in contact with HIS 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G TYR* 4.7 1.2 + - - -
261G HIS* 3.2 20.6 - + - -
262G ALA* 4.5 5.6 - - - -
265G VAL* 3.3 26.2 - - + +
293G ALA 2.8 18.5 + - - +
294G SER* 2.9 24.2 + - - +
295G ALA 3.5 0.2 - - - -
296G ILE* 1.3 74.7 - - - +
298G ASP* 1.3 79.7 + - + +
330G HIS* 2.9 21.0 - - - +
365G VAL* 4.1 17.7 - - + +
368G THR* 4.3 21.6 + - + -
411G VAL* 5.3 1.6 - - + -
415G ASP* 2.8 13.5 + - - -
2013G ZN 2.3 28.0 - - - -
2014G MG 3.9 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
------------------------------------------------------------
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