Contacts of the helix formed by residues 283 - 297 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL 5.3 1.3 - - - +
282A PHE* 1.3 77.4 - - - +
284A ASP* 1.3 64.7 + - - +
285A LEU* 3.3 9.7 + - - +
286A GLU* 2.7 43.2 + - - +
287A ILE* 3.0 22.3 + - - +
403A ARG* 5.3 5.6 - - - +
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG 5.6 1.6 - - - +
228A LEU* 4.4 8.0 - - + +
231A THR* 3.8 21.4 + - + +
232A PHE* 3.5 22.5 - - + -
283A THR* 1.3 73.7 - - - +
285A LEU* 1.3 58.7 + - - +
287A ILE* 3.4 16.0 + - - +
288A LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.6 25.4 - - + -
283A THR* 3.2 9.2 + - - +
284A ASP* 1.3 79.1 - - - +
286A GLU* 1.3 56.4 + - + +
288A LEU* 3.2 4.1 + - + +
289A ALA* 2.9 28.9 + - - +
349A LEU* 4.1 15.7 - - + -
353A GLN* 3.7 38.6 - - + +
356A SER* 3.9 19.5 - - - +
357A LEU* 3.9 19.3 - - + -
360A MET* 3.9 10.8 - - + -
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 3.1 20.6 - - + -
283A THR* 2.7 46.1 + - - +
285A LEU* 1.3 72.9 - - + +
287A ILE* 1.3 65.3 + - - +
289A ALA* 3.3 2.3 + - - +
290A ALA* 3.0 24.6 + - - +
360A MET* 3.9 27.7 - - + +
400A TYR* 5.1 5.2 - - - -
403A ARG* 2.8 41.2 + - - +
407A LEU* 4.0 19.9 - - + +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG* 3.9 28.7 - - + +
228A LEU* 4.8 8.5 - - + -
273A LEU* 3.8 30.7 - - + -
282A PHE* 3.9 24.2 - - + +
283A THR 3.0 21.3 + - - +
284A ASP* 3.6 17.7 - - - +
286A GLU* 1.3 75.1 - - - +
288A LEU* 1.3 64.4 + - - +
290A ALA* 3.4 2.4 + - - +
291A ILE* 3.1 33.9 + - + +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.8 34.1 - - + -
228A LEU* 4.1 13.5 - - + -
232A PHE* 3.8 35.0 - - + -
234A ILE* 4.9 2.5 - - + -
284A ASP 2.9 18.3 + - - +
285A LEU* 3.4 8.3 - - + +
287A ILE* 1.3 77.7 - - - +
289A ALA* 1.3 57.3 + - - +
291A ILE* 3.3 1.8 + - + +
292A PHE* 2.8 32.7 + - + +
346A PHE* 3.7 26.2 - - + -
349A LEU* 4.4 2.0 - - + -
357A LEU* 3.5 23.3 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU 2.9 16.9 + - - +
286A GLU* 3.6 5.2 - - - +
287A ILE 3.3 0.2 - - - -
288A LEU* 1.3 76.3 - - - +
290A ALA* 1.3 57.0 + - - +
292A PHE* 4.5 0.7 - - - -
293A ALA* 2.8 33.4 + - - +
357A LEU* 3.8 17.9 - - + +
360A MET* 3.9 32.3 - - + -
361A VAL* 3.8 14.1 - - + +
364A ILE* 4.4 2.9 - - + -
407A LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A THR* 4.2 15.7 - - + -
273A LEU* 4.4 7.0 - - + -
286A GLU 3.0 16.3 + - - +
287A ILE 3.8 3.8 - - - +
289A ALA* 1.3 75.9 - - - +
291A ILE* 1.3 58.7 + - - +
293A ALA* 3.5 2.3 + - - +
294A SER* 2.9 31.5 + - - -
364A ILE* 3.9 16.0 - - + +
407A LEU* 4.1 22.7 - - + -
410A MET* 5.3 0.2 - - - -
411A VAL* 4.0 7.6 - - + +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.8 22.1 - - - +
222A ILE* 4.0 14.6 - - + -
223A PHE* 4.1 13.9 - - + -
226A ARG* 3.6 36.8 - - - +
228A LEU* 4.5 7.4 - - + -
266A VAL* 4.1 11.1 - - + +
269A THR* 4.5 6.5 - - + -
270A HIS* 4.7 6.5 - - + +
273A LEU* 3.8 13.5 - - + -
287A ILE* 3.1 23.1 + - + +
288A LEU* 3.8 3.1 - - - +
290A ALA* 1.3 73.1 - - - +
292A PHE* 1.3 67.1 + - - +
294A SER* 3.2 7.8 + - - -
295A ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A MET* 4.6 12.3 - - + -
223A PHE* 5.7 2.0 - + + -
242A TYR* 3.5 43.1 - + - -
288A LEU* 2.8 25.0 + - + +
289A ALA* 3.8 4.0 - - - +
291A ILE* 1.3 73.4 - - - +
293A ALA* 1.3 63.2 + - - +
295A ALA* 3.1 15.1 + - + +
296A ILE* 3.2 38.0 + - + +
334A GLY 4.3 3.4 - - - -
335A PHE* 4.2 16.8 - + - -
338A LEU* 4.1 8.5 - - + -
345A ILE* 4.1 9.2 - - + -
346A PHE* 3.7 43.5 - + + -
361A VAL* 3.8 20.2 - - + -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA 2.8 22.6 + - - +
290A ALA 3.6 4.9 - - - +
292A PHE* 1.3 74.8 - - - +
294A SER* 1.3 56.6 + - - +
296A ILE* 3.3 3.3 + - - +
297A HIS* 2.8 32.7 + - - +
361A VAL* 4.2 14.8 - - + -
364A ILE* 3.9 30.3 - - + -
365A VAL* 3.8 16.6 - - + +
411A VAL* 5.3 1.1 - - - -
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A TYR* 4.5 0.3 + - - -
262A ALA* 4.3 3.5 - - - +
265A VAL* 4.0 6.2 - - - +
266A VAL* 3.8 28.7 - - - +
269A THR* 2.8 24.9 + - - +
290A ALA 2.9 15.1 + - - -
291A ILE 3.5 8.3 - - - -
292A PHE 3.2 0.2 - - - -
293A ALA* 1.3 77.1 - - - +
295A ALA* 1.3 63.5 + - - +
297A HIS* 2.9 30.7 + - - -
411A VAL* 3.7 11.8 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.0 5.9 - - + +
219A MET* 3.6 35.9 - - + -
246A LEU* 3.8 16.6 - - + +
250A TYR* 2.7 30.7 + - - -
262A ALA* 3.9 4.2 - - - +
266A VAL* 3.4 11.6 - - + +
291A ILE 3.1 4.6 + - - +
292A PHE* 3.1 11.2 + - + +
294A SER* 1.3 80.5 - - - +
296A ILE* 1.3 54.0 + - + +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A TYR* 3.6 22.7 - - - +
246A LEU* 3.8 23.1 - - + -
250A TYR* 3.5 2.9 - - - -
292A PHE* 3.2 36.9 + - + +
293A ALA* 3.6 9.4 - - - +
295A ALA* 1.3 77.2 - - + +
297A HIS* 1.3 61.7 + - - +
298A ASP 2.9 11.2 + - - -
299A VAL* 3.1 16.9 + - + +
330A HIS* 3.6 5.5 - - - +
331A LEU* 4.2 22.2 - - + +
334A GLY* 4.2 19.7 - - - -
335A PHE* 4.9 1.8 - - + +
361A VAL* 4.0 16.4 - - + -
365A VAL* 4.4 3.4 - - + -
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A TYR* 4.7 1.6 + - - -
261A HIS* 3.3 21.5 - + - -
262A ALA* 4.5 5.8 - - - -
265A VAL* 3.4 24.9 - - + +
293A ALA 2.8 18.3 + - - +
294A SER* 2.9 24.1 + - - +
296A ILE* 1.3 74.5 - - - +
298A ASP* 1.3 77.9 + - + +
330A HIS* 3.0 21.3 - - - +
365A VAL* 4.1 18.7 - - + +
368A THR* 4.3 21.1 + - + -
411A VAL* 5.2 1.6 - - + -
415A ASP* 2.7 13.5 + - + -
2001A ZN 2.3 28.8 - - - -
2002A 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