Contacts of the helix formed by residues 283 - 297 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D VAL 5.3 1.8 - - - +
282D PHE* 1.3 76.5 - - - +
284D ASP* 1.3 64.2 + - - +
285D LEU* 3.3 9.7 + - - +
286D GLU* 2.7 45.9 + - - +
287D ILE* 3.0 22.2 + - - +
403D ARG* 5.3 5.4 - - - +
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Residues in contact with ASP 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ARG 5.6 2.1 - - - +
228D LEU* 4.4 8.6 - - + +
231D THR* 3.9 21.4 + - + +
232D PHE* 3.5 22.6 - - + -
283D THR* 1.3 74.5 - - - +
285D LEU* 1.3 58.5 + - - +
287D ILE* 3.4 16.1 + - - +
288D LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PHE* 3.6 26.5 - - + -
283D THR* 3.2 8.6 + - - +
284D ASP* 1.3 79.6 - - - +
286D GLU* 1.3 57.8 + - + +
288D LEU* 3.2 3.6 + - + +
289D ALA* 2.8 28.8 + - - +
349D LEU* 4.0 15.5 - - + -
353D GLN* 3.7 39.5 - - + +
356D SER* 3.8 19.7 - - - -
357D LEU* 3.8 22.7 - - + -
360D MET* 3.9 11.2 - - + -
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D VAL 4.1 0.2 - - - +
282D PHE* 3.2 20.8 - - + +
283D THR* 2.7 48.3 + - - +
285D LEU* 1.3 73.2 - - - +
287D ILE* 1.3 65.7 + - - +
289D ALA* 3.3 2.4 + - - +
290D ALA* 3.0 24.6 + - - +
360D MET* 3.9 27.1 - - + +
400D TYR* 5.2 5.4 - - - -
403D ARG* 2.8 41.2 + - - +
407D LEU* 4.0 18.1 - - + +
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ARG* 3.9 33.4 - - + +
228D LEU* 4.8 7.2 - - + -
273D LEU* 3.9 26.9 - - + -
282D PHE* 3.9 24.9 - - + +
283D THR 3.0 17.9 + - - +
284D ASP* 3.6 17.9 - - - +
286D GLU* 1.3 75.2 - - - +
288D LEU* 1.3 64.6 + - - +
290D ALA* 3.4 2.4 + - - +
291D ILE* 3.1 35.1 + - + +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 3.8 35.4 - - + -
228D LEU* 4.1 13.5 - - + -
232D PHE* 3.7 36.1 - - + -
234D ILE* 4.9 2.9 - - + -
284D ASP 2.9 18.7 + - - +
285D LEU* 3.4 8.1 - - + +
287D ILE* 1.3 79.3 - - - +
289D ALA* 1.3 57.0 + - - +
291D ILE* 3.3 2.1 + - - +
292D PHE* 2.8 32.6 + - + +
346D PHE* 3.7 26.5 - - + -
349D LEU* 4.3 1.8 - - + -
357D LEU* 3.6 22.4 - - + -
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Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU 2.8 16.5 + - - +
286D GLU* 3.3 6.0 + - - +
288D LEU* 1.3 76.5 - - - +
290D ALA* 1.3 53.6 + - - +
292D PHE* 3.3 1.1 + - - -
293D ALA* 2.7 38.7 + - - +
357D LEU* 3.9 16.8 - - + -
360D MET* 3.9 32.8 - - + -
361D VAL* 3.7 14.0 - - + +
364D ILE* 4.5 3.1 - - + -
407D LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D THR* 4.2 15.7 - - + -
273D LEU* 4.4 6.7 - - + -
286D GLU 3.0 17.0 + - - +
287D ILE 3.8 4.0 - - - +
289D ALA* 1.3 75.9 - - - +
291D ILE* 1.3 58.9 + - - +
293D ALA* 3.5 2.3 + - - +
294D SER* 2.9 32.1 + - - -
364D ILE* 3.9 15.2 - - + +
407D LEU* 4.1 22.2 - - + -
410D MET* 5.3 0.4 - - - -
411D VAL* 4.0 7.9 - - + +
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET* 3.9 22.2 - - - -
222D ILE* 4.0 14.4 - - + -
223D PHE* 4.1 14.4 - - + -
226D ARG* 3.6 35.7 - - - +
228D LEU* 4.5 7.0 - - + -
266D VAL* 4.1 12.3 - - + +
269D THR* 4.6 6.7 - - + -
270D HIS* 4.6 6.1 - - + +
273D LEU* 3.8 14.6 - - + -
287D ILE* 3.1 21.8 + - + +
288D LEU* 3.8 3.4 - - - +
290D ALA* 1.3 74.4 - - - +
292D PHE* 1.3 65.3 + - - +
294D SER* 3.3 7.7 + - - -
295D ALA* 3.0 21.1 + - - +
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Residues in contact with PHE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET* 4.6 12.8 - - + -
223D PHE* 5.7 2.0 - + + -
242D TYR* 3.4 42.8 - + - -
288D LEU* 2.8 25.7 + - + +
289D ALA* 3.8 3.6 - - - +
291D ILE* 1.3 73.7 - - - +
293D ALA* 1.3 62.6 + - - +
295D ALA* 3.2 8.9 + - + +
296D ILE* 3.2 46.4 + - + +
334D GLY 4.3 3.1 - - - -
335D PHE* 4.3 17.0 - + - -
338D LEU* 4.2 7.9 - - + -
345D ILE* 4.1 9.0 - - + -
346D PHE* 3.7 42.2 - + + -
357D LEU* 4.7 0.4 - - + -
361D VAL* 3.8 19.7 - - + -
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Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D ALA 2.7 22.9 + - - +
290D ALA 3.6 5.2 - - - +
292D PHE* 1.3 74.5 - - - +
294D SER* 1.3 56.4 + - - +
296D ILE* 3.3 3.7 + - - +
297D HIS* 2.8 33.3 + - - +
361D VAL* 4.2 15.0 - - + -
364D ILE* 3.9 30.3 - - + -
365D VAL* 3.8 17.1 - - + +
411D VAL* 5.3 0.9 - - - -
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D TYR* 4.5 0.2 + - - -
262D ALA* 4.3 3.6 - - - +
265D VAL* 4.0 6.1 - - - -
266D VAL* 3.7 28.9 - - - +
269D THR* 2.8 26.7 + - - +
290D ALA 2.9 14.9 + - - -
291D ILE 3.5 9.0 - - - -
292D PHE 3.2 0.2 - - - -
293D ALA* 1.3 76.0 - - - +
295D ALA* 1.3 63.3 + - - +
297D HIS* 2.9 31.2 + - - -
411D VAL* 3.8 10.6 - - - +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 4.0 4.1 - - + +
219D MET* 3.6 33.4 - - + -
246D LEU* 3.8 17.0 - - + +
250D TYR* 2.7 30.8 + - - -
262D ALA* 3.9 4.4 - - - +
266D VAL* 3.4 17.4 - - + +
291D ILE 3.0 4.9 + - - +
292D PHE* 3.4 10.8 - - + +
294D SER* 1.3 80.0 - - - +
296D ILE* 1.3 54.0 + - + +
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D TYR* 3.7 23.3 - - - +
246D LEU* 3.8 21.1 - - + -
250D TYR* 3.5 2.9 - - - -
292D PHE* 3.2 37.9 + - + +
293D ALA* 3.6 9.4 - - - +
295D ALA* 1.3 77.8 - - - +
297D HIS* 1.3 60.6 - - - +
298D ASP 2.8 11.5 + - - -
299D VAL* 3.1 16.2 + - + +
330D HIS* 3.6 5.0 - - - +
331D LEU* 4.2 21.3 - - + +
334D GLY* 4.1 22.4 - - - -
335D PHE* 4.8 1.8 - - + +
361D VAL* 4.1 15.7 - - + -
365D VAL* 4.4 3.8 - - + -
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Residues in contact with HIS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D TYR* 4.7 1.6 + - - -
261D HIS* 3.2 22.0 - + - -
262D ALA* 4.5 5.4 - - - -
265D VAL* 3.4 24.4 - - + +
293D ALA 2.8 17.5 + - - +
294D SER* 2.9 25.1 + - - +
295D ALA 3.5 0.2 - - - -
296D ILE* 1.3 75.0 - - - +
298D ASP* 1.3 80.2 + - + +
330D HIS* 3.0 21.0 - - - +
365D VAL* 4.2 17.3 - - + +
368D THR* 4.3 21.3 + - + -
411D VAL* 5.3 2.0 - - + -
415D ASP* 2.8 13.8 + - + -
2007D ZN 2.3 29.0 - - - -
2008D MG 4.0 4.3 - - - -
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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