Contacts of the helix formed by residues 283 - 297 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281I VAL 5.4 1.1 - - - +
282I PHE* 1.3 77.1 - - - +
284I ASP* 1.3 64.8 + - - +
285I LEU* 3.3 9.3 + - - +
286I GLU* 2.7 44.4 + - - +
287I ILE* 3.0 22.3 + - - +
403I ARG* 5.3 5.6 - - - +
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Residues in contact with ASP 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ARG 5.6 1.7 - - - +
228I LEU* 4.4 8.4 - - + +
231I THR* 3.9 20.1 + - + +
232I PHE* 3.6 22.0 - - + -
283I THR* 1.3 75.1 - - - +
285I LEU* 1.3 58.7 + - - +
287I ILE* 3.3 15.6 + - - +
288I LEU* 2.8 28.9 + - - +
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Residues in contact with LEU 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I PHE* 3.6 24.8 - - + -
283I THR* 3.2 7.9 + - - +
284I ASP* 1.3 79.8 - - - +
286I GLU* 1.3 58.5 + - - +
288I LEU* 3.2 4.2 + - + +
289I ALA* 2.9 27.9 + - - +
349I LEU* 4.0 15.3 - - + -
353I GLN* 3.8 40.2 - - + +
356I SER* 3.9 19.3 - - - +
357I LEU* 3.9 21.1 - - + -
360I MET* 3.9 11.7 - - + -
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Residues in contact with GLU 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I PHE* 3.1 20.1 - - + +
283I THR* 2.7 46.1 + - - +
285I LEU* 1.3 73.8 - - + +
287I ILE* 1.3 66.6 + - - +
289I ALA* 3.3 2.4 + - - +
290I ALA* 3.0 24.6 + - - +
360I MET* 3.9 27.9 - - + +
400I TYR* 5.1 5.0 - - - -
403I ARG* 2.8 41.4 + - - +
407I LEU* 4.1 19.9 - - + +
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Residues in contact with ILE 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ARG* 3.9 27.4 - - + +
228I LEU* 4.8 7.6 - - + -
273I LEU* 3.8 29.8 - - + -
282I PHE* 4.0 24.7 - - + +
283I THR 3.0 21.3 + - - +
284I ASP* 3.6 17.3 - - - +
286I GLU* 1.3 76.5 - - - +
288I LEU* 1.3 64.4 + - - +
290I ALA* 3.8 2.3 - - - +
291I ILE* 3.1 34.9 + - + +
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Residues in contact with LEU 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I PHE* 3.8 35.0 - - + -
228I LEU* 4.1 14.1 - - + -
232I PHE* 3.7 36.1 - - + -
234I ILE* 4.9 2.5 - - + -
284I ASP 2.8 17.6 + - - +
285I LEU* 3.4 7.9 - - + +
286I GLU 3.2 0.2 - - - -
287I ILE* 1.3 79.6 - - - +
289I ALA* 1.3 56.5 + - - +
291I ILE* 3.3 1.8 + - - +
292I PHE* 2.8 32.4 + - + +
346I PHE* 3.7 25.1 - - + -
349I LEU* 4.4 1.8 - - + -
357I LEU* 3.5 23.1 - - + -
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Residues in contact with ALA 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I LEU 2.9 16.5 + - - +
286I GLU* 3.6 5.4 - - - +
288I LEU* 1.3 77.6 - - - +
290I ALA* 1.3 57.2 + - - +
292I PHE* 4.5 0.4 - - - -
293I ALA* 2.8 34.6 + - - +
357I LEU* 3.9 17.0 - - + -
360I MET* 3.9 32.8 - - + -
361I VAL* 3.8 12.9 - - + +
364I ILE* 4.4 3.1 - - + -
407I LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I THR* 4.2 16.6 - - + -
273I LEU* 4.4 7.4 - - + -
286I GLU 3.0 16.9 + - - +
287I ILE 3.8 3.6 - - - +
289I ALA* 1.3 75.7 - - - +
291I ILE* 1.3 59.0 + - - +
293I ALA* 3.6 1.9 - - - +
294I SER* 2.9 31.5 + - - -
364I ILE* 3.9 15.4 - - + +
407I LEU* 4.1 22.2 - - + -
410I MET* 5.4 0.2 - - - -
411I VAL* 4.0 7.7 - - + +
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Residues in contact with ILE 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I MET* 3.8 22.0 - - - -
222I ILE* 4.0 15.0 - - + -
223I PHE* 4.1 14.1 - - + -
226I ARG* 3.6 36.1 - - - +
228I LEU* 4.5 6.7 - - + -
266I VAL* 4.1 11.8 - - + +
269I THR* 4.6 6.3 - - + -
270I HIS* 4.7 5.8 - - - +
273I LEU* 3.8 14.1 - - + -
287I ILE* 3.1 24.6 + - + +
288I LEU* 3.8 3.8 - - - +
290I ALA* 1.3 74.3 - - - +
292I PHE* 1.3 66.7 + - - +
294I SER* 3.3 7.7 + - - -
295I ALA* 3.0 21.0 + - - +
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Residues in contact with PHE 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I MET* 4.6 11.9 - - + -
223I PHE* 5.7 2.4 - + + -
242I TYR* 3.4 43.7 - + - -
288I LEU* 2.8 25.3 + - + +
289I ALA* 3.9 3.8 - - - +
291I ILE* 1.3 72.4 - - - +
293I ALA* 1.3 62.9 + - - +
295I ALA* 3.1 15.3 + - + +
296I ILE* 3.2 39.5 + - + +
334I GLY 4.2 2.9 - - - -
335I PHE* 4.2 17.5 - + - -
338I LEU* 4.1 8.5 - - + -
345I ILE* 4.1 8.7 - - + -
346I PHE* 3.7 41.5 - + + -
361I VAL* 3.8 19.3 - - + -
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Residues in contact with ALA 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I ALA 2.8 19.1 + - - +
290I ALA 3.6 5.2 - - - +
292I PHE* 1.3 77.7 - - - +
294I SER* 1.3 56.9 + - - +
296I ILE* 3.3 4.0 + - - +
297I HIS* 2.9 31.9 + - - +
361I VAL* 4.2 14.4 - - + -
364I ILE* 3.9 29.4 - - + -
365I VAL* 3.7 17.3 - - + +
411I VAL* 5.2 0.9 - - - -
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Residues in contact with SER 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I TYR* 4.5 0.3 + - - -
262I ALA* 4.3 3.8 - - - +
265I VAL* 4.0 5.8 - - - -
266I VAL* 3.7 28.1 - - - +
269I THR* 2.8 24.8 + - - -
290I ALA 2.9 15.2 + - - -
291I ILE* 3.5 8.5 - - - -
293I ALA* 1.3 75.1 - - - +
295I ALA* 1.3 64.0 + - - +
296I ILE 3.3 0.5 + - - -
297I HIS* 3.0 31.2 + - - -
411I VAL* 3.7 11.6 - - - +
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Residues in contact with ALA 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LEU* 4.0 4.0 - - + +
219I MET* 3.6 34.1 - - + -
246I LEU* 3.8 17.2 - - + +
250I TYR* 2.7 30.7 + - - -
262I ALA* 3.9 4.6 - - - +
266I VAL* 3.4 16.5 - - + +
291I ILE 3.0 7.6 + - - +
292I PHE* 3.1 10.7 + - + +
294I SER* 1.3 77.6 - - - +
296I ILE* 1.3 53.9 + - + +
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Residues in contact with ILE 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I TYR* 3.7 23.6 - - - +
246I LEU* 3.8 20.2 - - + -
250I TYR* 3.5 3.4 - - - -
292I PHE* 3.2 36.9 + - + +
293I ALA* 3.6 10.3 - - - +
295I ALA* 1.3 78.1 - - + +
297I HIS* 1.3 61.3 + - - +
298I ASP 2.9 10.9 + - - -
299I VAL* 3.1 17.6 + - + +
330I HIS* 3.6 5.4 - - - +
331I LEU* 4.2 21.5 - - + +
334I GLY* 4.1 22.7 - - - -
335I PHE* 4.8 1.6 - - + +
361I VAL* 4.1 15.7 - - + -
365I VAL* 4.4 3.4 - - + -
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Residues in contact with HIS 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I TYR* 4.7 1.2 + - - -
261I HIS* 3.3 17.3 - + - -
262I ALA* 4.6 5.6 - - - -
265I VAL* 3.3 26.8 - - + +
293I ALA 2.9 18.1 + - - +
294I SER* 3.0 23.0 + - - +
296I ILE* 1.3 75.1 - - - +
298I ASP* 1.3 79.1 + - + +
330I HIS* 2.9 21.8 - - - +
365I VAL* 4.1 19.9 - - + +
368I THR* 4.3 19.6 + - + -
411I VAL* 5.2 2.0 - - + -
415I ASP* 2.8 12.5 + - - -
2017I ZN 2.2 32.9 - - - -
2018I MG 4.0 3.9 - - - -
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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