Contacts of the helix formed by residues 235 - 249 (chain J) 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 PRO 235 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233J LYS 3.4 9.2 - - - +
234J ILE* 1.3 85.3 - - + +
236J VAL* 1.3 56.7 + - - +
237J ASP* 3.1 15.5 - - - +
238J THR* 2.7 47.3 + - + +
239J LEU* 2.9 11.3 + - - +
345J ILE 5.0 0.7 - - - +
347J GLN* 3.8 29.6 - - + +
348J ASN* 4.6 2.0 - - - +
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Residues in contact with VAL 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220J HIS* 4.0 14.4 - - + +
224J GLN* 4.9 3.4 - - - +
229J LEU* 4.2 28.7 - - + -
234J ILE 3.1 3.4 + - - +
235J PRO* 1.3 70.7 - - - +
237J ASP* 1.3 65.1 + - - +
239J LEU* 3.2 2.6 + - - +
240J ILE* 3.0 47.0 + - + +
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Residues in contact with ASP 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J PRO* 3.9 14.1 - - - +
236J VAL* 1.3 80.4 + - - +
238J THR* 1.3 66.7 + - - +
240J ILE* 3.6 4.9 + - - +
241J THR* 2.6 38.9 + - - +
342J ASN* 3.2 18.4 + - - +
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Residues in contact with THR 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J PRO* 2.7 32.5 + - + +
237J ASP* 1.3 79.2 + - - +
239J LEU* 1.3 63.3 + - - +
241J THR* 3.2 2.3 + - - -
242J TYR* 2.9 22.5 + - - +
342J ASN* 2.9 45.5 + - - +
343J CYS 3.9 0.2 - - - -
344J ASP 3.7 5.2 - - - +
345J ILE* 3.6 34.1 - - + +
347J GLN* 3.9 7.0 + - - +
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Residues in contact with LEU 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J MET* 5.5 0.2 - - + -
220J HIS* 4.1 22.9 - - + -
223J PHE* 3.9 37.9 - - + -
229J LEU* 3.5 26.0 - - + -
234J ILE* 4.3 11.9 - - + -
235J PRO 2.9 10.5 + - - +
236J VAL* 3.2 10.1 + - - +
238J THR* 1.3 76.3 - - - +
240J ILE* 1.3 58.7 + - + +
242J TYR* 3.2 3.5 + - + +
243J LEU* 2.9 58.2 + - + +
345J ILE* 3.5 18.3 - - + +
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Residues in contact with ILE 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J THR* 4.6 9.4 - - + -
220J HIS* 3.5 35.2 - - + +
236J VAL* 3.0 35.3 + - + +
237J ASP* 4.1 5.2 - - - +
239J LEU* 1.3 83.1 - - + +
241J THR* 1.3 64.2 + - - +
243J LEU* 3.9 7.3 - - + +
244J MET* 2.9 57.7 + - + +
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Residues in contact with THR 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J ASP* 2.6 24.1 + - - +
238J THR 3.5 4.7 - - - -
239J LEU 3.2 0.2 - - - -
240J ILE* 1.3 78.2 - - - +
242J TYR* 1.3 60.8 + - - +
244J MET* 3.7 5.7 - - - +
245J THR* 2.8 29.1 + - - +
341J GLU* 3.6 26.5 - - + +
342J ASN* 3.7 15.3 + - - +
343J CYS* 3.7 10.1 - - - -
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Residues in contact with TYR 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J MET* 6.2 0.9 - - + -
238J THR 2.9 8.8 + - - +
239J LEU 3.5 6.1 - - - +
241J THR* 1.3 75.7 - - - +
243J LEU* 1.3 72.5 + - + +
245J THR* 3.0 6.2 + - - -
246J LEU* 2.8 52.5 + - + +
292J PHE* 3.4 32.8 - + - -
296J ILE* 3.7 8.0 - - - +
334J GLY* 2.8 23.3 + - - -
337J LEU* 3.8 24.2 - - + -
338J LEU* 3.5 15.9 - - + -
343J CYS* 3.3 41.3 - - + +
345J ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LEU* 4.8 3.9 - - + +
216J THR* 3.4 47.1 + - + +
219J MET* 3.6 44.4 - - + -
220J HIS* 3.9 9.4 - - + +
239J LEU* 2.9 45.8 + - + +
240J ILE* 3.9 2.7 - - - +
242J TYR* 1.3 83.5 - - + +
244J MET* 1.3 58.4 + - - +
246J LEU* 3.7 10.8 - - + +
247J GLU* 2.8 33.3 + - - +
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Residues in contact with MET 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J ARG* 3.0 48.3 + - + +
216J THR* 3.6 25.1 + - + -
240J ILE* 2.9 41.0 + - + +
241J THR* 3.7 7.2 - - - +
243J LEU* 1.3 76.7 - - - +
245J THR* 1.3 56.9 + - - +
248J ASP* 2.9 32.7 + - - +
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Residues in contact with THR 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J THR* 2.8 16.2 + - - +
242J TYR* 3.0 8.2 + - - -
244J MET* 1.3 73.4 - - - +
246J LEU* 1.3 63.6 + - - +
248J ASP* 3.1 15.5 + - + +
249J HIS* 2.7 47.4 + - + -
337J LEU* 3.7 14.1 - - + -
340J GLU* 3.5 22.3 + - - +
343J CYS* 3.7 13.5 - - - -
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Residues in contact with LEU 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LEU* 4.0 16.4 - - + -
242J TYR* 2.8 43.9 + - + +
243J LEU* 3.7 9.4 - - + +
245J THR* 1.3 72.9 - - - +
247J GLU* 1.3 58.5 + - - +
249J HIS* 2.8 24.4 + - - +
250J TYR* 3.5 9.2 - - + -
295J ALA* 3.8 26.7 - - + +
296J ILE* 3.8 30.1 - - + -
299J VAL* 3.7 29.6 - - + -
334J GLY* 4.6 1.6 - - - -
337J LEU* 3.7 15.0 - - + +
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Residues in contact with GLU 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J ASN* 4.5 2.5 - - - +
213J ARG* 3.4 30.3 - - - +
214J PRO* 3.1 3.1 - - - +
215J LEU* 2.9 39.6 + - + +
216J THR* 2.6 37.1 + - - -
243J LEU 2.8 20.4 + - - +
246J LEU* 1.3 73.3 - - - +
248J ASP* 1.3 62.0 + - - +
250J TYR* 3.1 22.9 + - - +
259J ASN* 2.7 36.6 + - + +
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Residues in contact with ASP 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J ARG* 2.8 27.8 + - - -
244J MET* 2.9 27.6 + - - +
245J THR* 3.3 13.6 - - - +
246J LEU 3.1 0.2 - - - -
247J GLU* 1.3 76.5 - - - +
249J HIS* 1.3 66.3 + - + +
250J TYR 3.2 8.5 + - - +
251J HIS* 5.9 0.2 - - - -
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Residues in contact with HIS 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J THR* 2.7 33.5 + - + +
246J LEU 2.8 11.3 + - - +
248J ASP* 1.3 80.7 - - + +
250J TYR* 1.3 60.9 + - - +
251J HIS* 3.7 6.0 - - - -
299J VAL* 3.6 15.0 - - + -
300J ASP* 3.0 35.6 + - + +
333J VAL* 4.4 12.6 - - + -
337J LEU* 3.6 33.0 - - + +
340J GLU* 5.5 1.3 - - - -
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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