Contacts of the helix formed by residues 235 - 249 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233K LYS 3.4 9.9 - - - +
234K ILE* 1.3 85.4 - - + +
236K VAL* 1.3 57.9 + - - +
237K ASP* 3.1 15.0 - - - +
238K THR* 2.7 46.9 + - + +
239K LEU* 2.9 11.1 + - - +
345K ILE 5.0 0.2 - - - +
347K GLN* 3.9 29.8 - - + +
348K ASN* 4.6 1.6 - - - +
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Residues in contact with VAL 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K HIS* 4.0 14.6 - - + +
224K GLN* 4.9 3.6 - - - +
229K LEU* 4.2 30.1 - - + -
234K ILE 3.1 4.7 + - - +
235K PRO* 1.3 69.6 - - - +
237K ASP* 1.3 64.9 + - - +
239K LEU* 3.2 1.5 + - - +
240K ILE* 3.0 46.8 + - + +
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Residues in contact with ASP 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235K PRO* 3.9 14.5 - - - +
236K VAL* 1.3 80.5 + - - +
238K THR* 1.3 66.7 + - - +
240K ILE* 3.5 5.3 + - - +
241K THR* 2.6 39.6 + - - +
342K ASN* 3.2 17.3 + - - +
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Residues in contact with THR 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K PRO* 2.7 38.8 + - + +
237K ASP* 1.3 73.6 + - - +
239K LEU* 1.3 62.7 + - - +
241K THR* 3.2 2.1 + - - -
242K TYR* 2.9 23.2 + - - +
342K ASN* 2.9 47.6 + - - +
343K CYS 4.0 0.4 - - - -
344K ASP 3.7 5.6 - - - +
345K ILE* 3.7 32.5 - - + +
347K GLN* 3.9 6.3 + - - +
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Residues in contact with LEU 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K HIS* 4.2 22.9 - - + -
223K PHE* 3.9 39.5 - - + -
229K LEU* 3.6 25.4 - - + -
234K ILE* 4.3 11.7 - - + -
235K PRO 2.9 9.2 + - - +
236K VAL* 3.2 11.0 + - - +
238K THR* 1.3 77.3 - - - +
240K ILE* 1.3 58.1 + - + +
242K TYR* 3.2 2.0 + - + +
243K LEU* 2.8 53.1 + - + +
345K ILE* 3.5 19.0 - - + +
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Residues in contact with ILE 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K THR* 4.5 9.6 - - + -
220K HIS* 3.4 36.1 - - + +
236K VAL* 3.0 37.5 + - + +
237K ASP* 4.1 5.4 - - - +
239K LEU* 1.3 80.1 - - + +
241K THR* 1.3 66.8 + - - +
243K LEU* 3.9 6.5 - - + +
244K MET* 2.9 58.4 + - + +
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Residues in contact with THR 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K ASP* 2.6 25.0 + - - +
238K THR 3.5 4.9 - - - -
240K ILE* 1.3 77.8 - - - +
242K TYR* 1.3 60.5 + - - +
244K MET* 3.5 5.6 + - - +
245K THR* 2.9 29.2 + - - +
341K GLU* 3.6 26.2 - - + +
342K ASN* 3.8 15.5 + - - +
343K CYS* 3.7 9.6 - - - -
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Residues in contact with TYR 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K MET* 6.2 0.9 - - + -
238K THR 2.9 13.2 + - - +
239K LEU* 3.5 3.6 - - + +
241K THR* 1.3 74.5 - - - +
243K LEU* 1.3 68.8 + - + +
245K THR* 3.0 4.8 + - - -
246K LEU* 2.8 57.0 + - + +
292K PHE* 3.4 32.5 - + - -
296K ILE* 3.7 8.0 - - - +
334K GLY* 2.7 24.3 + - - -
337K LEU* 3.7 24.4 - - + +
338K LEU* 3.6 15.9 - - + -
343K CYS* 3.3 44.6 - - + +
345K ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K LEU* 5.0 3.2 - - + +
216K THR* 3.4 47.9 + - + +
219K MET* 3.5 45.3 - - + -
220K HIS* 3.9 9.9 - - + +
239K LEU* 2.8 46.0 + - + +
240K ILE* 3.9 2.9 - - - +
242K TYR* 1.3 79.9 - - + +
244K MET* 1.3 58.1 + - - +
246K LEU* 3.6 12.5 - - + +
247K GLU* 2.8 33.4 + - - +
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Residues in contact with MET 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K ARG* 3.0 48.8 + - + +
216K THR* 3.6 25.1 + - + -
240K ILE* 2.9 42.7 + - + +
241K THR* 3.6 6.5 - - - +
243K LEU* 1.3 76.1 - - - +
245K THR* 1.3 56.8 + - - +
248K ASP* 2.9 32.3 + - - +
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Residues in contact with THR 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K THR* 2.9 15.6 + - - +
242K TYR* 3.0 8.2 + - - -
244K MET* 1.3 75.3 - - - +
246K LEU* 1.3 63.8 + - - +
248K ASP* 3.1 10.7 + - + +
249K HIS* 2.7 52.2 + - + -
337K LEU* 3.7 12.6 - - + -
340K GLU* 3.4 23.1 + - - +
343K CYS* 3.8 12.8 - - - -
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Residues in contact with LEU 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K LEU* 3.9 16.2 - - + -
242K TYR* 2.8 43.3 + - + +
243K LEU* 3.6 10.3 - - + +
245K THR* 1.3 72.0 - - - +
247K GLU* 1.3 55.7 + - - +
249K HIS* 2.8 28.2 + - - +
250K TYR* 3.5 10.7 - - + -
295K ALA* 3.7 26.9 - - + +
296K ILE* 3.7 29.8 - - + -
299K VAL* 3.7 27.4 - - + -
334K GLY* 4.7 1.6 - - - -
337K LEU* 3.7 13.9 - - + +
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Residues in contact with GLU 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K ASN* 4.4 2.5 - - - +
213K ARG* 3.4 33.6 - - - +
214K PRO* 3.1 3.1 - - - +
215K LEU* 2.9 41.1 + - + +
216K THR* 2.5 36.4 + - - +
243K LEU 2.8 19.8 + - - +
246K LEU* 1.3 73.6 - - - +
248K ASP* 1.3 61.9 + - - +
250K TYR* 3.1 24.1 + - - +
259K ASN* 2.8 34.9 + - + +
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Residues in contact with ASP 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213K ARG* 2.8 27.9 + - - -
244K MET* 2.9 28.6 + - - +
245K THR* 3.3 13.6 - - + +
246K LEU 3.1 0.2 - - - -
247K GLU* 1.3 76.2 - - - +
249K HIS* 1.3 63.0 + - + +
250K TYR 3.1 10.2 + - - +
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Residues in contact with HIS 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245K THR* 2.7 35.0 + - + -
246K LEU 2.8 12.2 + - - +
248K ASP* 1.3 79.9 - - + +
250K TYR* 1.3 59.8 + - - +
251K HIS* 3.7 6.2 + - - -
299K VAL* 3.6 14.6 - - + -
300K ASP* 2.9 35.9 + - + +
333K VAL* 4.4 12.6 - - + -
337K LEU* 3.5 33.0 - - + +
340K GLU* 5.5 1.6 - - - -
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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