Contacts of the helix formed by residues 235 - 249 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233H LYS 3.4 9.4 - - - +
234H ILE* 1.3 86.4 - - + +
236H VAL* 1.3 57.8 + - - +
237H ASP* 3.1 14.6 - - - +
238H THR* 2.7 48.0 + - + +
239H LEU* 2.9 10.4 + - - +
345H ILE 5.0 0.9 - - - +
347H GLN* 3.8 31.6 - - + +
348H ASN* 4.6 1.6 - - - +
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Residues in contact with VAL 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220H HIS* 4.0 14.8 - - + +
224H GLN* 4.9 3.6 - - - +
229H LEU* 4.2 29.6 - - + -
234H ILE 3.1 5.3 + - - +
235H PRO* 1.3 70.3 - - - +
237H ASP* 1.3 64.4 + - - +
239H LEU* 3.2 2.2 + - - +
240H ILE* 3.0 46.6 + - + +
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Residues in contact with ASP 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H PRO* 3.8 14.5 - - - +
236H VAL* 1.3 79.7 + - - +
238H THR* 1.3 67.5 + - - +
240H ILE* 3.9 4.9 - - - +
241H THR* 2.6 39.1 + - - +
342H ASN* 3.1 17.9 + - - +
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Residues in contact with THR 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H PRO* 2.7 39.1 + - + +
237H ASP* 1.3 72.9 + - - +
239H LEU* 1.3 63.7 + - - +
241H THR* 3.2 2.5 + - - -
242H TYR* 2.9 23.2 + - - +
342H ASN* 2.9 46.5 + - - +
343H CYS 4.0 0.2 - - - -
344H ASP 3.7 6.3 - - - +
345H ILE* 3.7 32.1 - - + +
347H GLN* 4.0 6.9 + - - +
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Residues in contact with LEU 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H MET* 5.5 0.2 - - + -
220H HIS* 4.2 21.3 - - + -
223H PHE* 3.8 38.8 - - + -
229H LEU* 3.6 25.1 - - + -
234H ILE* 4.3 12.3 - - + -
235H PRO 2.9 9.6 + - - +
236H VAL* 3.5 11.0 - - - +
238H THR* 1.3 78.1 - - - +
240H ILE* 1.3 57.5 + - + +
242H TYR* 3.2 1.6 + - + +
243H LEU* 2.9 51.0 + - + +
345H ILE* 3.5 18.5 - - + +
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Residues in contact with ILE 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H THR* 4.6 9.2 - - + -
220H HIS* 3.5 37.2 - - + +
236H VAL* 3.0 36.6 + - + +
237H ASP* 4.1 5.2 - - - +
239H LEU* 1.3 81.9 - - + +
241H THR* 1.3 65.2 + - - +
243H LEU* 3.8 7.1 - - + +
244H MET* 2.9 58.1 + - + +
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Residues in contact with THR 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H ASP* 2.6 27.2 + - - +
238H THR 3.2 4.9 + - - -
240H ILE* 1.3 78.9 - - - +
242H TYR* 1.3 61.0 + - - +
244H MET* 3.6 5.5 - - - +
245H THR* 2.8 29.5 + - - +
341H GLU* 3.6 25.8 - - + +
342H ASN* 3.8 16.4 + - - +
343H CYS* 3.7 9.4 - - - -
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Residues in contact with TYR 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H MET* 6.2 0.2 - - + -
238H THR 2.9 13.4 + - - +
239H LEU 3.6 3.4 - - - +
241H THR* 1.3 74.7 - - - +
243H LEU* 1.3 67.2 + - + +
245H THR* 3.0 6.9 + - - -
246H LEU* 2.8 56.4 + - + +
292H PHE* 3.4 33.3 - + - -
296H ILE* 3.7 8.1 - - - +
334H GLY* 2.8 23.6 + - - -
337H LEU* 3.7 24.2 - - + -
338H LEU* 3.6 17.0 - - + -
343H CYS* 3.3 42.1 - - + +
345H ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 4.8 4.0 - - + +
216H THR* 3.4 46.8 + - + +
219H MET* 3.5 44.9 - - + -
220H HIS* 3.9 9.6 - - + +
239H LEU* 2.9 42.5 + - + +
240H ILE* 3.8 3.1 - - - +
242H TYR* 1.3 84.0 - - + +
244H MET* 1.3 56.9 + - - +
246H LEU* 3.6 12.8 - - + +
247H GLU* 2.8 33.8 + - - +
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Residues in contact with MET 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H ARG* 3.0 49.0 + - + +
216H THR* 3.6 24.9 - - + -
240H ILE* 2.9 41.2 + - + +
241H THR* 3.6 6.7 - - - +
243H LEU* 1.3 76.4 - - - +
245H THR* 1.3 57.1 + - - +
248H ASP* 2.9 32.9 + - - +
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Residues in contact with THR 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H THR* 2.8 16.3 + - - +
242H TYR* 3.0 8.1 + - - -
244H MET* 1.3 74.0 - - - +
246H LEU* 1.3 63.6 + - - +
248H ASP* 3.1 10.2 + - + +
249H HIS* 2.7 53.2 + - + -
337H LEU* 3.7 13.7 - - + -
340H GLU* 3.4 22.6 + - - +
343H CYS* 3.8 12.8 - - - -
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 4.0 16.2 - - + -
219H MET* 5.8 0.2 - - + -
242H TYR* 2.8 44.2 + - + +
243H LEU* 3.6 9.2 - - + +
245H THR* 1.3 72.9 - - - +
247H GLU* 1.3 64.8 + - - +
249H HIS* 2.9 18.2 + - - +
250H TYR* 3.5 9.6 - - + -
295H ALA* 3.8 27.1 - - + +
296H ILE* 3.8 31.0 - - + -
299H VAL* 3.8 26.7 - - + -
334H GLY* 4.6 1.6 - - - -
337H LEU* 3.7 15.4 - - + +
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Residues in contact with GLU 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H ASN* 4.4 2.5 - - - +
213H ARG* 3.4 32.7 - - - +
214H PRO* 3.1 2.8 - - - +
215H LEU* 2.9 40.2 + - + +
216H THR* 2.6 37.8 + - - -
243H LEU 2.8 19.5 + - - +
246H LEU* 1.3 72.7 - - - +
248H ASP* 1.3 62.9 + - - +
250H TYR* 3.0 23.6 + - - +
259H ASN* 2.7 35.4 + - + +
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Residues in contact with ASP 248 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H ARG* 2.7 28.6 + - - -
244H MET* 2.9 27.8 + - - +
245H THR* 3.1 13.9 + - + +
247H GLU* 1.3 76.0 - - - +
249H HIS* 1.3 64.2 + - + +
250H TYR 3.2 10.0 + - - +
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Residues in contact with HIS 249 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H THR* 2.7 34.6 + - + -
246H LEU 2.9 12.2 + - - +
248H ASP* 1.3 81.0 - - + +
250H TYR* 1.3 58.9 + - - +
251H HIS* 3.7 5.9 + - - -
299H VAL* 3.6 14.1 - - + -
300H ASP* 2.9 36.0 + - + +
333H VAL* 4.5 11.7 - - + -
337H LEU* 3.5 32.8 - - + +
340H 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
------------------------------------------------------------
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