Contacts of the helix formed by residues 235 - 249 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233E LYS 3.4 9.4 - - - +
234E ILE* 1.3 85.3 - - + +
236E VAL* 1.3 58.6 + - - +
237E ASP* 3.1 14.4 - - - +
238E THR* 2.7 48.5 + - + +
239E LEU* 2.9 10.7 + - - +
347E GLN* 3.9 30.3 - - + +
348E ASN* 4.6 2.0 - - - +
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E HIS* 4.0 15.7 - - + +
224E GLN* 4.9 3.1 - - - +
229E LEU* 4.2 28.3 - - + -
234E ILE 3.1 3.8 + - - +
235E PRO* 1.3 70.8 - - - +
237E ASP* 1.3 64.4 + - - +
239E LEU* 3.3 2.0 + - - +
240E ILE* 3.0 46.7 + - + +
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Residues in contact with ASP 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E PRO* 3.9 14.6 - - - +
236E VAL* 1.3 81.3 + - - +
238E THR* 1.3 67.3 + - - +
240E ILE* 4.0 4.9 - - - +
241E THR* 2.7 38.7 + - - +
342E ASN* 3.2 18.3 + - - +
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Residues in contact with THR 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E PRO* 2.7 39.4 + - + +
237E ASP* 1.3 72.9 + - - +
239E LEU* 1.3 64.0 + - - +
241E THR* 3.2 2.3 + - - -
242E TYR* 2.9 23.4 + - - +
342E ASN* 2.9 45.2 + - - +
343E CYS 4.0 0.2 - - - -
344E ASP 3.7 5.6 - - - +
345E ILE* 3.6 33.9 - - + +
347E GLN* 3.9 6.4 + - - +
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Residues in contact with LEU 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E MET* 5.5 0.2 - - + -
220E HIS* 4.2 22.2 - - + -
223E PHE* 3.8 39.3 - - + -
229E LEU* 3.6 24.7 - - + -
234E ILE* 4.3 12.3 - - + -
235E PRO 2.9 9.4 + - - +
236E VAL* 3.5 11.0 - - - +
238E THR* 1.3 79.0 - - - +
240E ILE* 1.3 57.7 + - + +
242E TYR* 3.2 1.4 + - + +
243E LEU* 2.9 52.5 + - + +
345E ILE* 3.5 18.8 - - + +
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Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E THR* 4.5 9.6 - - + -
220E HIS* 3.5 36.1 - - + +
236E VAL* 3.0 35.5 + - + +
237E ASP* 4.1 5.2 - - - +
239E LEU* 1.3 75.3 - - + +
241E THR* 1.3 67.9 + - - +
243E LEU* 3.9 7.6 - - + +
244E MET* 2.9 58.3 + - + +
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Residues in contact with THR 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ASP* 2.7 23.9 + - - +
238E THR 3.5 4.7 - - - -
240E ILE* 1.3 78.3 - - - +
242E TYR* 1.3 61.3 + - - +
244E MET* 3.6 5.7 - - - +
245E THR* 2.8 28.7 + - - +
341E GLU* 3.6 25.1 - - + +
342E ASN* 3.8 15.7 + - - +
343E CYS* 3.8 9.9 - - - -
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Residues in contact with TYR 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E MET* 6.2 0.9 - - + -
238E THR 2.9 12.9 + - - +
239E LEU* 3.6 3.1 - - + +
241E THR* 1.3 74.4 - - - +
243E LEU* 1.3 67.7 + - + +
245E THR* 3.0 7.3 + - - -
246E LEU* 2.7 57.4 + - + +
292E PHE* 3.4 33.3 - + - -
296E ILE* 3.7 7.4 - - - +
334E GLY* 2.7 23.8 + - - -
337E LEU* 3.7 24.0 - - + +
338E LEU* 3.5 15.3 - - + -
343E CYS* 3.3 41.0 - - + +
345E ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.7 3.4 - - + +
216E THR* 3.4 47.4 + - + +
219E MET* 3.5 45.3 - - + -
220E HIS* 3.9 9.2 - - + +
239E LEU* 2.9 47.6 + - + +
240E ILE* 3.9 2.9 - - - +
242E TYR* 1.3 81.2 - - + +
244E MET* 1.3 57.1 + - - +
246E LEU* 3.7 11.2 - - + +
247E GLU* 2.8 33.3 + - - +
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Residues in contact with MET 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ARG* 3.0 48.3 + - + +
216E THR* 3.6 25.1 - - + -
240E ILE* 2.9 40.6 + - + +
241E THR* 3.6 7.0 - - - +
243E LEU* 1.3 76.9 - - - +
245E THR* 1.3 56.2 + - - +
248E ASP* 2.9 32.7 + - - +
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Residues in contact with THR 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E THR* 2.8 16.0 + - - +
242E TYR* 3.0 7.9 + - - -
244E MET* 1.3 75.1 - - - +
246E LEU* 1.3 64.1 + - - +
248E ASP* 3.1 15.4 + - + +
249E HIS* 2.8 47.3 + - + -
337E LEU* 3.7 12.8 - - + -
340E GLU* 3.4 23.4 + - - +
343E CYS* 3.9 13.0 - - - -
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Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.0 16.6 - - + -
242E TYR* 2.7 45.0 + - + +
243E LEU* 3.7 10.1 - - + +
245E THR* 1.3 72.2 - - - +
247E GLU* 1.3 64.7 + - - +
249E HIS* 2.8 18.9 + - - +
250E TYR* 3.5 11.4 - - + -
295E ALA* 3.7 26.7 - - + +
296E ILE* 3.8 29.4 - - + -
299E VAL* 3.8 26.9 - - + -
334E GLY* 4.7 1.6 - - - -
337E LEU* 3.7 14.5 - - + +
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Residues in contact with GLU 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ASN* 4.4 2.5 - - - +
213E ARG* 3.4 31.2 - - - +
214E PRO* 3.1 3.5 - - - +
215E LEU* 3.0 40.6 + - + +
216E THR* 2.6 36.6 + - - -
243E LEU 2.8 19.8 + - - +
246E LEU* 1.3 74.0 - - - +
248E ASP* 1.3 62.6 + - - +
250E TYR* 3.1 23.4 + - - +
259E ASN* 2.7 36.6 + - + +
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Residues in contact with ASP 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ARG* 2.7 28.4 + - - -
244E MET* 2.9 27.9 + - - +
245E THR* 3.1 14.1 + - + +
247E GLU* 1.3 76.7 - - - +
249E HIS* 1.3 62.3 + - + +
250E TYR 3.3 10.2 + - - +
251E HIS* 5.9 0.2 - - - -
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Residues in contact with HIS 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E THR* 2.8 35.2 + - + -
246E LEU 2.8 12.6 + - - +
248E ASP* 1.3 80.4 - - + +
250E TYR* 1.3 59.4 + - - +
251E HIS* 3.7 5.8 + - - -
299E VAL* 3.6 15.0 - - + -
300E ASP* 3.0 36.8 + - + +
333E VAL* 4.4 12.8 - - + -
337E LEU* 3.5 33.2 - - + +
340E 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