Contacts of the helix formed by residues 235 - 249 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233G LYS 3.4 9.9 - - - +
234G ILE* 1.3 86.3 - - + +
236G VAL* 1.3 56.7 + - - +
237G ASP* 3.1 15.3 - - - +
238G THR* 2.7 47.4 + - + +
239G LEU* 2.9 10.9 + - - +
345G ILE 5.0 0.4 - - - +
347G GLN* 3.8 30.1 - - + +
348G ASN* 4.6 2.2 - - - +
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Residues in contact with VAL 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G HIS* 4.0 15.3 - - + +
224G GLN* 5.0 3.4 - - - +
229G LEU* 4.2 28.9 - - + -
234G ILE 3.1 5.1 + - - +
235G PRO* 1.3 70.4 - - - +
237G ASP* 1.3 64.9 + - - +
239G LEU* 3.3 1.7 + - - +
240G ILE* 3.0 47.5 + - + +
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Residues in contact with ASP 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G PRO* 3.9 14.4 - - - +
236G VAL* 1.3 80.2 + - - +
238G THR* 1.3 65.9 + - - +
240G ILE* 3.6 4.9 + - - +
241G THR* 2.6 38.2 + - - +
342G ASN* 3.2 17.8 + - - +
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Residues in contact with THR 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G PRO* 2.7 39.4 + - + +
237G ASP* 1.3 72.5 + - - +
239G LEU* 1.3 63.1 + - - +
241G THR* 3.2 2.4 + - - -
242G TYR* 2.9 23.9 + - - +
342G ASN* 2.9 43.8 + - - +
343G CYS 4.0 0.2 - - - -
344G ASP 3.7 5.8 - - - +
345G ILE* 3.6 34.3 - - + +
347G GLN* 3.9 6.9 + - - +
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Residues in contact with LEU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G MET* 5.5 0.4 - - + -
220G HIS* 4.2 21.3 - - + -
223G PHE* 3.8 39.7 - - + -
229G LEU* 3.5 26.5 - - + -
234G ILE* 4.2 12.1 - - + -
235G PRO 2.9 9.4 + - - +
236G VAL* 3.5 10.8 - - - +
238G THR* 1.3 78.5 - - - +
240G ILE* 1.3 58.6 + - + +
242G TYR* 3.6 1.3 - - + +
243G LEU* 2.9 51.8 + - + +
345G ILE* 3.5 18.6 - - + +
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Residues in contact with ILE 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G THR* 4.5 9.0 - - + -
220G HIS* 3.4 36.6 - - + +
236G VAL* 3.0 37.6 + - + +
237G ASP* 4.1 4.3 - - - +
239G LEU* 1.3 82.5 - - + +
241G THR* 1.3 64.8 + - - +
243G LEU* 3.9 6.7 - - + +
244G MET* 2.9 52.1 + - + +
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Residues in contact with THR 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G ASP* 2.6 24.9 + - - +
238G THR 3.5 4.5 - - - -
240G ILE* 1.3 78.7 - - - +
242G TYR* 1.3 60.8 - - - +
244G MET* 3.6 6.1 - - - +
245G THR* 2.9 29.3 + - - +
341G GLU* 3.6 25.6 - - + +
342G ASN* 3.8 16.0 + - - +
343G CYS* 3.8 9.0 - - - -
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Residues in contact with TYR 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G MET* 6.2 1.3 - - + -
238G THR 2.9 13.0 + - - +
239G LEU 3.6 3.1 - - - +
241G THR* 1.3 75.3 - - - +
243G LEU* 1.3 67.1 + - + +
245G THR* 3.0 6.9 + - - -
246G LEU* 2.8 56.0 + - + +
292G PHE* 3.4 32.6 - + - -
296G ILE* 3.6 8.5 - - - +
334G GLY* 2.7 24.6 + - - -
337G LEU* 3.7 25.4 - - + -
338G LEU* 3.7 16.2 - - + -
343G CYS* 3.4 40.6 - - + +
345G ILE* 3.8 17.5 - - + -
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Residues in contact with LEU 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G LEU* 5.0 3.6 - - + +
216G THR* 3.4 47.6 + - + +
219G MET* 3.5 44.9 - - + -
220G HIS* 3.9 9.4 - - + +
239G LEU* 2.9 46.3 + - + +
240G ILE* 3.9 2.5 - - - +
242G TYR* 1.3 81.0 - - + +
244G MET* 1.3 57.3 + - - +
246G LEU* 3.7 12.2 - - + +
247G GLU* 2.8 33.6 + - - +
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Residues in contact with MET 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G ARG* 3.0 48.8 + - + +
216G THR* 3.5 25.1 + - + -
240G ILE* 2.9 41.4 + - + +
241G THR* 3.6 7.4 - - - +
243G LEU* 1.3 77.1 - - - +
245G THR* 1.3 58.1 + - - +
248G ASP* 2.9 32.6 + - - +
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Residues in contact with THR 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G THR* 2.9 16.0 + - - +
242G TYR* 3.0 8.8 + - - -
244G MET* 1.3 74.6 - - - +
246G LEU* 1.3 63.5 + - - +
248G ASP* 3.1 15.5 + - + +
249G HIS* 2.7 48.3 + - + -
337G LEU* 3.8 12.6 - - + -
340G GLU* 3.4 22.1 + - - +
343G CYS* 3.9 12.8 - - - -
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Residues in contact with LEU 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G LEU* 4.0 16.2 - - + -
242G TYR* 2.8 43.5 + - + +
243G LEU* 3.7 11.0 - - + +
245G THR* 1.3 73.5 - - - +
247G GLU* 1.3 59.2 + - - +
249G HIS* 2.8 24.3 + - - +
250G TYR* 3.5 10.3 - - + -
295G ALA* 3.8 26.9 - - + +
296G ILE* 3.7 31.0 - - + -
299G VAL* 3.8 27.1 - - + -
334G GLY* 4.7 1.3 - - - -
337G LEU* 3.7 14.3 - - + +
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Residues in contact with GLU 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ASN* 4.4 2.7 - - - +
213G ARG* 3.3 30.6 - - - +
214G PRO* 3.1 3.5 - - - +
215G LEU* 2.9 40.7 + - + +
216G THR* 2.6 37.1 + - - -
243G LEU 2.8 20.0 + - - +
246G LEU* 1.3 73.5 - - - +
248G ASP* 1.3 63.5 + - - +
250G TYR* 3.0 22.9 + - - +
259G ASN* 2.7 36.2 + - + +
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Residues in contact with ASP 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ARG* 2.8 28.8 + - - -
244G MET* 2.9 28.0 + - - +
245G THR* 3.1 14.1 + - + +
247G GLU* 1.3 76.7 - - - +
249G HIS* 1.3 63.3 + - + +
250G TYR 3.1 10.0 + - - +
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Residues in contact with HIS 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G THR* 2.7 35.2 + - + -
246G LEU 2.8 12.6 + - - +
248G ASP* 1.3 79.8 - - + +
250G TYR* 1.3 59.9 + - - +
251G HIS* 3.7 5.8 + - - -
299G VAL* 3.6 15.0 - - + -
300G ASP* 2.9 36.3 + - + +
333G VAL* 4.4 11.7 - - + -
337G LEU* 3.6 33.4 - - + +
340G 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