Contacts of the helix formed by residues 235 - 249 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233I LYS 3.4 9.0 - - - +
234I ILE* 1.3 84.9 - - + +
236I VAL* 1.3 57.0 + - - +
237I ASP* 3.1 14.1 - - - +
238I THR* 2.7 49.0 + - + +
239I LEU* 2.9 10.6 + - - +
347I GLN* 3.8 31.2 - - + +
348I ASN* 4.6 2.2 - - - +
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Residues in contact with VAL 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I HIS* 4.0 15.0 - - + +
224I GLN* 4.9 3.6 - - - +
229I LEU* 4.2 29.6 - - + -
234I ILE 3.2 4.0 + - - +
235I PRO* 1.3 70.2 - - - +
237I ASP* 1.3 65.4 + - - +
239I LEU* 3.2 2.5 + - - +
240I ILE* 3.0 46.9 + - + +
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Residues in contact with ASP 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235I PRO* 3.9 14.3 - - - +
236I VAL* 1.3 79.8 + - - +
238I THR* 1.3 66.9 + - - +
240I ILE* 4.0 4.8 - - - +
241I THR* 2.6 39.4 + - - +
342I ASN* 3.2 17.3 + - - +
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Residues in contact with THR 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235I PRO* 2.7 33.5 + - + +
237I ASP* 1.3 78.1 + - - +
239I LEU* 1.3 62.5 + - - +
241I THR* 3.3 2.4 + - - -
242I TYR* 3.0 22.9 + - - +
342I ASN* 2.9 43.8 + - - +
343I CYS 4.0 0.2 - - - -
344I ASP 3.7 5.2 - - - +
345I ILE* 3.7 34.3 - - + +
347I GLN* 3.9 6.7 + - - +
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Residues in contact with LEU 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I MET* 5.5 0.2 - - + -
220I HIS* 4.2 21.8 - - + -
223I PHE* 3.9 38.4 - - + -
229I LEU* 3.6 25.4 - - + -
234I ILE* 4.2 11.7 - - + -
235I PRO 2.9 9.8 + - - +
236I VAL* 3.2 11.4 + - - +
238I THR* 1.3 77.0 - - - +
240I ILE* 1.3 58.6 + - + +
242I TYR* 3.3 3.0 + - + +
243I LEU* 2.9 51.7 + - + +
345I ILE* 3.5 18.8 - - + +
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Residues in contact with ILE 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I THR* 4.6 9.0 - - + -
220I HIS* 3.5 35.9 - - + +
236I VAL* 3.0 36.4 + - + +
237I ASP* 4.1 5.2 - - - +
239I LEU* 1.3 79.0 - - + +
241I THR* 1.3 68.1 + - - +
243I LEU* 3.8 6.4 - - + +
244I MET* 2.9 58.2 + - + +
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Residues in contact with THR 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I ASP* 2.6 25.0 + - - +
238I THR 3.6 4.7 - - - -
239I LEU 3.3 0.2 - - - -
240I ILE* 1.3 78.0 - - - +
242I TYR* 1.3 61.1 + - - +
244I MET* 3.5 6.5 + - - +
245I THR* 2.8 29.1 + - - +
341I GLU* 3.6 26.0 - - + +
342I ASN* 3.8 14.8 + - - +
343I CYS* 3.7 9.6 - - - -
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Residues in contact with TYR 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I MET* 6.2 0.9 - - + -
238I THR 3.0 12.9 + - - +
239I LEU 3.6 3.4 - - - +
241I THR* 1.3 74.5 - - - +
243I LEU* 1.3 66.4 + - + +
245I THR* 3.0 7.1 + - - -
246I LEU* 2.7 56.2 + - + +
292I PHE* 3.4 32.3 - + - -
296I ILE* 3.7 7.8 - - - +
334I GLY* 2.7 24.1 + - - -
337I LEU* 3.7 24.9 - - + +
338I LEU* 3.6 17.3 - - + -
343I CYS* 3.3 41.5 - - + +
345I ILE* 3.9 17.0 - - + -
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Residues in contact with LEU 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU* 4.8 3.8 - - + +
216I THR* 3.4 46.5 + - + +
219I MET* 3.5 45.5 - - + -
220I HIS* 3.9 9.9 - - + +
239I LEU* 2.9 47.3 + - + +
240I ILE* 3.8 3.1 - - - +
242I TYR* 1.3 80.6 - - + +
244I MET* 1.3 57.4 + - - +
246I LEU* 3.7 12.2 - - + +
247I GLU* 2.8 33.1 + - - +
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Residues in contact with MET 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I ARG* 3.0 48.5 + - + +
216I THR* 3.5 26.2 - - + -
240I ILE* 2.9 41.0 + - + +
241I THR* 3.6 7.6 - - - +
243I LEU* 1.3 76.2 - - - +
245I THR* 1.3 58.6 + - - +
248I ASP* 2.9 32.9 + - - +
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Residues in contact with THR 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I THR* 2.8 15.6 + - - +
242I TYR* 3.0 8.1 + - - -
244I MET* 1.3 74.6 - - - +
246I LEU* 1.3 63.9 + - - +
248I ASP* 3.1 9.9 + - + +
249I HIS* 2.7 52.8 + - + -
337I LEU* 3.7 13.7 - - + -
340I GLU* 3.5 22.2 + - - +
343I CYS* 3.8 13.1 - - - -
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Residues in contact with LEU 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LEU* 4.0 16.4 - - + -
219I MET* 5.8 0.2 - - + -
242I TYR* 2.7 44.6 + - + +
243I LEU* 3.7 9.9 - - + +
245I THR* 1.3 74.1 - - - +
247I GLU* 1.3 63.0 + - - +
249I HIS* 2.9 18.5 + - - +
250I TYR* 3.5 10.3 - - + -
295I ALA* 3.8 26.2 - - + +
296I ILE* 3.8 29.4 - - + -
299I VAL* 3.7 27.8 - - + -
334I GLY* 4.7 1.3 - - - -
337I LEU* 3.7 13.6 - - + +
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Residues in contact with GLU 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I ASN* 4.1 2.5 - - - +
213I ARG* 3.3 30.3 - - - +
214I PRO* 3.1 3.1 - - - +
215I LEU* 2.9 40.4 + - + +
216I THR* 2.6 37.4 + - - -
243I LEU 2.8 16.8 + - - +
246I LEU* 1.3 77.7 - - - +
248I ASP* 1.3 61.4 - - - +
250I TYR* 3.1 22.1 + - - +
259I ASN* 2.7 36.4 + - + +
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Residues in contact with ASP 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213I ARG* 2.7 28.0 + - - -
244I MET* 2.9 27.3 + - - +
245I THR* 3.3 14.1 - - + +
246I LEU 3.1 0.4 - - - -
247I GLU* 1.3 75.8 - - - +
249I HIS* 1.3 64.8 + - + +
250I TYR 3.2 10.1 + - - +
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Residues in contact with HIS 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I THR* 2.7 33.4 + - + +
246I LEU 2.9 11.8 + - - +
248I ASP* 1.3 79.5 - - + +
250I TYR* 1.3 60.1 + - - +
251I HIS* 3.7 5.4 + - - -
299I VAL* 3.6 14.4 - - + -
300I ASP* 2.9 36.3 + - + +
333I VAL* 4.4 12.8 - - + -
337I LEU* 3.6 33.6 - - + +
340I 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