Contacts of the helix formed by residues 235 - 249 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D LYS 3.4 9.6 - - - +
234D ILE* 1.3 85.5 - - + +
236D VAL* 1.3 58.7 + - - +
237D ASP* 3.1 14.8 - - - +
238D THR* 2.7 48.4 + - + +
239D LEU* 2.9 10.7 + - - +
345D ILE 5.0 0.4 - - - +
347D GLN* 3.9 29.8 - - + +
348D ASN* 4.4 2.2 - - - +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D HIS* 4.0 15.5 - - + +
224D GLN* 4.9 3.4 - - - +
229D LEU* 4.2 29.6 - - + -
234D ILE 3.1 4.3 + - - +
235D PRO* 1.3 70.3 - - - +
237D ASP* 1.3 63.7 + - - +
239D LEU* 3.3 2.0 + - - +
240D ILE* 3.0 46.5 + - + +
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Residues in contact with ASP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D PRO* 3.9 15.0 - - - +
236D VAL* 1.3 77.2 + - - +
238D THR* 1.3 67.0 + - - +
240D ILE* 3.6 5.3 + - - +
241D THR* 2.6 39.6 + - - +
342D ASN* 3.2 18.1 + - - +
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D PRO* 2.7 39.6 + - + +
237D ASP* 1.3 72.7 + - - +
239D LEU* 1.3 62.9 + - - +
241D THR* 3.2 2.4 + - - -
242D TYR* 2.9 23.2 + - - +
342D ASN* 2.9 44.2 + - - +
343D CYS 4.0 0.2 - - - -
344D ASP 3.7 5.6 - - - +
345D ILE* 3.7 34.1 - - + +
347D GLN* 3.9 6.2 + - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET* 5.4 0.2 - - + -
220D HIS* 4.2 22.2 - - + -
223D PHE* 3.9 39.0 - - + -
229D LEU* 3.6 26.2 - - + -
234D ILE* 4.3 12.1 - - + -
235D PRO 2.9 9.2 + - - +
236D VAL* 3.5 10.8 - - - +
238D THR* 1.3 76.4 - - - +
240D ILE* 1.3 58.9 + - - +
242D TYR* 3.2 3.2 + - + +
243D LEU* 2.9 52.0 + - + +
345D ILE* 3.5 18.8 - - + +
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Residues in contact with ILE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D THR* 4.6 9.4 - - + -
220D HIS* 3.5 35.7 - - + +
236D VAL* 3.0 35.7 + - + +
237D ASP* 4.1 4.9 - - - +
239D LEU* 1.3 82.4 - - + +
241D THR* 1.3 63.6 + - - +
243D LEU* 3.8 6.7 - - + +
244D MET* 2.9 57.7 + - + +
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Residues in contact with THR 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ASP* 2.6 28.0 + - - +
238D THR 3.5 4.3 - - - -
240D ILE* 1.3 78.5 - - - +
242D TYR* 1.3 60.5 + - - +
244D MET* 3.6 6.0 - - - +
245D THR* 2.8 28.9 + - - +
341D GLU* 3.6 27.1 - - + +
342D ASN* 3.8 15.2 + - - +
343D CYS* 3.7 9.2 - - - -
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Residues in contact with TYR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET* 6.2 1.1 - - + -
238D THR 2.9 13.4 + - - +
239D LEU 3.6 3.1 - - - +
241D THR* 1.3 74.9 - - - +
243D LEU* 1.3 67.6 + - + +
245D THR* 2.9 8.2 + - - -
246D LEU* 2.7 56.8 + - + +
292D PHE* 3.4 33.2 - + - -
296D ILE* 3.7 7.6 - - - +
334D GLY* 2.8 24.6 + - - -
337D LEU* 3.7 24.4 - - + +
338D LEU* 3.6 16.4 - - + -
343D CYS* 3.3 41.7 - - + +
345D ILE* 3.9 17.0 - - + -
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 4.7 3.2 - - + +
216D THR* 3.4 47.0 + - + +
219D MET* 3.5 44.2 - - + -
220D HIS* 3.9 9.4 - - + +
239D LEU* 2.9 46.0 + - + +
240D ILE* 3.8 2.9 - - + +
242D TYR* 1.3 79.8 - - + +
244D MET* 1.3 57.9 + - - +
246D LEU* 3.7 12.9 - - + +
247D GLU* 2.8 33.6 + - - +
345D ILE* 6.4 0.2 - - + -
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Residues in contact with MET 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ARG* 3.0 49.3 + - + +
216D THR* 3.6 24.9 - - + -
240D ILE* 2.9 40.4 + - + +
241D THR* 3.6 7.2 - - - +
243D LEU* 1.3 76.0 - - - +
245D THR* 1.3 57.9 + - - +
248D ASP* 2.9 32.6 + - - +
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Residues in contact with THR 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D THR* 2.8 16.1 + - - +
242D TYR* 2.9 8.1 + - - -
244D MET* 1.3 74.4 - - - +
246D LEU* 1.3 63.8 + - - +
248D ASP* 3.0 16.1 + - + +
249D HIS* 2.8 46.3 + - + -
337D LEU* 3.7 13.9 - - + -
340D GLU* 3.4 22.5 + - - +
343D CYS* 3.9 12.7 - - - -
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Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 4.0 15.9 - - + -
242D TYR* 2.7 43.2 + - + +
243D LEU* 3.7 10.3 - - + +
245D THR* 1.3 73.2 - - - +
247D GLU* 1.3 58.7 + - - +
249D HIS* 2.8 25.8 + - - +
250D TYR* 3.5 10.1 - - + -
295D ALA* 3.8 25.8 - - + +
296D ILE* 3.8 29.2 - - + -
299D VAL* 3.7 27.8 - - + -
334D GLY* 4.7 1.6 - - - -
337D LEU* 3.7 14.7 - - + +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ASN* 4.4 2.7 - - - +
213D ARG* 3.4 31.1 - - - +
214D PRO* 3.1 3.3 - - - +
215D LEU* 2.9 40.3 + - + +
216D THR* 2.6 37.2 + - - -
243D LEU 2.8 18.9 + - - +
246D LEU* 1.3 72.2 - - - +
248D ASP* 1.3 63.4 + - - +
250D TYR* 3.0 23.6 + - - +
259D ASN* 2.7 35.5 + - + +
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Residues in contact with ASP 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ARG* 2.8 27.3 + - - -
244D MET* 2.9 27.1 + - - +
245D THR* 3.0 14.6 + - + +
247D GLU* 1.3 76.2 - - - +
249D HIS* 1.3 62.2 + - + +
250D TYR 3.2 9.8 + - - +
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Residues in contact with HIS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D THR* 2.8 34.9 + - + -
246D LEU 2.8 12.6 + - - +
248D ASP* 1.3 80.1 - - + +
250D TYR* 1.3 60.7 + - - +
251D HIS* 3.7 5.7 + - - -
299D VAL* 3.6 14.6 - - + -
300D ASP* 2.9 37.4 + - + +
333D VAL* 4.4 13.0 - - + -
337D LEU* 3.6 33.2 - - + +
340D 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