Contacts of the helix formed by residues 213 - 226 (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 ARG 213 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210H SER* 2.9 26.2 + - - +
211H GLY 4.0 5.6 + - - +
212H ASN* 1.3 84.0 + - - +
214H PRO* 1.3 65.2 - - - +
215H LEU 3.3 2.7 - - - -
216H THR* 3.5 4.0 + - - -
217H VAL* 3.0 28.8 + - + +
244H MET* 3.0 63.9 + - + +
247H GLU* 3.4 26.8 - - - +
248H ASP* 2.7 28.6 + - - -
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Residues in contact with PRO 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H VAL* 4.5 6.3 - - + +
206H ILE* 4.5 4.0 - - + -
207H ALA* 3.9 28.5 - - + +
210H SER* 3.4 5.3 - - - +
212H ASN* 3.3 5.6 - - - +
213H ARG* 1.3 91.1 - - - +
215H LEU* 1.3 57.7 + - - +
217H VAL* 4.5 3.6 - - + -
218H ILE* 2.8 44.1 + - + +
247H GLU* 3.1 7.6 - - - +
259H ASN* 3.1 28.9 - - - +
260H ILE* 4.0 9.6 - - + -
263H ALA* 3.7 11.2 - - + -
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Residues in contact with LEU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H PRO* 1.3 79.7 - - - +
216H THR* 1.3 56.8 + - - +
218H ILE* 4.2 0.2 - - - +
219H MET* 2.8 54.6 + - + +
243H LEU* 5.0 3.8 - - + +
246H LEU* 4.0 18.6 - - + -
247H GLU* 2.9 29.7 + - + +
250H TYR* 3.8 33.7 - - + -
259H ASN* 3.9 8.1 - - + +
262H ALA* 4.0 6.1 - - + -
263H ALA* 3.7 26.7 - - - +
266H VAL* 3.9 12.6 - - + -
295H ALA* 4.1 5.8 - - + +
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Residues in contact with THR 216 (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* 3.9 13.6 - - - -
215H LEU* 1.3 73.2 - - - +
217H VAL* 1.3 59.2 + - + +
220H HIS* 3.0 34.4 + - + +
240H ILE* 4.6 12.8 - - + -
243H LEU* 3.4 45.5 + - + +
244H MET* 3.6 29.7 + - + -
247H GLU* 2.6 28.6 + - - -
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Residues in contact with VAL 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H LEU* 4.6 10.8 - - + -
193H LEU* 3.4 37.5 - - + -
206H ILE* 4.5 6.5 - - + -
210H SER* 3.7 20.6 - - - -
213H ARG* 3.0 27.2 + - + +
214H PRO* 3.9 4.5 - - + +
216H THR* 1.3 79.7 - - + +
218H ILE* 1.3 52.1 + - + +
220H HIS* 3.7 4.9 + - - +
221H THR* 2.7 36.3 + - + +
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Residues in contact with ILE 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H LEU* 4.2 16.8 - - + -
196H VAL* 4.7 5.2 - - + -
201H LEU* 4.1 16.8 - - + -
203H VAL* 4.0 17.9 - - + -
206H ILE* 4.3 11.4 - - + -
214H PRO 2.8 26.9 + - - +
215H LEU* 4.2 1.1 - - + +
217H VAL* 1.3 70.3 - - - +
219H MET* 1.3 66.0 + - - +
221H THR* 3.0 7.6 + - - -
222H ILE* 3.0 44.1 + - + +
263H ALA* 3.9 27.6 - - + +
266H VAL* 4.8 2.2 - - + -
267H GLN* 4.1 17.5 - - + +
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Residues in contact with MET 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 2.8 42.5 + - + +
218H ILE* 1.3 72.5 - - - +
220H HIS* 1.3 65.0 + - - +
222H ILE* 3.1 4.7 + - - +
223H PHE* 2.9 56.8 + - + -
239H LEU* 5.5 0.4 - - + -
242H TYR* 6.2 0.9 - - + -
243H LEU* 3.5 33.7 - - + -
246H LEU* 5.8 0.4 - - + -
266H VAL* 3.6 25.1 - - + -
291H ILE* 3.8 16.6 - - + +
292H PHE* 4.6 11.7 - - + -
295H ALA* 3.6 23.1 - - + -
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Residues in contact with HIS 220 (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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216H THR* 3.0 20.4 + - + +
217H VAL* 3.7 4.7 + - - +
219H MET* 1.3 77.9 - - - +
221H THR* 1.3 63.8 + - + +
223H PHE* 3.2 7.6 + - - +
224H GLN* 3.0 67.5 + - + +
229H LEU* 4.7 0.4 - - + -
236H VAL* 4.0 13.6 - - + +
239H LEU* 4.2 13.2 - - + -
240H ILE* 3.5 29.7 - - + +
243H LEU* 3.9 8.6 - - + +
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Residues in contact with THR 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H LEU* 3.8 37.2 - - + +
196H VAL* 4.8 12.4 - - - +
217H VAL* 2.7 23.9 + - + +
218H ILE* 3.0 16.3 + - - +
220H HIS* 1.3 81.5 - - - +
222H ILE* 1.3 57.0 + - - +
224H GLN* 3.6 9.3 - - + +
225H GLU* 2.9 28.9 + - - +
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Residues in contact with ILE 222 (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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196H VAL* 3.6 19.3 - - + -
218H ILE* 3.0 39.3 + - + +
219H MET* 3.6 4.3 - - - +
221H THR* 1.3 74.2 - - - +
223H PHE* 1.3 63.2 + - + +
225H GLU* 3.3 5.8 + - - +
226H ARG* 2.8 29.6 + - - +
266H VAL* 3.8 17.9 - - + -
267H GLN* 4.0 5.6 - - - -
270H HIS* 3.3 47.6 - - + +
291H ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 223 (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* 2.9 56.9 + - + +
220H HIS 3.6 7.2 - - - +
222H ILE* 1.3 75.9 - - + +
224H GLN* 1.3 61.1 + - - +
226H ARG 3.4 0.3 + - - -
227H ASP* 2.9 23.7 + - - -
228H LEU* 3.0 35.5 + - + -
229H LEU* 4.0 10.6 + - + -
234H ILE* 3.7 25.4 - - + -
239H LEU* 3.8 34.1 - - + -
288H LEU* 3.8 25.6 - - + -
291H ILE* 4.1 13.9 - - + -
292H PHE* 5.7 2.9 - - + -
345H ILE* 5.1 10.8 - - + -
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Residues in contact with GLN 224 (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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220H HIS* 3.0 53.3 + - + +
221H THR* 3.6 9.9 - - + +
223H PHE* 1.3 75.2 - - - +
225H GLU* 1.3 56.8 + - - +
227H ASP* 2.8 25.6 + - - +
229H LEU* 3.1 25.5 - - - +
236H VAL* 4.9 5.3 - - - +
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Residues in contact with GLU 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H VAL* 4.5 9.8 - - + +
197H ASN* 3.4 37.7 + - - +
221H THR 2.9 19.2 + - - +
222H ILE* 3.4 8.7 - - - +
224H GLN* 1.3 78.5 - - - +
226H ARG* 1.3 59.0 + - + +
227H ASP* 3.6 1.2 + - - +
270H HIS* 4.1 13.9 - - + +
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Residues in contact with ARG 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ILE* 2.8 20.2 + - - +
225H GLU* 1.3 74.6 - - + +
227H ASP* 1.3 72.2 + - - +
228H LEU* 3.0 22.2 + - + +
231H THR* 4.7 2.1 + - - -
270H HIS* 2.9 43.8 + - + -
273H LEU* 3.5 15.9 - - - +
274H SER* 2.9 29.0 + - - +
284H ASP* 5.6 1.4 - - - +
287H ILE* 3.9 33.9 - - + +
291H ILE* 3.6 26.0 - - - +
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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