Contacts of the helix formed by residues 213 - 226 (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 ARG 213 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210I SER* 2.9 28.2 + - - +
211I GLY 4.0 5.0 + - - +
212I ASN* 1.3 83.4 + - - +
214I PRO* 1.3 66.3 - - - +
215I LEU 3.3 2.5 - - - -
216I THR* 3.9 4.3 - - - -
217I VAL* 3.0 28.4 + - + +
244I MET* 3.0 63.7 + - + +
247I GLU* 3.3 26.3 - - - +
248I ASP* 2.7 28.5 + - - -
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Residues in contact with PRO 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I VAL* 4.5 6.1 - - + +
206I ILE* 4.5 5.4 - - + -
207I ALA* 3.9 27.1 - - + +
210I SER* 3.3 7.7 - - - +
212I ASN* 3.3 4.7 - - - -
213I ARG* 1.3 90.5 - - - +
215I LEU* 1.3 58.6 + - - +
217I VAL* 4.5 3.1 - - + -
218I ILE* 2.8 42.1 + - + +
247I GLU* 3.1 7.6 - - - +
259I ASN* 3.2 28.7 - - - +
260I ILE* 4.1 10.8 - - + -
263I ALA* 3.7 12.3 - - + -
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Residues in contact with LEU 215 (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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214I PRO* 1.3 79.7 - - - +
216I THR* 1.3 59.8 + - - +
218I ILE* 4.9 0.2 - - - -
219I MET* 2.8 55.1 + - + +
243I LEU* 5.0 3.1 - - + +
246I LEU* 4.0 19.5 - - + -
247I GLU* 2.9 28.3 + - + +
250I TYR* 3.8 33.2 - - + -
259I ASN* 3.9 7.6 - - + +
262I ALA* 4.0 6.7 - - + -
263I ALA* 3.7 27.1 - - - +
266I VAL* 3.9 13.2 - - + -
295I ALA* 4.0 5.2 - - + +
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Residues in contact with THR 216 (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* 3.9 12.8 - - - -
215I LEU* 1.3 72.5 - - - +
217I VAL* 1.3 65.0 + - + +
220I HIS* 3.0 27.8 + - + +
240I ILE* 4.6 11.4 - - + -
243I LEU* 3.4 45.1 + - + +
244I MET* 3.5 31.3 + - + -
247I GLU* 2.6 26.6 + - - -
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Residues in contact with VAL 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 4.6 10.8 - - + -
193I LEU* 3.4 38.1 - - + -
206I ILE* 4.5 6.5 - - + -
210I SER* 3.7 20.0 - - - -
213I ARG* 3.0 24.3 + - + +
214I PRO* 3.9 4.5 - - + +
216I THR* 1.3 80.3 - - + +
218I ILE* 1.3 52.6 + - - +
220I HIS* 3.4 4.5 + - - +
221I THR* 2.7 36.3 + - + +
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Residues in contact with ILE 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I LEU* 4.2 16.6 - - + -
196I VAL* 4.7 5.4 - - + -
201I LEU* 4.1 15.9 - - + -
203I VAL* 4.0 18.4 - - + -
206I ILE* 4.3 11.0 - - + -
214I PRO 2.8 28.1 + - - +
215I LEU* 4.2 1.3 - - + +
217I VAL* 1.3 69.2 - - - +
219I MET* 1.3 65.6 + - - +
221I THR* 3.1 8.0 + - - -
222I ILE* 2.9 43.9 + - + +
263I ALA* 3.8 26.9 - - + +
266I VAL* 4.8 2.2 - - + -
267I GLN* 4.1 17.3 - - + +
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Residues in contact with MET 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU* 2.8 39.9 + - + +
218I ILE* 1.3 72.0 - - + +
220I HIS* 1.3 63.7 + - - +
222I ILE* 3.1 4.3 + - - +
223I PHE* 2.9 56.7 + - + -
239I LEU* 5.5 0.9 - - + -
242I TYR* 6.2 1.1 - - + -
243I LEU* 3.5 32.8 - - + -
246I LEU* 5.8 0.2 - - + -
266I VAL* 3.5 25.8 - - + -
291I ILE* 3.8 15.5 - - + +
292I PHE* 4.6 11.7 - - + -
295I ALA* 3.6 23.6 - - + -
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Residues in contact with HIS 220 (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* 3.0 20.8 + - + +
217I VAL* 3.6 4.3 - - - +
219I MET* 1.3 76.6 - - - +
221I THR* 1.3 64.0 + - + +
223I PHE* 3.2 8.1 + - - +
224I GLN* 3.0 64.8 + - + +
229I LEU* 4.8 0.4 - - + -
236I VAL* 4.0 14.2 - - + +
239I LEU* 4.2 13.2 - - + -
240I ILE* 3.5 27.5 - - + +
243I LEU* 3.9 8.6 - - + +
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Residues in contact with THR 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I LEU* 3.7 38.2 - - + +
196I VAL* 4.8 12.1 - - - +
217I VAL* 2.7 18.8 + - + +
218I ILE* 3.1 16.3 + - - +
220I HIS* 1.3 81.4 - - - +
222I ILE* 1.3 55.9 + - - +
224I GLN* 3.6 8.7 - - + +
225I GLU* 2.9 28.9 + - - +
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Residues in contact with ILE 222 (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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196I VAL* 3.6 20.0 - - + -
218I ILE* 2.9 38.4 + - + +
219I MET* 3.1 5.1 + - - +
221I THR* 1.3 74.1 - - - +
223I PHE* 1.3 63.3 + - + +
225I GLU* 3.3 6.1 + - - +
226I ARG* 2.8 29.2 + - - +
266I VAL* 3.8 18.2 - - + -
267I GLN* 4.0 6.1 - - - -
270I HIS* 3.3 47.3 - - + +
291I ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 223 (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* 2.9 55.1 + - + +
220I HIS 3.6 7.6 - - - +
222I ILE* 1.3 75.8 - - + +
224I GLN* 1.3 59.7 + - - +
226I ARG 3.4 0.5 + - - -
227I ASP* 2.9 24.1 + - - -
228I LEU* 3.0 35.9 + - + -
229I LEU* 4.0 10.8 + - + -
234I ILE* 3.7 26.9 - - + -
239I LEU* 3.9 34.1 - - + -
288I LEU* 3.8 26.2 - - + -
291I ILE* 4.1 17.0 - - + -
292I PHE* 5.7 3.6 - + + -
345I ILE* 5.2 10.5 - - + -
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Residues in contact with GLN 224 (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* 3.0 52.9 + - + +
221I THR* 3.6 10.8 - - + +
223I PHE* 1.3 75.5 - - - +
225I GLU* 1.3 60.5 + - - +
227I ASP* 2.9 22.7 + - - +
229I LEU* 3.2 24.6 - - - +
236I VAL* 4.9 5.3 - - - +
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Residues in contact with GLU 225 (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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196I VAL* 4.5 9.9 - - + +
197I ASN* 3.4 37.9 + - - +
221I THR 2.9 20.2 + - - +
222I ILE* 3.4 8.3 - - - +
224I GLN* 1.3 77.9 - - - +
226I ARG* 1.3 58.7 + - + +
227I ASP* 5.0 1.4 - - - +
270I HIS* 4.1 13.9 - - + +
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Residues in contact with ARG 226 (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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222I ILE* 2.8 21.2 + - - +
225I GLU* 1.3 74.6 - - + +
227I ASP* 1.3 71.2 + - - +
228I LEU* 3.1 22.0 + - + +
231I THR* 4.7 1.7 + - - -
270I HIS* 2.9 44.5 + - + -
273I LEU* 3.5 15.2 - - - +
274I SER* 2.9 28.4 + - - +
284I ASP* 5.6 1.6 - - - +
287I ILE* 3.9 32.9 - - - +
291I ILE* 3.6 25.4 - - - +
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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