Contacts of the helix formed by residues 220 - 233 (chain M) in PDB entry 1MVW
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 ASP 220 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206M LYS 5.5 0.3 - - - +
213M LYS* 2.8 65.7 + - + +
214M MET 3.5 3.8 - - - +
217M THR* 2.8 40.3 + - - +
218M LEU 2.9 1.4 - - - -
219M GLU* 1.3 88.4 - - - +
221M GLN* 1.3 51.4 + - - +
222M ILE 3.0 0.9 - - - -
223M ILE* 2.7 7.9 + - - +
224M SER* 2.3 41.6 + - - +
340M ILE* 4.8 1.3 - - + -
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Residues in contact with GLN 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M LYS* 4.5 3.6 - - - +
216M GLY* 3.6 7.1 + - - +
217M THR* 2.6 37.8 + - - +
218M LEU* 2.4 47.5 - - + +
220M ASP* 1.3 69.9 - - - +
222M ILE* 1.3 63.0 - - - +
224M SER* 4.2 4.5 - - - -
225M ALA* 2.8 24.5 + - - +
340M ILE* 3.6 21.4 - - + +
341M LEU* 3.4 20.7 - - + +
448M GLN* 4.0 22.9 - - - +
449M LEU* 3.6 15.3 - - + -
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Residues in contact with ILE 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M ILE* 4.0 26.9 - - + +
197M ALA* 5.2 5.8 - - + -
218M LEU* 2.9 38.6 - - + -
219M GLU* 3.5 20.4 - - - +
221M GLN* 1.3 81.7 - - - +
223M ILE* 1.3 69.2 + - + +
225M ALA* 3.3 12.8 - - - +
226M ASN* 4.2 5.5 - - - +
250M ILE* 6.0 0.9 - - + -
252M ILE* 5.0 9.2 - - + -
260M LEU* 5.3 11.4 - - + -
262M SER 5.1 1.3 - - - -
263M ALA* 3.2 30.5 - - + -
449M LEU* 4.6 7.2 - - + +
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Residues in contact with ILE 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M ILE* 5.3 4.3 - - + -
194M GLN* 3.2 48.7 - - + +
197M ALA* 4.9 6.1 - - + -
219M GLU 2.8 25.8 - - - +
220M ASP* 2.7 9.6 + - - +
222M ILE* 1.3 84.7 - - + +
224M SER* 1.3 56.4 + - - +
225M ALA 2.6 16.8 + - - -
226M ASN* 2.9 36.7 + - - +
227M PRO* 3.2 5.9 - - + +
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Residues in contact with SER 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M LYS 4.2 4.0 + - - -
220M ASP 2.3 32.5 + - - -
221M GLN* 3.7 6.1 - - - -
223M ILE* 1.3 68.0 - - - +
225M ALA* 1.3 63.1 + - - +
226M ASN 3.3 0.2 - - - -
227M PRO* 3.0 21.7 - - - +
228M LEU 3.9 0.5 + - - -
337M ALA* 3.7 18.2 - - - +
340M ILE* 3.8 25.1 - - - +
341M LEU* 3.4 21.1 - - - +
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Residues in contact with ALA 225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221M GLN 2.8 11.2 + - - +
222M ILE* 3.3 17.0 - - - +
223M ILE 2.6 5.5 + - - -
224M SER* 1.3 72.3 - - - +
226M ASN* 1.3 68.2 + - - +
228M LEU* 3.0 20.3 + - - +
229M LEU* 3.4 11.1 + - + +
265M ILE* 4.1 25.4 - - + -
341M LEU* 3.6 10.7 - - - +
445M ILE* 4.4 14.5 - - + +
449M LEU* 5.2 1.6 - - + -
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Residues in contact with ASN 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M MLY 4.1 30.1 - - + +
193M ILE* 5.6 8.7 - - - +
194M GLN* 6.0 0.4 + - - -
222M ILE 4.2 6.1 + - - +
223M ILE* 2.9 31.2 + - - +
225M ALA* 1.3 78.2 - - - +
227M PRO* 1.3 58.8 - - + +
228M LEU 2.8 11.8 + - - -
229M LEU* 3.0 8.3 + - - +
230M GLU* 2.8 33.8 + - + +
248M MLY 2.8 37.3 - - - -
250M ILE* 5.4 1.2 - - - +
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Residues in contact with PRO 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M MLY 6.2 2.0 - - - -
223M ILE* 3.2 9.9 - - + +
224M SER* 3.0 21.8 - - - +
226M ASN* 1.3 98.9 - - + +
228M LEU* 1.3 58.1 + - - +
230M GLU* 4.1 12.2 - - + +
231M ALA* 3.7 8.7 + - - +
333M ALA* 4.9 16.4 - - + +
334M THR* 3.8 19.7 + - - -
337M ALA* 4.8 9.0 - - + -
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Residues in contact with LEU 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224M SER 3.9 5.3 + - - +
225M ALA 3.0 10.0 + - - +
226M ASN 2.8 2.6 + - - -
227M PRO* 1.3 73.9 - - - +
229M LEU* 1.3 70.4 + - + +
230M GLU 3.0 0.9 - - - -
231M ALA* 2.8 15.5 + - - +
232M PHE* 3.2 39.7 - - + -
334M THR* 4.2 10.3 - - + +
337M ALA* 4.6 5.8 - - + -
338M ILE* 3.5 30.5 - - + -
341M LEU* 4.5 9.4 - - + -
343M PHE* 4.1 21.5 - - + -
441M MET* 4.3 16.4 - - - -
445M ILE* 3.9 24.0 - - + -
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Residues in contact with LEU 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M ALA* 3.4 13.9 + - + +
226M ASN* 3.0 9.6 + - - +
228M LEU* 1.3 83.2 - - + +
230M GLU* 1.3 53.3 + - + +
232M PHE* 3.1 2.8 + - - +
233M GLY* 2.4 39.2 + - - -
246M PHE* 4.0 21.4 - - + -
248M MLY 5.4 9.9 - - + +
265M ILE* 4.2 30.3 - - + -
267M THR* 5.6 0.4 - - - +
438M PHE* 3.9 23.0 - - + -
441M MET* 5.1 5.6 - - + -
442M VAL* 4.1 21.5 - - + +
445M ILE* 3.9 23.3 - - + -
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Residues in contact with GLU 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M THR* 3.6 12.5 - - + +
190M MLY 2.8 46.5 - - - +
226M ASN* 2.8 31.1 + - + +
227M PRO* 4.1 9.4 - - + +
229M LEU* 1.3 75.6 - - + +
231M ALA* 1.3 63.5 + - - +
232M PHE 3.1 0.7 - - - -
234M ASN* 2.9 45.3 + - + +
242M ASN* 2.6 31.4 + - - +
246M PHE* 6.1 0.7 - - + -
248M MLY 5.5 4.0 - - - -
286M HIS* 3.3 9.6 - - + -
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Residues in contact with ALA 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M PRO 3.7 5.0 + - - +
228M LEU 2.8 11.8 + - - +
230M GLU* 1.3 81.1 - - - +
232M PHE* 1.3 66.2 - - + +
285M TYR 4.0 0.2 - - - -
286M HIS* 3.2 17.3 + - - -
287M ILE* 2.7 37.3 + - + +
290M GLN* 3.5 29.2 - - - +
334M THR* 3.8 9.9 - - + +
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Residues in contact with PHE 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M LEU* 3.2 45.0 + - + -
229M LEU* 3.1 4.1 + - - +
231M ALA* 1.3 80.4 - - + +
233M GLY* 1.3 59.4 + - - +
270M LEU* 5.0 0.2 - - - +
285M TYR* 2.8 20.8 - - - -
287M ILE* 3.0 39.7 - - + -
334M THR* 4.9 1.1 - - + -
338M ILE* 5.6 0.7 - - + -
351M ILE* 3.7 21.3 - - + -
355M THR* 3.8 20.2 - - - -
434M TYR* 2.8 38.8 + + + +
437M MET* 4.0 9.2 - - + -
438M PHE* 3.8 19.7 - - + -
441M MET* 3.8 23.3 - - + -
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Residues in contact with GLY 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229M LEU 2.4 19.7 + - - -
232M PHE* 1.3 72.7 - - - +
234M ASN* 1.3 60.9 + - - +
245M ARG* 2.9 27.4 + - - -
246M PHE* 3.0 22.8 - - - -
270M LEU* 4.1 3.4 - - - -
285M TYR* 3.3 13.0 - - - -
438M PHE* 3.8 6.7 - - - -
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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