Contacts of the helix formed by residues 220 - 233 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206P LYS 5.5 0.3 - - - +
213P LYS* 2.8 65.4 + - + +
214P MET 3.5 4.2 - - - +
217P THR* 2.8 41.0 + - - +
218P LEU 2.9 1.0 - - - -
219P GLU* 1.3 88.6 - - - +
221P GLN* 1.3 50.5 + - - +
222P ILE 3.0 0.9 - - - -
223P ILE* 2.7 7.9 + - - +
224P SER* 2.3 41.7 + - - +
340P ILE* 4.8 0.4 - - + -
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Residues in contact with GLN 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P LYS* 4.5 3.8 - - - +
216P GLY* 3.6 6.5 + - - +
217P THR* 2.6 37.7 + - - +
218P LEU* 2.4 47.0 - - + +
220P ASP* 1.3 68.9 - - - +
222P ILE* 1.3 64.4 + - - +
224P SER* 4.2 4.5 - - - -
225P ALA* 2.8 24.0 + - - +
340P ILE* 3.6 20.9 - - + +
341P LEU* 3.4 20.7 - - + +
448P GLN* 4.0 22.9 - - - +
449P LEU* 3.6 15.3 - - + -
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Residues in contact with ILE 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P ILE* 4.0 27.5 - - + +
197P ALA* 5.2 6.1 - - + -
218P LEU* 2.9 38.4 - - + -
219P GLU* 3.5 19.7 - - - +
221P GLN* 1.3 80.9 - - - +
223P ILE* 1.3 69.4 + - + +
225P ALA* 3.3 13.0 - - - +
226P ASN* 4.2 5.4 - - - +
250P ILE* 6.0 1.1 - - + -
252P ILE* 5.0 9.9 - - + -
260P LEU* 5.3 10.3 - - + -
262P SER 5.1 1.1 - - - -
263P ALA* 3.2 30.7 - - + +
449P LEU* 4.6 7.4 - - + +
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Residues in contact with ILE 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P ILE* 5.3 4.3 - - + -
194P GLN* 3.2 49.8 - - + +
197P ALA* 4.9 6.3 - - + -
219P GLU 2.8 25.4 - - - +
220P ASP* 2.7 9.6 + - - +
222P ILE* 1.3 86.6 - - + +
224P SER* 1.3 57.2 + - - +
225P ALA 2.6 16.3 + - - -
226P ASN* 2.9 36.3 + - - +
227P PRO* 3.2 5.2 - - + +
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Residues in contact with SER 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213P LYS 4.2 4.0 + - - -
220P ASP 2.3 33.2 + - - -
221P GLN* 3.7 6.1 - - - -
223P ILE* 1.3 67.6 - - - +
225P ALA* 1.3 62.3 - - - +
226P ASN 3.2 0.2 - - - -
227P PRO* 3.0 22.0 - - - +
228P LEU 3.9 0.3 + - - -
337P ALA* 3.7 17.3 - - - +
340P ILE* 3.8 24.5 - - - +
341P LEU* 3.4 21.8 - - - +
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Residues in contact with ALA 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221P GLN 2.8 10.9 + - - +
222P ILE* 3.3 16.6 - - - +
223P ILE 2.6 5.5 + - - -
224P SER* 1.3 73.6 - - - +
226P ASN* 1.3 67.8 + - - +
228P LEU* 3.0 19.9 + - - +
229P LEU* 3.4 10.5 + - + +
265P ILE* 4.1 25.6 - - + -
341P LEU* 3.7 10.3 - - - -
445P ILE* 4.4 14.7 - - + +
449P LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MLY 4.1 30.6 - - + +
193P ILE* 5.6 8.7 - - - +
194P GLN* 6.0 0.4 + - - -
222P ILE 4.2 6.1 - - - +
223P ILE* 2.9 31.0 + - - +
225P ALA* 1.3 78.6 - - - +
227P PRO* 1.3 58.1 - - + +
228P LEU 2.8 11.8 + - - -
229P LEU* 3.0 9.2 + - - +
230P GLU* 2.8 33.9 + - + +
248P MLY 2.8 36.9 - - - -
250P ILE* 5.4 1.6 - - - +
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Residues in contact with PRO 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MLY 6.2 1.8 - - - -
223P ILE* 3.2 10.1 - - + +
224P SER* 3.0 21.1 - - - +
226P ASN* 1.3 97.9 - - + +
228P LEU* 1.3 59.4 + - - +
230P GLU* 4.1 12.4 - - + +
231P ALA* 3.7 8.3 + - - +
333P ALA* 4.9 16.2 - - + +
334P THR* 3.8 20.2 + - - -
337P ALA* 4.8 9.0 - - + -
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Residues in contact with LEU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224P SER 3.9 6.0 + - - +
225P ALA 3.0 9.8 + - - +
226P ASN 2.8 3.4 + - - -
227P PRO* 1.3 74.6 - - - +
229P LEU* 1.3 70.3 + - + +
230P GLU 3.0 0.9 - - - -
231P ALA* 2.8 14.7 + - - +
232P PHE* 3.2 39.7 - - + -
334P THR* 4.2 8.7 - - + +
337P ALA* 4.6 6.5 - - + -
338P ILE* 3.5 31.6 - - + -
341P LEU* 4.5 8.5 - - + -
343P PHE* 4.1 21.1 - - + -
441P MET* 4.3 15.7 - - - -
445P ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225P ALA* 3.4 14.5 + - + +
226P ASN* 3.4 9.4 - - - +
228P LEU* 1.3 83.0 - - + +
230P GLU* 1.3 53.7 + - + +
232P PHE* 3.1 2.9 + - - +
233P GLY* 2.4 38.6 + - - -
246P PHE* 4.1 20.2 - - + -
248P MLY 5.4 10.1 - - + +
265P ILE* 4.2 29.4 - - + -
267P THR* 5.6 0.7 - - - +
438P PHE* 3.9 21.5 - - + -
441P MET* 5.1 6.1 - - + -
442P VAL* 4.1 22.9 - - + +
445P ILE* 3.9 22.7 - - + -
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Residues in contact with GLU 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P THR* 3.6 12.2 - - + +
190P MLY 2.8 46.3 - - - +
226P ASN* 2.8 30.3 + - + +
227P PRO* 4.1 9.9 - - + +
229P LEU* 1.3 75.7 - - + +
231P ALA* 1.3 62.7 + - - +
232P PHE 3.1 0.9 - - - -
234P ASN* 2.9 45.5 + - + +
242P ASN* 2.6 31.9 + - - +
246P PHE* 6.1 0.9 - - + -
248P MLY 5.0 4.0 - - - -
286P HIS* 3.3 9.9 - - + -
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Residues in contact with ALA 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P PRO 3.7 5.4 + - - +
228P LEU 2.8 10.7 + - - +
230P GLU* 1.3 81.3 - - - +
232P PHE* 1.3 65.5 - - + +
285P TYR 4.0 0.2 - - - -
286P HIS* 3.2 17.0 + - - -
287P ILE* 2.7 37.9 + - + +
290P GLN* 3.5 28.9 - - - +
334P THR* 3.8 10.3 - - + +
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Residues in contact with PHE 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228P LEU* 3.2 45.2 + - + -
229P LEU* 3.1 4.6 + - - +
231P ALA* 1.3 81.7 - - + +
233P GLY* 1.3 59.1 + - - +
270P LEU* 5.0 0.3 - - - +
285P TYR* 2.8 20.6 - - - -
287P ILE* 3.0 38.6 - - + -
334P THR* 4.9 1.1 - - + -
338P ILE* 5.5 1.1 - - + -
351P ILE* 3.7 20.9 - - + -
355P THR* 3.8 20.4 - - - -
434P TYR* 2.8 38.6 + + + +
437P MET* 4.0 9.2 - - + -
438P PHE* 3.8 19.7 - - + -
441P MET* 3.8 22.4 - - + -
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Residues in contact with GLY 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229P LEU 2.4 24.6 + - - -
232P PHE* 1.3 68.5 - - - +
234P ASN* 1.3 60.5 + - - +
245P ARG* 2.9 27.5 + - - -
246P PHE* 3.0 22.3 - - - -
270P LEU* 4.1 3.4 - - - -
285P TYR* 3.3 13.0 - - - -
438P 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