Contacts of the helix formed by residues 219 - 228 (chain B) in PDB entry 1MPX
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 ASN 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B ASP* 2.8 42.2 + - - +
209B TRP* 3.6 16.8 - - + +
215B PHE* 5.9 0.2 - - + -
216B ARG* 3.5 18.6 + - - +
217B GLN 3.1 2.0 - - - -
218B VAL* 1.3 86.9 - - - +
220B PHE* 1.3 64.4 + - - +
221B ASP 3.2 2.5 - - - -
222B TYR* 3.1 22.2 + - + +
223B PHE* 3.2 38.4 + - + -
309B GLU* 5.8 4.7 - - - +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 3.6 26.9 - + - -
216B ARG 4.9 0.4 + - - -
217B GLN* 3.2 31.6 + - + +
218B VAL 3.3 0.2 - - - -
219B ASN* 1.3 76.7 - - - +
221B ASP* 1.3 64.7 + - - +
223B PHE* 3.2 27.6 + + - +
224B THR* 3.5 3.3 + - - +
236B ILE* 3.4 25.1 - - + +
238B ARG* 5.9 1.3 - - - +
247B PHE* 3.6 29.6 - + + -
253B ALA* 3.5 21.3 - - + -
256B PHE* 3.7 13.9 - + + -
257B ALA* 3.8 4.0 - - + -
262B LEU* 3.3 26.2 - - + +
268B TRP* 3.5 28.7 - + - -
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLN 5.7 0.3 - - - +
218B VAL 4.0 9.1 + - - +
219B ASN 3.2 0.6 - - - -
220B PHE* 1.3 74.4 - - - +
222B TYR* 1.3 59.4 + - - +
224B THR* 3.3 7.4 + - - -
225B GLY* 3.0 24.9 + - - -
234B ALA 4.0 1.9 - - - +
235B GLY* 3.8 8.9 - - - -
236B ILE* 3.1 19.7 + - - +
238B ARG* 2.9 44.0 + - - -
459B PHE* 4.3 12.1 - - - +
460B ALA* 5.4 2.3 + - - +
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 2.6 37.5 + + - -
129B TYR* 5.1 0.3 + - - -
131B MSE 3.9 26.9 - - + -
175B TYR* 3.4 21.3 - - - -
200B MSE 5.2 2.3 - - + -
209B TRP* 4.0 25.1 - + - -
218B VAL 4.7 1.0 + - - +
219B ASN* 3.1 25.5 + - + +
221B ASP* 1.3 78.3 - - - +
223B PHE* 1.3 59.4 + + - +
225B GLY* 4.4 1.8 - - - +
226B GLN* 2.9 55.1 + - + +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B MSE 4.2 6.5 - - + -
209B TRP* 3.7 22.4 - + - -
215B PHE* 4.4 7.2 - + - -
219B ASN* 3.2 27.8 + - + -
220B PHE* 3.2 34.5 + + - +
222B TYR* 1.3 79.9 - + - +
224B THR* 1.3 59.6 + - + +
227B LEU* 2.9 43.0 + - + +
262B LEU* 4.5 7.2 - - + -
265B LEU* 4.0 17.1 - - + +
267B TRP* 3.3 28.9 - + - -
268B TRP* 4.3 10.5 - + + -
271B LEU* 3.5 29.4 - - + -
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B PHE 3.5 1.1 + - - -
221B ASP 3.3 7.4 + - - -
223B PHE* 1.3 74.4 - - - +
225B GLY* 1.3 65.0 + - - +
228B SER* 2.4 36.1 + - - +
234B ALA 2.7 26.0 + - - +
235B GLY 3.5 13.0 - - - +
236B ILE* 3.5 19.3 - - + +
262B LEU* 3.5 31.2 - - + -
265B LEU* 4.5 2.7 - - + -
36D PHE* 3.8 20.6 - - + -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TYR* 5.4 0.7 + - - -
221B ASP 3.0 16.9 + - - -
222B TYR* 3.4 2.4 + - - -
223B PHE 3.3 0.2 - - - -
224B THR* 1.3 78.4 - - - +
226B GLN* 1.3 67.6 + - - +
231B GLY 4.3 3.3 - - - +
232B LYS* 4.7 0.9 - - - -
233B GLY* 3.2 23.0 + - - -
234B ALA* 3.1 18.0 + - - -
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Residues in contact with GLN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.0 36.2 + - - +
82B TYR* 3.6 25.2 - - - -
122B LYS* 2.9 35.0 + - - +
123B TYR* 4.8 7.6 + - - -
129B TYR* 4.6 6.6 + - - +
131B MSE 5.5 0.2 - - + -
222B TYR* 2.9 48.8 + - + +
225B GLY* 1.3 88.4 - - - +
227B LEU* 1.3 69.8 + - + +
228B SER 3.7 1.1 - - - -
229B LYS 3.9 1.1 - - - +
31D ILE* 3.5 8.8 - - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR* 3.6 33.7 - - + -
131B MSE 4.0 22.9 - - + -
223B PHE* 2.9 30.7 + - + +
226B GLN* 1.3 80.6 - - + +
228B SER* 1.3 65.9 + - - +
229B LYS 3.3 2.5 - - - -
265B LEU* 3.7 24.1 - - + +
267B TRP* 3.5 33.0 - - + -
30D ASP* 3.7 27.9 - - + +
31D ILE* 3.7 16.8 - - + +
32D THR 5.1 0.7 + - - -
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE 4.0 0.6 + - - -
224B THR* 2.4 39.2 + - - +
225B GLY 5.0 0.2 - - - -
226B GLN 3.7 0.4 - - - -
227B LEU* 1.3 78.5 - - - +
229B LYS* 1.3 71.9 + - - +
233B GLY* 4.2 12.3 - - - -
234B ALA 4.5 2.5 + - - -
265B LEU* 5.0 1.1 - - - -
31D ILE* 5.0 1.4 - - - +
34D LYS 4.6 6.6 - - - +
35D PRO* 5.5 0.5 - - - +
36D PHE* 3.9 43.5 + - - +
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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