Contacts of the helix formed by residues 219 - 228 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D ASP* 2.7 43.3 + - - +
209D TRP* 3.7 16.4 - - + +
215D PHE* 6.1 0.2 - - - -
216D ARG* 3.5 18.0 + - - +
217D GLN 3.1 1.8 - - - -
218D VAL* 1.3 86.4 - - - +
220D PHE* 1.3 62.8 + - - +
221D ASP 3.2 2.7 - - - -
222D TYR* 3.0 23.9 + - + +
223D PHE* 3.1 39.5 + - + -
309D GLU* 5.8 3.5 - - - +
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Residues in contact with PHE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 3.6 27.1 - + - -
216D ARG 4.8 0.2 + - - -
217D GLN* 3.2 34.5 + - + +
219D ASN* 1.3 77.0 - - - +
221D ASP* 1.3 62.2 + - - +
223D PHE* 3.2 28.0 + + - +
224D THR 3.5 3.3 + - - -
236D ILE* 3.3 24.8 - - + +
238D ARG* 5.9 1.3 - - - +
247D PHE* 3.6 29.8 - + + -
253D ALA* 3.6 21.1 - - + -
256D PHE* 3.8 12.1 - + + -
257D ALA* 3.8 4.3 - - + -
262D LEU* 3.3 26.7 - - + -
268D TRP* 3.5 28.0 - + - -
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Residues in contact with ASP 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLN 5.0 0.2 + - - -
218D VAL 4.0 9.9 + - - +
219D ASN 3.2 0.4 - - - -
220D PHE* 1.3 74.2 - - - +
222D TYR* 1.3 60.5 + - - +
224D THR* 3.3 8.6 + - - -
225D GLY* 3.0 25.5 + - - -
234D ALA 4.0 2.1 - - - +
235D GLY* 3.8 8.8 - - - -
236D ILE* 3.1 19.0 + - - +
238D ARG* 2.9 43.9 + - - -
459D PHE* 4.2 13.2 - - - +
460D ALA* 5.2 4.2 + - - +
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Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 2.7 36.5 + + - -
129D TYR* 5.1 0.3 + - - -
131D MSE 3.9 21.5 - - + -
175D TYR* 3.4 20.8 - - - -
200D MSE 5.2 1.9 - - + -
209D TRP* 3.8 32.1 - + - -
218D VAL 4.6 1.3 + - - +
219D ASN* 3.0 27.4 + - + +
221D ASP* 1.3 77.6 - - - +
223D PHE* 1.3 60.6 + + - +
225D GLY* 4.4 1.6 - - - +
226D GLN* 2.9 50.8 + - + +
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Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D MSE 4.2 6.7 - - + -
209D TRP* 3.7 22.7 - + - -
215D PHE* 4.3 9.6 - + - -
219D ASN* 3.1 28.8 + - + -
220D PHE* 3.2 33.8 + + - +
222D TYR* 1.3 80.2 - + - +
224D THR* 1.3 59.7 + - + +
227D LEU* 2.9 43.0 + - + +
262D LEU* 4.5 6.3 - - + -
265D LEU* 4.1 17.8 - - + +
267D TRP* 3.3 28.9 - + + -
268D TRP* 4.3 10.5 - + + -
271D LEU* 3.5 29.2 - - + -
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Residues in contact with THR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 4.1 19.3 - - + -
220D PHE 3.5 1.1 + - - +
221D ASP 3.3 7.6 + - - -
223D PHE* 1.3 74.6 - - - +
225D GLY* 1.3 63.8 + - - +
228D SER* 2.4 38.3 + - - +
234D ALA 2.7 26.2 + - - +
235D GLY 3.5 12.2 - - - +
236D ILE* 3.5 26.8 - - + +
262D LEU* 3.5 24.2 - - + -
265D LEU* 4.7 2.7 - - + -
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Residues in contact with GLY 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TYR* 5.5 0.3 + - - -
221D ASP 3.0 17.7 + - - -
222D TYR* 3.3 2.8 + - - -
224D THR* 1.3 78.3 - - - +
226D GLN* 1.3 67.6 + - - +
229D LYS 5.8 0.2 + - - -
231D GLY 4.4 3.6 - - - +
232D LYS* 4.8 0.5 - - - -
233D GLY* 3.2 23.2 + - - -
234D ALA 3.1 17.2 + - - -
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Residues in contact with GLN 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.5 8.3 - - - +
81D PRO* 2.9 34.1 + - - +
82D TYR* 3.5 25.9 - - - -
122D LYS* 2.7 38.2 + - - +
123D TYR* 4.8 8.3 + - - -
129D TYR* 4.6 6.2 + - - +
222D TYR* 2.9 47.3 + - + +
225D GLY* 1.3 87.3 - - - +
227D LEU* 1.3 69.3 + - + +
228D SER 3.7 1.3 - - - -
229D LYS 3.7 0.6 - - - +
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 3.8 24.9 - - + +
31B ILE* 3.6 17.3 - - - +
32B THR 5.1 0.7 + - - -
36B PHE* 5.0 0.7 - - - +
129D TYR* 3.5 35.4 - - + -
131D MSE 3.9 22.7 - - + -
223D PHE* 2.9 29.5 + - + +
226D GLN* 1.3 80.1 - - + +
228D SER* 1.3 64.7 + - - +
229D LYS 3.4 2.0 - - - -
265D LEU* 3.8 23.7 - - + +
267D TRP* 3.5 35.2 - - + -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.9 3.2 - - - +
35B PRO* 5.2 2.3 - - - +
36B PHE* 3.9 44.5 + - - +
223D PHE 4.0 0.4 + - - -
224D THR* 2.4 39.8 + - - -
226D GLN 3.7 0.4 - - - -
227D LEU* 1.3 78.6 - - - +
229D LYS* 1.3 76.9 + - - +
233D GLY* 4.4 8.3 - - - -
234D ALA 4.7 1.5 + - - -
265D LEU* 5.1 0.2 - - - -
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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