Contacts of the helix formed by residues 219 - 228 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ASP* 2.7 42.4 + - - +
209A TRP* 3.6 17.1 - - + +
215A PHE* 6.0 0.4 - - + -
216A ARG* 3.5 18.9 + - - +
217A GLN 3.1 1.8 - - - -
218A VAL* 1.3 84.9 - - - +
220A PHE* 1.3 64.0 + - - +
221A ASP 3.2 3.1 - - - -
222A TYR* 3.0 24.2 + - + +
223A PHE* 3.2 37.7 + - + -
309A GLU* 5.8 4.7 - - - +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.6 26.0 - + - -
216A ARG 4.9 0.2 + - - -
217A GLN* 3.3 34.6 + - + +
219A ASN* 1.3 76.8 - - - +
221A ASP* 1.3 63.4 + - - +
223A PHE* 3.2 27.3 + + - +
224A THR 3.6 2.8 + - - -
236A ILE* 3.3 25.3 - - + +
238A ARG* 5.8 1.3 - - - +
247A PHE* 3.6 29.6 - + + -
253A ALA* 3.6 20.9 - - + -
256A PHE* 3.8 13.2 - + + -
257A ALA* 3.7 12.3 - - + -
262A LEU* 3.3 19.2 - - + +
268A TRP* 3.5 28.5 - + - -
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL 4.0 9.6 + - - +
219A ASN 3.2 0.4 - - - -
220A PHE* 1.3 75.7 - - - +
222A TYR* 1.3 60.1 + - - +
224A THR* 3.2 8.6 + - - -
225A GLY* 2.9 25.3 + - - -
234A ALA 3.9 1.9 - - - +
235A GLY* 3.7 8.8 - - - -
236A ILE* 3.0 19.9 + - - +
238A ARG* 3.0 42.1 + - - -
459A PHE* 4.3 12.3 - - - +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 2.6 36.8 + + - -
129A TYR* 5.1 0.3 + - - -
131A MSE 3.8 28.7 - - + -
175A TYR* 3.4 21.5 - - - -
200A MSE 5.2 2.3 - - + -
209A TRP* 3.8 24.9 - + - -
218A VAL 4.7 0.6 + - - +
219A ASN* 3.0 26.0 + - + +
221A ASP* 1.3 78.0 - - - +
223A PHE* 1.3 59.7 + + - +
225A GLY* 4.4 1.8 - - - +
226A GLN* 2.9 51.5 + - + +
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A MSE 4.1 7.0 - - + -
209A TRP* 3.6 23.1 - + - -
215A PHE* 4.5 7.2 - + - -
219A ASN* 3.3 29.4 - - + -
220A PHE* 3.2 30.0 + + - +
222A TYR* 1.3 80.0 - + - +
224A THR* 1.3 58.8 + - - +
227A LEU* 2.9 42.2 + - + +
262A LEU* 4.4 7.9 - - + -
265A LEU* 3.9 18.8 - - + +
267A TRP* 3.3 28.9 - + - -
268A TRP* 4.2 11.9 - + + -
271A LEU* 3.5 29.4 - - + -
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE 3.6 0.4 + - - -
221A ASP 3.2 9.2 + - - -
223A PHE* 1.3 74.4 - - - +
225A GLY* 1.3 62.0 + - - +
228A SER* 2.4 37.1 + - - +
234A ALA 2.6 26.7 + - - +
235A GLY 3.5 13.9 - - - +
236A ILE* 3.6 19.5 - - + +
262A LEU* 3.5 31.0 - - + -
265A LEU* 4.6 2.9 - - + -
36C PHE* 3.9 20.0 - - + -
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 5.4 0.3 + - - -
221A ASP 2.9 17.5 + - - -
222A TYR* 3.7 2.5 - - - -
223A PHE 3.3 0.2 - - - -
224A THR* 1.3 78.5 - - - +
226A GLN* 1.3 68.9 + - - +
229A LYS 5.8 0.2 + - - -
231A GLY 4.4 3.6 - - - +
232A LYS* 4.7 0.7 - - - -
233A GLY* 3.2 23.0 + - - -
234A ALA* 3.1 17.4 + - - -
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Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.0 35.3 + - - +
82A TYR* 3.5 25.0 - - - -
122A LYS* 2.8 35.0 + - - +
123A TYR* 4.8 7.8 + - - -
129A TYR* 4.4 6.9 + - - +
222A TYR* 2.9 49.9 + - + +
225A GLY* 1.3 87.9 - - - +
227A LEU* 1.3 67.6 + - + +
228A SER 3.7 1.1 - - - -
229A LYS 4.5 0.7 - - - -
31C ILE* 3.6 8.5 - - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.6 32.3 - - + -
131A MSE 4.0 20.4 - - + -
223A PHE* 2.9 34.3 + - + +
226A GLN* 1.3 79.9 - - + +
228A SER* 1.3 65.8 + - - +
229A LYS 3.4 2.2 - - - -
265A LEU* 3.8 24.0 - - + +
267A TRP* 3.5 31.0 - - + -
30C ASP* 3.7 28.4 - - + +
31C ILE* 3.7 16.8 - - - +
32C THR 5.1 0.9 + - - -
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE 4.0 0.4 + - - -
224A THR* 2.4 39.2 + - - +
225A GLY 4.9 0.2 - - - -
226A GLN 3.7 0.4 - - - -
227A LEU* 1.3 79.7 - - - +
229A LYS* 1.3 74.9 + - - +
233A GLY* 4.2 9.6 - - - -
234A ALA 4.6 1.9 + - - -
265A LEU* 4.9 1.3 - - - -
31C ILE* 4.9 2.5 - - - +
34C LYS 4.8 5.0 - - - +
35C PRO* 5.6 0.3 - - - +
36C PHE* 4.0 42.6 + - - +
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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