Contacts of the helix formed by residues 285 - 291 (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 ALA 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D ILE 3.6 8.3 - - - -
202D ASP* 3.5 26.9 - - - +
277D TYR* 3.7 9.2 - - - +
281D TRP 3.2 5.4 + - - +
282D GLN 3.4 15.1 + - - +
283D GLU 5.3 0.3 - - - -
284D GLN* 1.3 73.4 - - - +
286D LEU* 1.3 63.7 + - - +
287D ASP* 3.2 12.3 - - - +
288D LYS* 3.3 25.6 + - + +
289D VAL* 3.5 9.1 + - - +
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Residues in contact with LEU 286 (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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135D LEU* 4.2 14.8 - - + -
178D PHE* 3.7 25.4 - - + +
181D VAL* 3.7 26.7 - - + -
182D MSE 3.9 28.5 - - + -
185D THR* 5.2 1.1 - - + -
200D MSE 3.7 20.9 - - - +
201D ILE* 3.1 23.8 + - + +
283D GLU 6.2 0.2 - - - +
284D GLN* 2.9 17.1 + - - +
285D ALA* 1.3 69.4 - - - +
287D ASP* 1.3 60.6 + - - +
288D LYS 3.2 0.2 - - - -
289D VAL* 3.2 13.4 + - + +
290D MSE 2.9 32.0 + - - +
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Residues in contact with ASP 287 (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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201D ILE* 3.3 23.2 - - + +
202D ASP* 4.4 3.5 - - - +
285D ALA* 3.5 19.4 - - - +
286D LEU* 1.3 73.6 - - - +
288D LYS* 1.3 77.1 + - - +
290D MSE 3.5 3.8 + - - -
291D ALA* 3.2 17.5 + - - +
312D TRP* 3.3 25.2 + - - -
316D HIS* 3.8 24.6 - - - +
317D SER* 3.8 13.5 - - - +
320D ALA* 3.4 13.5 - - + +
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Residues in contact with LYS 288 (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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202D ASP* 5.1 1.0 + - - -
205D MSE 6.2 0.4 - - - +
277D TYR* 4.0 21.4 + - - -
282D GLN 5.0 6.5 - - - +
285D ALA* 3.5 23.0 - - + +
286D LEU 3.2 0.2 - - - -
287D ASP* 1.3 87.8 + - - +
289D VAL* 1.3 65.2 + - + +
291D ALA* 3.3 19.5 + - + +
292D ARG* 3.6 19.1 + - - +
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Residues in contact with VAL 289 (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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135D LEU* 4.1 20.0 - - + -
185D THR* 3.7 31.0 - - + -
283D GLU 5.2 8.3 - - - +
285D ALA 3.7 13.5 - - - +
286D LEU* 3.2 16.3 + - + +
288D LYS* 1.3 77.1 - - + +
290D MSE 1.3 60.1 + - + +
292D ARG* 3.2 45.2 + - - +
293D THR* 2.7 27.7 + - - +
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Residues in contact with MSE 290 (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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181D VAL* 3.6 22.7 - - + +
184D LEU* 4.3 11.7 - - - -
185D THR* 3.6 37.0 - - + +
286D LEU 2.9 19.3 + - - +
287D ASP* 3.8 7.6 - - - +
288D LYS 3.3 0.2 - - - -
289D VAL* 1.3 79.4 - - + +
291D ALA* 1.3 58.7 + - - +
293D THR* 3.2 26.4 + - - +
301D TRP* 4.0 28.3 - - + -
317D SER* 4.6 6.1 - - - +
320D ALA* 4.5 4.0 - - + -
321D MSE 3.6 42.3 - - + +
324D ARG* 2.8 19.9 + - - -
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Residues in contact with ALA 291 (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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287D ASP 3.2 13.1 + - - +
288D LYS* 3.4 16.4 - - + +
289D VAL 3.1 0.4 - - - -
290D MSE 1.3 77.1 - - - +
292D ARG* 1.3 55.2 + - - +
293D THR 3.5 0.7 - - - -
320D ALA* 3.7 22.8 - - + +
324D ARG* 3.3 17.2 + - - -
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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