Contacts of the helix formed by residues 285 - 292 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ILE 3.5 8.3 - - - -
202C ASP* 3.5 24.5 - - - +
277C TYR* 3.8 3.1 - - - +
281C TRP 3.2 6.4 + - - +
282C GLN 3.4 14.9 + - - +
283C GLU 5.2 0.3 - - - +
284C GLN* 1.3 74.0 - - - +
286C LEU* 1.3 62.7 + - - +
287C ASP* 3.3 12.3 - - - +
288C LYS* 3.4 28.7 + - - +
289C VAL* 3.5 13.9 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.9 28.7 - - + -
178C PHE* 3.6 35.4 - - + +
181C VAL* 3.7 26.5 - - + -
182C MSE 4.0 13.0 - - + -
185C THR* 5.3 1.1 - - + -
200C MSE 3.7 9.9 - - - +
201C ILE* 3.1 25.5 + - + +
283C GLU 6.0 0.2 - - - +
284C GLN* 3.0 19.6 + - - +
285C ALA* 1.3 69.6 - - - +
287C ASP* 1.3 59.5 + - - +
288C LYS 3.2 0.2 - - - -
289C VAL* 3.3 14.8 + - + +
290C MSE 2.9 32.5 + - - +
317C SER* 4.8 0.2 - - - -
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 3.2 21.5 - - + +
202C ASP* 4.5 3.5 - - - +
285C ALA* 3.6 18.0 - - - +
286C LEU* 1.3 70.2 - - - +
288C LYS* 1.3 75.9 + - - +
290C MSE 3.4 4.3 + - - +
291C ALA* 3.1 17.8 + - - +
312C TRP* 3.2 25.7 + - - -
316C HIS* 3.7 27.1 - - + +
317C SER* 3.8 14.1 - - - +
320C ALA* 3.4 13.6 - - + +
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASP* 4.9 1.0 + - - -
277C TYR* 3.3 33.4 + - - -
282C GLN* 4.0 17.7 - - + +
285C ALA* 3.4 18.6 + - + +
286C LEU 3.2 0.4 - - - -
287C ASP* 1.3 91.8 + - - +
289C VAL* 1.3 63.2 + - + +
291C ALA* 3.3 21.0 + - - +
292C ARG* 3.6 16.8 + - - +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 4.5 11.2 - - + -
185C THR* 3.9 27.4 - - + -
283C GLU 5.2 9.0 - - - +
285C ALA 3.5 13.7 + - - +
286C LEU* 3.3 22.2 + - + +
287C ASP 3.3 0.2 - - - -
288C LYS* 1.3 76.7 - - + +
290C MSE 1.3 59.3 + - + +
292C ARG* 3.2 45.4 + - - +
293C THR* 2.5 31.4 + - - +
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Residues in contact with MSE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C VAL* 3.7 31.2 - - + +
184C LEU* 4.4 11.2 - - - -
185C THR* 3.7 24.9 - - + +
286C LEU* 2.9 20.7 + - + +
287C ASP* 3.7 7.9 - - - +
288C LYS 3.3 0.4 - - - -
289C VAL* 1.3 79.5 - - + +
291C ALA* 1.3 58.2 + - - +
293C THR* 3.2 22.9 + - + +
301C TRP* 4.0 28.9 - - + -
317C SER* 4.5 8.5 - - - +
320C ALA* 4.6 0.4 - - + -
321C MSE 3.6 39.8 - - + +
324C ARG* 2.9 20.3 + - - -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP 3.1 13.0 + - - +
288C LYS* 3.3 15.3 - - - +
289C VAL 3.2 0.2 - - - -
290C MSE 1.3 78.6 - - - +
292C ARG* 1.3 57.2 + - + +
293C THR 3.5 0.7 - - - -
320C ALA* 3.6 21.9 - - + +
324C ARG* 3.2 19.2 + - - -
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Residues in contact with ARG 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 6.2 0.6 - - - +
283C GLU* 5.9 1.2 + - - -
288C LYS* 3.9 11.9 + - - +
289C VAL* 3.5 45.0 + - - +
291C ALA* 1.3 77.2 - - + +
293C THR* 1.3 59.0 + - - +
294C PRO* 3.7 7.0 - - - +
324C ARG* 4.6 2.2 - - - +
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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