Contacts of the helix formed by residues 358 - 367 (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 ASP 358 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355C PHE 5.4 0.2 + - - -
356C GLU* 3.1 17.5 + - - +
345D TYR 4.3 1.9 - - - +
346D ASP* 3.2 23.9 - - - +
347D GLY 2.9 18.1 + - - -
348D SER* 3.2 17.0 + - - +
357D GLY* 1.3 67.5 - - - -
359D THR* 1.3 57.4 + - - +
360D ALA* 3.3 1.7 + - - +
361D ARG* 3.1 32.4 + - + +
362D GLN* 2.9 30.5 + - - +
364D ARG* 5.0 1.6 + - - -
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Residues in contact with THR 359 (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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337D PRO* 3.6 9.0 - - + +
338D TRP* 3.0 32.6 + - - -
347D GLY 2.7 21.2 + - - +
355D PHE* 3.9 11.0 - - + -
356D GLU 4.3 3.6 - - - +
357D GLY 2.9 19.3 + - - +
358D ASP* 1.3 70.4 - - - +
360D ALA* 1.3 56.9 + - - +
362D GLN* 3.5 17.5 - - - +
363D PHE 3.1 20.4 + - - -
391D TYR* 3.7 28.0 - - + -
398D TRP* 3.6 14.9 - - - -
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Residues in contact with ALA 360 (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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338D TRP* 3.9 12.1 - - - +
342D GLN 3.5 18.6 - - - +
343D VAL* 3.5 13.4 - - - +
345D TYR 3.3 24.7 - - - +
347D GLY* 3.6 8.2 - - - +
358D ASP* 3.2 5.0 + - - +
359D THR* 1.3 78.9 + - - +
361D ARG* 1.3 59.7 + - - +
363D PHE* 3.2 4.3 + - - +
364D ARG* 3.0 33.9 + - - +
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Residues in contact with ARG 361 (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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356C GLU* 6.0 2.2 - - - +
105D ASP* 2.9 31.7 + - - -
106D VAL* 3.3 27.5 - - - +
109D GLU* 3.2 23.1 + - - -
358D ASP* 3.1 31.9 + - + +
360D ALA* 1.3 77.0 - - - +
362D GLN* 1.3 66.8 + - + +
364D ARG* 3.8 13.6 - - - +
365D HIS* 3.0 51.3 + - + +
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Residues in contact with GLN 362 (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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356C GLU* 2.7 29.5 + - - +
356D GLU 2.9 28.4 + - - +
357D GLY* 3.5 9.3 - - - -
358D ASP 2.9 15.0 + - - +
359D THR* 3.5 12.8 - - - +
360D ALA 3.2 0.2 - - - -
361D ARG* 1.3 77.4 - - - +
363D PHE* 1.3 56.3 + - - +
366D ASP* 3.0 50.9 + - - +
367D VAL* 5.0 0.2 - - - +
389D PHE* 5.2 2.5 - - + -
398D TRP* 3.0 32.3 + - + +
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Residues in contact with PHE 363 (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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195D VAL* 4.9 2.0 - - + -
197D GLU* 4.2 4.9 - - - -
300D MSE 3.7 28.0 - - - -
302D LEU* 3.2 28.7 - - + -
334D VAL* 3.8 19.3 - - + -
338D TRP* 3.9 14.1 - + + -
343D VAL* 3.4 23.8 - - + -
359D THR 3.1 14.9 + - - +
360D ALA 3.2 5.4 + - - +
362D GLN* 1.3 77.4 - - - +
364D ARG* 1.3 68.3 + - + +
367D VAL* 3.0 24.5 + - + -
368D LEU* 2.9 52.6 + - + -
389D PHE* 4.2 17.7 - + + -
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Residues in contact with ARG 364 (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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102D ALA* 3.6 12.5 + - - +
103D GLY* 3.4 26.6 + - - -
105D ASP* 2.9 34.8 + - - -
106D VAL* 3.4 21.0 - - + +
343D VAL* 2.9 36.5 + - + +
344D ASN* 3.8 9.3 - - - -
345D TYR 3.2 23.0 + - - -
358D ASP* 5.0 1.2 + - - -
360D ALA* 3.0 22.3 + - - +
361D ARG* 3.4 22.5 + - - +
363D PHE* 1.3 85.9 - - + +
365D HIS* 1.3 57.1 + - - +
368D LEU* 3.4 18.1 - - + +
369D ARG 3.0 25.6 + - - -
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Residues in contact with HIS 365 (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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106D VAL* 3.8 6.7 - - + +
109D GLU* 4.0 10.5 + - - -
361D ARG* 3.0 54.4 + - + +
364D ARG* 1.3 77.7 - - - +
366D ASP* 1.3 77.5 + - - +
369D ARG* 3.7 13.7 + - + +
370D PRO* 3.4 17.4 - - - +
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Residues in contact with ASP 366 (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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362D GLN* 3.0 33.7 + - - +
365D HIS* 1.3 94.0 + - - +
367D VAL* 1.3 66.3 + - + +
370D PRO* 3.5 14.3 - - - +
389D PHE* 5.8 1.7 - - + -
400D ARG* 4.7 15.2 + - - +
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Residues in contact with VAL 367 (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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300D MSE 3.8 25.1 - - + -
334D VAL* 5.0 2.7 - - + -
363D PHE* 3.0 24.5 + - + +
365D HIS 3.5 0.2 - - - -
366D ASP* 1.3 86.9 - - + +
368D LEU* 1.3 66.5 + - - +
369D ARG 3.5 1.3 - - - -
370D PRO* 3.5 2.8 - - - +
371D PHE* 3.2 24.6 + - - +
385D THR* 4.4 11.8 + - + +
386D PRO* 4.4 14.8 - - + -
389D PHE* 3.8 41.5 - - + -
400D ARG* 4.6 5.6 - - - +
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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