Contacts of the helix formed by residues 358 - 367 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLU* 3.0 16.2 + - - +
345B TYR 4.4 1.7 - - - +
346B ASP* 3.3 22.9 - - - +
347B GLY 2.9 18.2 + - - -
348B SER* 3.2 15.5 + - - +
357B GLY* 1.3 69.7 - - - -
359B THR* 1.3 55.9 + - - +
360B ALA* 3.3 1.7 + - - +
361B ARG* 3.1 33.1 + - + +
362B GLN* 2.9 30.4 + - - +
364B ARG* 5.0 1.6 + - - -
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B PRO* 3.6 8.9 - - + +
338B TRP* 2.9 33.7 + - - -
347B GLY 2.7 21.1 + - - +
355B PHE* 4.0 10.5 - - + -
356B GLU 4.4 3.8 - - - +
357B GLY 2.9 18.2 + - - +
358B ASP* 1.3 71.2 - - - +
360B ALA* 1.3 56.9 + - - +
362B GLN* 3.5 18.8 - - - +
363B PHE 3.1 20.1 + - - -
391B TYR* 3.7 28.0 - - + -
398B TRP* 3.6 15.8 - - - -
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B TRP* 3.9 11.7 - - - +
342B GLN 3.4 18.6 - - - +
343B VAL* 3.5 13.4 - - - +
345B TYR 3.3 24.5 - - - +
347B GLY* 3.7 7.6 - - - +
358B ASP* 3.2 5.2 + - - +
359B THR* 1.3 79.1 + - - +
361B ARG* 1.3 65.3 + - - +
363B PHE* 3.2 3.8 + - - +
364B ARG* 3.0 29.9 + - - +
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Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLU* 6.0 2.0 - - - +
105B ASP* 3.0 27.2 + - - -
106B VAL* 3.2 24.7 - - - +
109B GLU* 3.2 31.7 + - - -
358B ASP* 3.1 32.4 + - + +
360B ALA* 1.3 77.7 - - - +
362B GLN* 1.3 57.9 + - + +
364B ARG* 3.8 14.2 - - - +
365B HIS* 2.9 54.6 + - + +
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLU* 2.7 29.3 + - - +
356B GLU 3.0 25.1 + - - +
357B GLY 3.6 8.5 - - - -
358B ASP 2.9 15.0 + - - +
359B THR* 3.5 14.0 - - - +
360B ALA 3.2 0.2 - - - -
361B ARG* 1.3 76.8 - - + +
363B PHE* 1.3 57.4 + - - +
365B HIS* 5.1 0.7 - - - -
366B ASP* 2.9 52.5 + - + +
367B VAL* 5.0 0.2 - - - +
389B PHE* 5.2 2.2 - - + -
398B TRP* 3.0 32.8 + - + +
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B VAL* 4.8 2.2 - - + -
197B GLU* 4.1 5.8 - - - -
300B MSE 3.7 28.3 - - - -
302B LEU* 3.3 27.8 - - + -
334B VAL* 3.9 17.9 - - + -
338B TRP* 3.9 13.7 - + + -
343B VAL* 3.3 24.2 - - + -
359B THR 3.1 11.4 + - - +
360B ALA 3.2 5.1 + - - +
362B GLN* 1.3 80.0 - - - +
364B ARG* 1.3 65.3 + - + +
367B VAL* 3.1 22.1 + - + -
368B LEU* 2.9 58.0 + - + -
389B PHE* 4.2 18.1 - + + -
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.7 12.5 + - - +
103B GLY* 3.4 26.3 - - - -
105B ASP* 2.9 34.9 + - - -
106B VAL* 3.5 22.8 - - + +
197B GLU* 6.1 0.2 - - - +
343B VAL* 2.9 29.4 + - + +
344B ASN* 3.8 7.6 - - - -
345B TYR 3.2 23.8 + - - -
358B ASP* 5.0 1.0 + - - -
360B ALA* 3.0 23.2 + - - +
361B ARG* 3.8 22.1 - - - +
363B PHE* 1.3 86.1 - - + +
365B HIS* 1.3 56.8 + - - +
368B LEU* 3.5 19.0 - - + +
369B ARG* 3.0 24.9 + - - +
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Residues in contact with HIS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.9 6.5 - - + -
109B GLU* 4.4 7.0 - - - -
361B ARG* 2.9 54.2 + - + +
362B GLN* 5.1 0.4 - - - -
364B ARG* 1.3 78.1 - - - +
366B ASP* 1.3 84.9 + - - +
367B VAL 3.5 0.2 - - - -
369B ARG* 3.7 10.9 - - + +
370B PRO* 3.4 17.2 - - - +
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLN* 2.9 38.0 + - - +
365B HIS* 1.3 95.9 + - - +
367B VAL* 1.3 67.3 + - + +
370B PRO* 3.6 14.2 - - - +
389B PHE* 5.7 1.9 - - + -
400B ARG* 4.5 15.8 + - - +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B MSE 3.7 25.8 - - + -
334B VAL* 5.0 2.0 - - + -
363B PHE* 3.1 22.1 + - + +
365B HIS 3.5 0.2 - - - -
366B ASP* 1.3 87.8 - - + +
368B LEU* 1.3 68.2 + - - +
369B ARG 3.4 1.3 - - - -
370B PRO* 3.5 3.1 - - - +
371B PHE* 3.2 23.9 + - - +
385B THR* 4.4 12.0 + - + +
386B PRO* 4.5 14.6 - - + +
389B PHE* 3.7 42.2 - - + -
400B ARG* 4.4 6.3 - - - +
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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