Contacts of the helix formed by residues 454 - 461 (chain B) in PDB entry 1MWR
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 454 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B ASP 4.4 11.5 - - - +
423B THR 3.3 22.4 - - - +
424B SER* 3.8 5.2 - - - -
452B ASN 3.3 6.5 + - - +
453B ILE* 1.3 74.9 - - - +
455B LEU* 1.3 60.3 + - - +
456B LYS* 4.2 15.8 + - - +
457B GLN* 3.2 21.7 + - - +
458B ALA* 2.8 27.9 + - - +
466B PHE* 3.5 6.3 - - - -
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Residues in contact with LEU 455 (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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410B ALA* 4.4 10.3 - - + -
414B LEU* 4.6 2.7 - - + -
419B LEU* 3.9 24.7 - - + -
420B ASP 4.5 7.0 - - - +
421B ASP* 5.3 2.2 - - - -
423B THR 4.4 2.0 + - - -
454B ASP* 1.3 72.2 - - - +
456B LYS* 1.3 69.2 + - - +
458B ALA* 2.7 15.2 + - - +
459B ILE* 2.9 34.5 + - + +
466B PHE* 3.3 30.7 - - + -
467B PHE* 4.3 10.3 - - + -
570B LEU* 3.5 41.1 - - + -
571B LEU* 4.0 13.2 - - + -
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Residues in contact with LYS 456 (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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454B ASP* 3.6 13.7 + - - +
455B LEU* 1.3 79.7 - - - +
457B GLN* 1.3 60.1 + - - +
459B ILE* 3.6 6.1 + - - +
460B GLU* 3.1 21.0 + - - +
570B LEU* 5.3 16.5 + - + +
573B ASP* 3.6 32.3 + - - +
574B GLY* 4.1 24.4 - - - +
577B GLN* 5.3 10.8 - - + -
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Residues in contact with GLN 457 (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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449B VAL* 4.3 23.4 - - + +
453B ILE* 3.8 26.2 - - + -
454B ASP* 3.2 25.1 + - - +
455B LEU 3.0 0.8 - - - -
456B LYS* 1.3 78.0 - - - +
458B ALA* 1.3 60.3 + - - +
460B GLU* 2.9 42.9 + - - +
461B SER* 2.9 45.6 + - - +
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Residues in contact with ALA 458 (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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453B ILE* 4.4 2.5 - - + -
454B ASP 2.8 8.3 + - - +
455B LEU 2.7 11.3 + - - +
457B GLN* 1.3 72.9 - - - +
459B ILE* 1.3 53.6 + - - +
461B SER* 4.4 0.2 - - - -
462B SER* 2.7 30.5 + - - -
463B ASP* 3.0 19.8 + - + -
466B PHE* 3.1 47.1 - - + -
467B PHE* 3.7 12.3 - - + -
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Residues in contact with ILE 459 (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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407B ILE* 4.3 10.8 - - + -
410B ALA* 5.8 0.2 - - + -
455B LEU* 2.9 31.1 + - + +
456B LYS* 3.8 6.7 - - - +
458B ALA* 1.3 76.3 - - - +
460B GLU* 1.3 62.4 + - - +
461B SER 3.4 0.3 + - - -
462B SER* 3.7 6.1 + - - +
467B PHE* 4.4 10.3 - - + -
570B LEU 4.7 0.9 - - - +
571B LEU* 3.7 42.2 - - + +
574B GLY* 3.8 7.4 - - - -
575B MSE 3.8 34.8 - - + +
578B VAL* 3.4 13.6 - - + +
597B LYS* 4.2 21.4 - - + +
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Residues in contact with GLU 460 (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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456B LYS 3.1 14.7 + - - +
457B GLN* 2.9 35.8 + - - +
459B ILE* 1.3 78.3 - - - +
461B SER* 1.3 57.1 + - - +
462B SER 3.6 0.2 - - - -
574B GLY 4.8 1.5 + - - +
577B GLN* 3.8 34.0 + - + +
578B VAL* 4.3 9.1 - - - +
581B LYS* 3.8 29.8 + - + +
582B THR* 2.8 37.3 + - + +
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Residues in contact with SER 461 (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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445B ARG* 5.8 0.3 + - - -
446B TYR* 5.3 2.1 - - - +
447B GLU* 3.7 44.6 + - - +
449B VAL* 4.9 2.5 - - - +
453B ILE* 5.6 0.3 - - - +
457B GLN* 2.9 32.8 + - - +
460B GLU* 1.3 78.0 - - - +
462B SER* 1.3 75.0 + - - +
463B ASP* 3.2 14.9 + - - +
582B THR* 4.5 4.5 - - - -
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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