Contacts of the helix formed by residues 454 - 461 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A ASP 5.3 7.4 - - - +
423A THR 3.8 11.2 - - - +
424A SER* 4.5 3.7 + - - +
452A ASN 3.9 3.6 + - - -
453A ILE* 1.3 79.6 - - - +
455A LEU* 1.3 61.1 + - - +
456A LYS* 3.7 18.6 - - + +
457A GLN* 2.4 43.6 + - - +
458A ALA* 3.0 15.6 + - - +
466A PHE* 3.9 0.9 - - - -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ALA* 4.9 4.7 - - + -
414A LEU* 4.8 1.6 - - + -
419A LEU* 3.2 33.9 - - + -
420A ASP 4.8 7.4 - - - +
421A ASP* 5.6 4.7 + - - -
423A THR 4.1 4.4 + - - +
454A ASP* 1.3 70.2 - - - +
456A LYS* 1.3 68.5 + - - +
458A ALA 3.1 0.9 + - - -
459A ILE* 2.8 46.3 + - + +
466A PHE* 3.5 24.1 - - + -
467A PHE* 3.8 24.5 - - + -
570A LEU* 4.3 24.2 - - + +
571A LEU* 4.7 13.0 - - + -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ASP* 3.3 17.6 - - + +
455A LEU* 1.3 80.1 - - - +
457A GLN* 1.3 62.1 + - - +
459A ILE* 3.2 6.3 + - - +
460A GLU* 3.0 23.6 + - - +
570A LEU* 5.1 17.1 - - - +
573A ASP* 4.1 30.9 + - + +
574A GLY* 4.1 18.5 - - - +
577A GLN* 5.0 14.1 - - + -
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Residues in contact with GLN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLU* 5.0 0.8 + - - -
449A VAL* 3.6 30.1 - - + +
452A ASN 5.6 0.2 - - - +
453A ILE* 3.8 20.9 - - + -
454A ASP* 2.4 39.8 + - - +
456A LYS* 1.3 65.6 - - - +
458A ALA* 1.3 67.6 + - - +
460A GLU* 3.0 25.2 + - - +
461A SER* 2.8 58.5 + - - +
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A ILE* 3.8 2.9 - - + +
454A ASP 3.0 10.9 + - - +
455A LEU 3.5 6.7 - - - +
457A GLN* 1.3 76.6 - - - +
459A ILE* 1.3 57.3 + - - +
462A SER* 2.9 24.8 + - - -
463A ASP* 3.0 19.4 + - + -
466A PHE* 3.2 49.6 - - + -
467A PHE* 3.7 10.4 - - + -
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ILE* 4.7 8.5 - - + -
455A LEU* 2.8 40.5 + - + +
456A LYS* 3.5 6.5 - - - +
458A ALA* 1.3 74.8 - - - +
460A GLU* 1.3 63.6 + - - +
462A SER* 3.1 13.0 + - - -
467A PHE* 4.2 10.8 - - + -
570A LEU 4.5 2.5 - - - +
571A LEU* 3.8 38.6 - - + +
574A GLY* 3.4 29.4 - - - +
575A MSE 3.7 10.5 - - + +
578A VAL* 3.7 12.6 - - + +
597A LYS* 4.2 20.1 + - + +
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LYS* 3.0 14.1 + - - +
457A GLN* 3.0 28.7 + - - +
459A ILE* 1.3 78.3 - - - +
461A SER* 1.3 57.9 + - - +
462A SER* 3.4 0.6 + - - -
574A GLY 4.2 0.8 + - - +
577A GLN* 3.6 32.6 - - + +
578A VAL* 3.8 16.4 - - - +
581A LYS* 3.5 29.6 + - - +
582A THR* 2.6 38.7 + - - +
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A TYR* 4.7 4.9 - - - -
447A GLU* 3.0 50.7 + - - +
449A VAL* 4.3 7.7 - - - +
457A GLN* 2.8 36.6 + - - +
458A ALA* 4.4 1.9 + - - -
460A GLU* 1.3 73.5 - - - +
462A SER* 1.3 72.2 + - - +
463A ASP* 3.3 7.6 + - - +
582A THR* 5.1 2.7 - - - -
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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