Contacts of the helix formed by residues 541 - 546 (chain A) in PDB entry 5IXM
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 THR 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ALA 4.7 14.4 - - - +
423A ASP* 5.6 1.1 - - - -
462A SER* 3.2 29.8 - - - +
470A ALA* 5.4 3.8 - - - +
472A VAL* 4.1 13.6 - - + +
492A GLN* 2.7 30.7 + - - -
501A ASN* 4.1 3.0 - - - +
540A GLY* 1.3 67.9 - - - -
542A ALA* 1.3 58.2 + - + +
544A MET* 2.9 14.2 + - - +
545A LEU* 2.7 39.6 + - + +
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Residues in contact with ALA 542 (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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540A GLY 2.8 3.7 + - - +
541A THR* 1.3 80.4 - - + +
543A GLN* 1.3 54.7 + - - +
545A LEU* 3.4 14.9 - - + +
546A ASN* 2.6 40.5 + - + +
552A TYR* 5.7 6.1 - - + -
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Residues in contact with GLN 543 (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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501A ASN* 4.9 1.4 - - - +
527A ASN* 3.7 24.2 + - - +
529A GLU* 4.8 19.6 + - - +
540A GLY* 3.2 32.9 + - - +
541A THR 3.1 0.6 - - - -
542A ALA* 1.3 78.0 - - - +
544A MET* 1.3 57.0 + - - +
546A ASN* 3.4 20.6 - - - +
547A SER* 4.0 5.2 - - - -
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Residues in contact with MET 544 (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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472A VAL* 3.8 27.4 - - + -
488A LEU* 3.6 19.7 - - + +
489A VAL 5.7 0.2 - - - +
490A GLY* 4.1 3.4 - - - -
491A LEU 3.9 22.7 - - - +
492A GLN* 5.1 1.3 - - + -
501A ASN* 4.0 25.8 - - + +
502A LEU 3.8 18.6 - - - +
503A GLY* 4.1 13.7 - - - -
540A GLY* 4.4 1.5 - - - -
541A THR* 2.9 15.6 + - - +
543A GLN* 1.3 78.5 - - - +
545A LEU* 1.3 59.2 + - - +
546A ASN 3.2 1.3 - - - -
547A SER* 2.4 27.4 + - - +
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Residues in contact with LEU 545 (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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425A MET* 4.9 6.7 - - - -
460A THR* 3.9 24.9 - - + -
461A ALA 4.1 4.5 - - - +
462A SER* 4.2 19.1 - - - -
472A VAL* 3.9 24.5 - - + -
473A GLY 4.4 4.0 - - - +
474A ALA* 5.3 1.3 - - + -
488A LEU* 5.0 9.5 - - + +
541A THR* 2.7 26.6 + - + +
542A ALA* 3.5 16.2 - - + +
544A MET* 1.3 72.3 - - - +
546A ASN* 1.3 57.7 + - + +
547A SER 3.4 4.9 + - - -
548A GLY 4.5 1.9 + - - -
550A LEU 5.0 0.5 - - - +
551A PRO* 3.7 3.8 - - - +
552A TYR* 3.3 48.7 + - + +
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Residues in contact with ASN 546 (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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542A ALA* 2.6 21.9 + - + +
543A GLN* 3.4 11.6 - - - +
545A LEU* 1.3 70.1 - - - +
547A SER* 1.3 59.7 + - - +
551A PRO* 3.5 23.4 - - - +
552A TYR* 4.6 9.2 + - + +
65B GLU* 4.7 10.5 + - - +
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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