Contacts of the helix formed by residues 476 - 484 (chain A) in PDB entry 3MTC
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 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A TYR 4.5 3.8 - - - +
451A ARG 3.8 8.6 - - - +
452A ILE* 4.1 10.6 - - + +
472A LEU 3.7 1.8 + - - -
473A TYR* 3.1 30.9 + - + +
475A TYR* 1.3 77.7 - - - +
477A GLN* 1.3 64.9 + - - +
478A LEU* 3.0 7.0 + - - +
479A LYS* 3.0 27.0 + - + +
480A ILE* 3.2 24.1 + - - +
522A TRP* 4.0 13.8 + - + +
525A ARG* 3.0 39.2 + - - -
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Residues in contact with GLN 477 (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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405A ILE* 2.7 30.7 + - - +
408A TYR* 3.9 15.2 - - + -
411A ARG* 2.9 23.5 + - - -
450A TYR* 3.7 15.1 - - + -
451A ARG* 2.9 42.3 + - - +
453A GLU* 3.2 40.3 + - + +
475A TYR 4.5 0.4 - - - -
476A ASP* 1.3 71.4 - - - +
478A LEU* 1.3 61.6 + - - +
480A ILE* 3.3 7.4 + - - +
481A GLN* 2.8 35.3 + - + +
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Residues in contact with LEU 478 (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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448A LEU* 4.1 20.4 - - + -
450A TYR* 3.7 35.6 - - + +
476A ASP* 3.0 11.2 + - - +
477A GLN* 1.3 75.7 - - - +
479A LYS* 1.3 60.7 + - - +
481A GLN* 3.2 1.8 + - - -
482A VAL* 2.8 51.9 + - + +
487A VAL* 4.2 6.1 - - + -
488A PHE* 3.8 22.0 - - + -
493A GLU* 4.2 7.4 - - - +
525A ARG* 3.8 29.4 - - + +
527A LEU* 4.4 13.9 - - + -
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Residues in contact with LYS 479 (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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473A TYR* 3.3 70.7 - - + +
474A ALA* 4.1 21.1 - - - +
476A ASP* 3.0 13.8 + - - +
478A LEU* 1.3 77.6 - - - +
480A ILE* 1.3 60.0 + - + +
482A VAL* 3.4 6.1 + - - +
483A ALA* 3.0 33.1 + - + +
525A ARG* 4.8 0.8 - - - +
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Residues in contact with ILE 480 (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 GLU* 4.7 13.9 - - + -
474A ALA 4.1 13.0 - - - +
475A TYR* 4.1 20.2 - - + +
476A ASP 3.2 17.3 + - - +
477A GLN* 3.7 9.0 - - - +
479A LYS* 1.3 84.1 - - + +
481A GLN* 1.3 70.8 + - - +
483A ALA* 3.2 8.1 + - - +
484A ALA* 3.0 29.2 + - + +
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Residues in contact with GLN 481 (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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408A TYR* 3.9 25.9 - - + -
412A ASN* 2.9 24.6 + - - +
450A TYR* 4.2 11.0 - - + -
477A GLN* 2.8 27.0 + - + +
478A LEU* 3.8 3.1 - - - +
480A ILE* 1.3 85.5 - - - +
482A VAL* 1.3 62.4 + - - +
484A ALA* 3.3 5.2 + - - +
485A LYS 3.1 17.2 + - - -
486A THR* 2.7 46.0 + - - +
487A VAL* 3.6 16.1 + - + -
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Residues in contact with VAL 482 (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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478A LEU* 2.8 46.7 + - + +
479A LYS* 3.7 6.1 - - - +
481A GLN* 1.3 71.6 - - - +
483A ALA* 1.3 64.1 + - - +
485A LYS* 3.1 17.7 + - - +
487A VAL* 4.0 17.3 - - + +
488A PHE* 4.2 21.8 - - + +
491A PHE 5.1 7.9 - - - +
527A LEU* 5.1 5.8 - - + -
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Residues in contact with ALA 483 (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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479A LYS* 3.0 19.1 + - + +
480A ILE* 3.2 11.4 + - - +
482A VAL* 1.3 77.4 - - - +
484A ALA* 1.3 61.3 + - - +
485A LYS* 3.3 11.4 + - - +
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Residues in contact with ALA 484 (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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480A ILE* 3.0 18.1 + - + +
481A GLN* 3.8 9.9 - - - +
482A VAL 3.3 0.4 - - - -
483A ALA* 1.3 74.1 - - - +
485A LYS* 1.3 69.9 + - - +
486A THR* 3.3 17.0 + - + +
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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