Contacts of the helix formed by residues 456 - 466 (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 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A GLU 3.7 1.3 + - - +
455A LEU* 1.3 76.0 - - - +
457A VAL* 1.3 65.6 + - - +
458A GLU* 3.1 21.5 - - - +
459A LYS* 2.9 48.6 + - - +
460A VAL* 3.0 12.3 + - - +
519A ALA* 5.9 0.2 - - - -
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Residues in contact with VAL 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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456A ASP* 1.3 74.5 - - - +
458A GLU* 1.3 66.6 + - + +
460A VAL* 3.4 7.0 + - - +
461A LYS* 3.0 56.7 + - + +
517A CYS* 4.5 16.6 - - - +
518A ARG 4.5 2.7 - - - +
519A ALA* 3.8 37.0 - - + +
520A PRO* 4.5 0.2 - - + -
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Residues in contact with GLU 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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456A ASP* 3.1 27.1 - - - +
457A VAL* 1.3 87.4 + - + +
459A LYS* 1.3 56.9 + - - +
461A LYS* 3.4 8.3 + - - +
462A LYS* 3.0 28.8 + - - +
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Residues in contact with LYS 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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455A LEU* 4.2 26.5 - - + -
456A ASP* 2.9 27.8 + - - +
458A GLU* 1.3 74.9 - - - +
460A VAL* 1.3 65.3 + - - +
462A LYS* 3.3 10.9 + - + +
463A LEU* 3.0 51.8 + - + +
466A GLU* 5.5 1.8 + - - -
471A MET* 5.4 11.6 - - - +
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Residues in contact with VAL 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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452A ILE* 4.1 20.0 - - + +
455A LEU* 3.9 21.8 - - + +
456A ASP 3.0 19.9 + - - +
457A VAL* 3.5 10.1 - - - +
459A LYS* 1.3 76.6 - - - +
461A LYS* 1.3 61.2 + - - +
463A LEU* 3.5 4.5 + - - +
464A ILE* 3.2 37.9 + - + +
472A LEU* 3.9 18.5 - - + +
519A ALA* 5.2 6.3 - - + -
520A PRO* 4.0 29.6 - - + +
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Residues in contact with LYS 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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457A VAL* 3.0 40.8 + - + +
458A GLU* 3.9 6.5 - - - +
460A VAL* 1.3 75.9 - - - +
462A LYS* 1.3 61.7 + - - +
464A ILE* 3.5 10.0 + - - +
465A GLU* 3.1 23.3 + - - +
511A TRP* 3.8 46.3 + - + +
512A ASP 4.7 4.2 + - - -
517A CYS* 4.4 15.8 - - - -
518A ARG 4.5 3.3 + - - -
520A PRO* 4.0 21.1 - - + -
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Residues in contact with LYS 462 (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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458A GLU 3.0 18.2 + - - +
459A LYS* 3.6 14.8 - - + +
460A VAL 3.3 0.2 - - - -
461A LYS* 1.3 74.3 - - - +
463A LEU* 1.3 66.0 + - - +
465A GLU* 3.0 21.4 + - + +
466A GLU* 2.9 61.7 + - + +
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Residues in contact with LEU 463 (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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455A LEU* 3.6 31.4 - - + -
459A LYS* 3.0 43.2 + - + +
460A VAL 3.7 4.3 - - - +
462A LYS* 1.3 76.1 - - + +
464A ILE* 1.3 57.4 + - - +
466A GLU* 3.3 19.1 + - - +
467A LYS 2.9 6.8 + - - -
468A ASP* 2.9 49.2 + - + +
471A MET* 3.9 30.5 - - + -
472A LEU* 4.1 18.6 - - + -
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A VAL* 3.2 23.1 + - + +
461A LYS* 3.7 7.9 - - - +
462A LYS 3.1 1.2 - - - -
463A LEU* 1.3 73.1 - - - +
465A GLU* 1.3 66.1 + - - +
467A LYS* 3.1 19.1 + - - +
469A PHE* 4.4 9.3 - - + -
472A LEU* 3.6 16.2 - - + -
499A GLN* 3.9 27.8 - - + +
500A PRO* 3.8 17.9 - - + -
511A TRP* 3.9 25.4 - - + +
520A PRO* 3.7 31.2 - - + -
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Residues in contact with GLU 465 (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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461A LYS 3.1 13.8 + - - +
462A LYS* 3.0 24.6 + - + +
464A ILE* 1.3 76.8 - - - +
466A GLU* 1.3 62.3 + - + +
467A LYS* 3.5 8.8 + - - +
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Residues in contact with GLU 466 (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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459A LYS* 5.5 1.9 + - - -
462A LYS* 2.9 56.6 + - - +
463A LEU* 3.5 26.9 - - - +
465A GLU* 1.3 75.9 - - - +
467A LYS* 1.3 67.9 + - - +
468A ASP* 3.4 10.2 + - + +
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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