Contacts of the helix formed by residues 464 - 472 (chain A) in PDB entry 3CTZ
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 LYS 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A GLY 3.5 2.9 + - - +
463A THR* 1.3 77.9 - - - +
465A GLY* 1.3 60.8 + - - +
466A HIS* 3.1 34.3 - - + +
467A LEU* 2.9 36.5 + - + +
468A LEU* 4.8 0.3 - - - +
509A PHE* 3.6 28.5 - - + +
510A SER* 5.3 1.3 - - - +
511A ASP* 3.4 27.8 - - - +
512A GLU* 4.2 1.6 - - - -
513A PRO* 4.0 29.0 - - + +
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Residues in contact with GLY 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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463A THR 3.5 2.6 + - - -
464A LYS* 1.3 71.4 - - - +
466A HIS* 1.3 64.1 + - - +
468A LEU* 2.8 16.9 + - - +
503A GLY 3.2 21.1 - - - -
504A ILE* 3.4 17.4 - - - +
511A ASP* 3.2 6.7 + - - -
512A GLU 4.2 2.6 + - - -
514A LEU* 3.7 28.1 - - - +
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 3.1 29.3 - - + +
465A GLY* 1.3 76.9 - - - +
467A LEU* 1.3 80.4 + - + +
468A LEU 3.1 4.7 + - - -
469A ASP* 3.2 18.4 + - - +
470A SER* 4.7 0.7 + - - -
503A GLY 3.7 0.2 + - - -
505A SER 3.2 32.0 - - - +
506A TYR* 5.5 0.4 - - - -
508A THR* 3.4 13.5 - - - +
509A PHE* 3.4 38.5 - + + +
511A ASP* 2.8 28.6 + - - +
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Residues in contact with LEU 467 (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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463A THR* 4.1 15.7 - - + -
464A LYS* 2.9 31.8 + - + +
466A HIS* 1.3 102.9 - - + +
468A LEU* 1.3 63.9 + - - +
469A ASP 3.5 0.4 - - - -
470A SER* 5.0 2.6 + - - -
471A PHE* 4.5 10.6 - - - -
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Residues in contact with LEU 468 (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 VAL* 3.7 15.0 - - + +
457A ALA* 4.6 2.9 - - + -
459A PHE* 3.7 45.3 - - + -
463A THR* 4.6 9.4 - - + -
464A LYS 4.8 1.1 - - - +
465A GLY* 2.8 15.8 + - - +
467A LEU* 1.3 83.4 - - - +
469A ASP* 1.3 65.5 + - - +
470A SER 3.3 2.5 - - - -
471A PHE* 3.1 46.8 + - + +
504A ILE* 3.9 15.7 - - + -
514A LEU* 3.8 20.2 - - + -
559A LEU* 4.5 13.9 - - + -
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Residues in contact with ASP 469 (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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466A HIS 3.2 15.1 + - - +
468A LEU* 1.3 79.6 - - - +
470A SER* 1.3 66.6 + - - +
472A ALA* 3.1 20.1 + - - +
473A ARG* 2.8 37.2 + - - +
477A TRP* 5.7 0.2 - - - -
487A THR* 2.6 33.4 + - - -
504A ILE* 3.6 19.0 - - + +
505A SER* 3.7 9.6 - - - -
506A TYR* 3.7 23.2 - - - +
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Residues in contact with SER 470 (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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466A HIS 4.7 1.0 + - - -
467A LEU 5.0 3.0 + - - -
468A LEU 3.3 0.6 - - - -
469A ASP* 1.3 80.7 + - - +
471A PHE* 1.3 67.6 + - - +
473A ARG* 2.9 14.7 + - - +
474A SER* 3.1 17.6 + - - -
477A TRP* 3.6 33.3 - - - -
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Residues in contact with PHE 471 (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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450A GLY* 3.9 3.3 - - - -
453A ALA* 3.4 41.7 - - + +
454A VAL* 4.2 5.8 - - + -
457A ALA* 4.2 11.9 - - + -
458A VAL 6.0 1.1 - - - -
459A PHE* 6.3 0.7 - - + -
467A LEU 4.5 8.5 + - - -
468A LEU* 3.1 43.1 + - + +
470A SER* 1.3 79.5 - - - +
472A ALA* 1.3 60.6 + - - +
473A ARG 3.3 0.5 + - - -
474A SER* 3.9 14.5 + - - -
475A ALA 5.3 0.2 + - - -
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Residues in contact with ALA 472 (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 4.8 2.4 - - - +
450A GLY* 3.3 29.4 - - - +
454A VAL* 3.7 10.3 - - + +
469A ASP 3.1 10.0 + - - +
470A SER 3.1 0.6 - - - -
471A PHE* 1.3 79.5 - - - +
473A ARG* 1.3 58.9 + - - +
475A ALA 5.3 0.3 + - - -
476A LEU* 4.5 5.2 + - - +
483A TYR* 3.2 23.5 + - - +
487A THR* 3.6 20.6 - - + -
524A PRO* 4.1 15.7 - - + +
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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