Contacts of the helix formed by residues 465 - 482 (chain A) in PDB entry 3TVX
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 SER 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A ASN 3.6 2.6 + - - -
464A LEU* 1.3 75.0 - - - +
466A LYS* 1.3 66.9 + - - +
467A ARG* 3.4 29.8 + - - -
468A GLN* 3.0 36.7 + - - +
469A ARG* 2.9 20.9 + - - +
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Residues in contact with LYS 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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465A SER* 1.3 71.4 - - - +
467A ARG* 1.3 65.7 + - + +
469A ARG* 3.1 31.9 + - - +
470A GLN* 2.9 52.4 + - + +
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Residues in contact with ARG 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A SER* 3.3 27.5 + - - -
466A LYS* 1.3 79.1 - - + +
468A GLN* 1.3 66.1 + - + +
470A GLN* 3.4 13.7 + - - +
471A SER* 3.0 30.0 + - - -
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Residues in contact with GLN 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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347A PHE* 4.4 18.8 - - - -
400A LEU* 3.8 32.1 - - + +
463A ASN 5.0 0.3 - - - +
464A LEU* 3.6 17.3 - - + +
465A SER* 3.0 37.4 + - - +
467A ARG* 1.3 85.5 - - - +
469A ARG* 1.3 55.9 - - - +
471A SER* 3.2 1.4 + - - -
472A LEU* 2.7 37.6 + - - +
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Residues in contact with ARG 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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459A ASP* 5.7 2.5 - - - -
461A PHE* 3.4 39.3 - - + +
462A GLN* 5.3 3.5 + - - +
464A LEU* 3.2 28.8 + - + +
465A SER 2.9 6.2 + - - +
466A LYS* 3.1 38.7 + - - +
468A GLN* 1.3 76.7 - - - +
470A GLN* 1.3 61.8 + - - +
472A LEU* 3.7 6.4 - - + +
473A ARG* 3.0 25.5 + - - +
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Residues in contact with GLN 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 LYS* 2.9 47.7 + - + +
467A ARG* 3.5 11.9 + - - +
469A ARG* 1.3 78.8 - - + +
471A SER* 1.3 61.6 + - - +
473A ARG* 3.5 8.9 + - - +
474A LYS* 3.3 22.9 + - - +
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Residues in contact with SER 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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400A LEU* 3.9 13.1 - - - +
467A ARG 3.0 18.0 + - - -
468A GLN* 3.2 4.7 + - - -
470A GLN* 1.3 74.3 - - - +
472A LEU* 1.3 65.7 + - - +
474A LYS* 3.4 7.5 + - - +
475A MET* 3.2 39.3 + - - +
515A TYR* 5.7 3.5 - - - -
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Residues in contact with LEU 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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400A LEU* 4.1 11.0 - - + -
403A LEU* 3.9 23.6 - - + -
404A ALA* 3.6 32.1 - - + +
407A PHE* 4.3 3.4 - - + -
450A PHE* 4.4 8.5 - - + -
461A PHE* 4.1 32.5 - - + -
464A LEU* 4.7 4.9 - - + -
468A GLN 2.7 21.9 + - - +
469A ARG* 3.7 6.5 - - + +
471A SER* 1.3 70.1 - - - +
473A ARG* 1.3 66.5 + - - +
475A MET* 3.2 12.9 + - - +
476A VAL* 2.9 44.1 + - + +
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Residues in contact with ARG 473 (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 PHE* 4.0 33.2 - - + -
469A ARG 3.0 18.3 + - - +
470A GLN* 3.6 8.2 + - - +
472A LEU* 1.3 76.9 - - - +
474A LYS* 1.3 70.5 + - - +
476A VAL* 3.3 1.9 + - - +
477A ILE* 2.9 54.6 + - + +
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Residues in contact with LYS 474 (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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470A GLN 3.3 11.4 + - - +
471A SER* 3.6 10.3 - - - +
472A LEU 3.3 0.8 - - - -
473A ARG* 1.3 82.9 - - - +
475A MET* 1.3 62.6 + - - +
477A ILE* 3.0 14.7 + - + +
478A ASP* 3.0 29.2 + - - +
515A TYR* 4.8 9.2 - - - +
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Residues in contact with MET 475 (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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400A LEU* 3.8 27.6 - - + +
401A GLU* 3.5 38.6 - - + +
404A ALA* 3.9 4.5 - - + -
471A SER* 3.2 38.7 + - - +
472A LEU* 3.6 9.4 - - - +
474A LYS* 1.3 77.8 - - + +
476A VAL* 1.3 58.0 + - - +
478A ASP* 3.3 4.2 + - - +
479A MET* 3.0 47.9 + - + +
515A TYR* 3.9 27.1 - - + +
519A ILE* 3.9 12.2 - - + +
522A LEU* 4.8 5.2 - - - -
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Residues in contact with VAL 476 (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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404A ALA* 3.7 25.4 - - + +
407A PHE* 3.9 9.0 - - + -
408A ALA* 4.2 10.5 - - - -
411A ILE* 3.9 15.7 - - + -
446A LEU* 3.9 8.5 - - + -
450A PHE* 3.7 24.7 - - + -
472A LEU* 2.9 40.4 + - + +
473A ARG 3.7 3.4 - - - +
475A MET* 1.3 71.0 - - - +
477A ILE* 1.3 65.2 + - - +
479A MET* 4.0 0.4 - - - +
480A VAL* 3.0 29.2 + - + +
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Residues in contact with ILE 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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446A LEU* 3.8 23.2 - - + +
450A PHE* 5.0 2.7 - - + -
473A ARG* 2.9 62.7 + - + +
474A LYS* 3.0 12.1 + - + +
476A VAL* 1.3 75.7 - - - +
478A ASP* 1.3 64.1 + - - +
481A LEU* 2.9 58.5 + - + +
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Residues in contact with ASP 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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474A LYS* 3.0 16.7 + - - +
475A MET 3.7 7.2 - - - +
477A ILE* 1.3 83.0 - - - +
479A MET* 1.3 61.7 + - - +
481A LEU* 4.7 2.6 - - - +
482A ALA* 3.2 7.6 + - - +
515A TYR* 4.5 4.5 + - - -
519A ILE* 4.0 28.6 - - + +
523A ARG* 2.9 47.3 + - - +
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Residues in contact with MET 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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404A ALA* 3.8 13.2 - - + +
405A ALA* 3.7 39.7 - - + +
408A ALA* 3.9 12.1 - - + -
475A MET* 3.0 37.5 + - + +
476A VAL* 4.0 1.6 - - - +
477A ILE 3.2 0.2 - - - -
478A ASP* 1.3 74.5 - - - +
480A VAL* 1.3 64.5 + - - +
482A ALA* 3.3 17.1 + - - +
483A THR* 3.7 12.7 + - - +
519A ILE* 4.2 8.3 - - + -
522A LEU* 3.7 43.3 - - + +
523A ARG* 4.0 4.2 - - - +
526A VAL* 3.9 24.0 - - + +
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Residues in contact with VAL 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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408A ALA* 3.9 31.9 - - + +
411A ILE* 4.3 7.0 - - + -
412A HIS* 4.2 22.2 - - + +
442A GLU* 3.8 19.4 - - - +
445A HIS* 4.3 4.3 - - + -
446A LEU* 3.6 30.1 - - + -
476A VAL* 3.0 20.0 + - + +
479A MET* 1.3 72.0 - - - +
481A LEU* 1.3 65.1 + - - +
483A THR* 2.5 33.5 + - - +
526A VAL* 5.8 0.2 - - - -
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Residues in contact with LEU 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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439A SER* 4.2 16.1 + - - +
442A GLU* 4.2 9.0 - - + -
443A ASN* 4.1 27.4 - - - +
446A LEU* 4.0 17.3 - - + -
477A ILE* 2.9 37.6 + - + +
478A ASP* 4.1 6.1 - - - +
480A VAL* 1.3 76.8 - - - +
482A ALA* 1.3 59.7 + - - +
483A THR 3.1 1.5 + - - -
484A ASP* 3.4 20.1 + - - +
487A LYS* 3.8 17.0 - - - +
523A ARG* 4.2 10.8 - - - +
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Residues in contact with ALA 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 ASP 3.2 18.9 + - - +
479A MET 3.4 9.2 - - - +
480A VAL 3.1 1.6 - - - -
481A LEU* 1.3 74.5 - - - +
483A THR* 1.3 60.7 + - - +
484A ASP 3.3 7.0 + - - +
487A LYS* 4.8 2.6 - - - +
488A HIS 5.6 0.7 + - - -
491A LEU* 3.7 30.1 - - + +
523A ARG* 3.8 28.5 - - + +
527A HIS* 3.8 20.3 + - - +
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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