Contacts of the helix formed by residues 465 - 482 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ASN 3.9 1.6 + - - -
464B LEU* 1.3 73.4 - - - +
466B LYS* 1.3 68.0 + - - +
467B ARG* 3.9 8.1 + - - +
468B GLN* 3.0 35.6 + - - +
469B ARG* 2.8 23.8 + - - +
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B SER* 1.3 72.2 - - - +
467B ARG* 1.3 58.4 + - + +
469B ARG* 3.1 32.0 + - - +
470B GLN* 2.8 58.7 + - + +
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Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B SER* 3.2 8.5 + - - +
466B LYS* 1.3 78.9 - - + +
468B GLN* 1.3 58.0 + - + +
470B GLN* 3.4 10.5 + - - +
471B SER* 3.0 31.2 + - - -
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B PHE* 4.2 20.1 - - - -
400B LEU* 3.7 23.3 - - + +
463B ASN 4.9 0.3 - - - +
464B LEU* 3.6 26.9 - - + +
465B SER* 3.0 34.6 + - - +
467B ARG* 1.3 76.5 - - + +
469B ARG* 1.3 57.6 - - - +
471B SER* 3.8 0.2 - - - -
472B LEU* 2.9 32.6 + - - +
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Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ASP* 5.7 2.7 - - - -
461B PHE* 3.6 28.8 + - + +
462B GLN* 4.8 6.4 + - - +
464B LEU* 3.0 40.5 + - + -
465B SER* 2.8 10.3 + - - +
466B LYS* 3.2 43.8 - - - +
468B GLN* 1.3 74.0 - - - +
470B GLN* 1.3 57.9 + - + +
472B LEU* 3.8 7.2 - - - +
473B ARG* 3.1 29.6 + - - +
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Residues in contact with GLN 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LYS* 2.8 53.0 + - + +
467B ARG* 3.9 9.5 - - - +
469B ARG* 1.3 72.5 - - + +
471B SER* 1.3 60.7 + - - +
473B ARG* 3.5 6.4 + - - +
474B LYS* 3.1 28.8 + - - +
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.0 12.2 - - - +
467B ARG 3.0 18.5 + - - -
468B GLN 3.8 2.9 - - - -
470B GLN* 1.3 75.9 - - - +
472B LEU* 1.3 64.8 + - - +
474B LYS* 3.4 7.0 + - - +
475B MET* 3.0 44.4 + - - +
515B TYR* 5.8 1.7 - - - -
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LEU* 4.1 11.0 - - + +
403B LEU* 3.9 23.6 - - + +
404B ALA* 3.6 33.7 - - + +
407B PHE* 4.8 0.9 - - + -
450B PHE* 4.5 8.3 - - + -
461B PHE* 3.9 34.8 - - + -
464B LEU* 4.7 5.2 - - + -
468B GLN 2.9 19.8 + - - +
469B ARG* 3.8 6.5 - - - +
471B SER* 1.3 76.9 - - - +
473B ARG* 1.3 59.7 + - - +
475B MET* 3.4 13.1 + - - +
476B VAL* 2.9 46.1 + - + +
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B PHE* 3.5 57.6 - - + +
469B ARG 3.1 20.2 + - - +
470B GLN* 3.7 7.2 - - - +
472B LEU* 1.3 74.7 - - + +
474B LYS* 1.3 64.8 + - - +
476B VAL* 3.2 1.6 + - - +
477B ILE* 3.0 51.7 + - + +
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Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B GLN 3.1 18.1 + - - +
471B SER* 3.7 7.6 - - - +
473B ARG* 1.3 75.8 - - - +
475B MET* 1.3 62.7 + - - +
477B ILE* 3.7 8.4 + - - +
478B ASP* 3.2 26.9 + - - +
515B TYR* 4.3 24.6 - - + +
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Residues in contact with MET 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.1 20.2 - - + +
401B GLU* 3.7 35.4 - - + +
404B ALA* 3.9 15.9 - - + -
471B SER* 3.0 44.9 + - - +
472B LEU* 3.6 11.2 - - - +
474B LYS* 1.3 74.8 - - + +
476B VAL* 1.3 58.2 + - - +
478B ASP* 3.2 9.2 - - - +
479B MET* 2.9 38.1 + - + +
515B TYR* 3.6 32.8 - - + +
519B ILE* 4.1 5.3 - - + +
522B LEU* 4.8 7.0 - - - -
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ALA* 3.6 28.7 - - - +
407B PHE* 3.9 9.2 - - + -
408B ALA* 4.0 11.4 - - - -
411B ILE* 4.0 15.3 - - + -
446B LEU* 3.9 7.0 - - + -
450B PHE* 3.7 26.7 - - + -
472B LEU* 2.9 37.5 + - + +
473B ARG 3.8 2.9 - - - +
475B MET* 1.3 71.9 - - - +
477B ILE* 1.3 60.9 + - - +
479B MET* 3.2 6.0 + - - +
480B VAL* 3.0 30.0 + - + +
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LEU* 3.5 26.6 - - + +
450B PHE* 4.5 5.4 - - + -
473B ARG* 3.0 57.4 + - + +
474B LYS* 3.9 7.0 - - - +
476B VAL* 1.3 74.3 - - - +
478B ASP* 1.3 63.9 + - - +
481B LEU* 3.0 44.7 + - + +
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Residues in contact with ASP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B LYS* 3.2 15.8 + - - +
475B MET* 3.2 11.2 - - - +
477B ILE* 1.3 82.9 - - - +
479B MET* 1.3 61.2 + - - +
481B LEU* 3.7 5.1 + - - +
482B ALA* 3.3 19.8 + - - +
515B TYR* 4.7 3.7 + - - +
519B ILE* 3.7 19.9 - - + +
523B ARG* 2.7 47.4 + - - +
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ALA* 3.7 14.8 - - + +
405B ALA* 3.6 37.9 - - + +
408B ALA* 3.9 9.6 - - + -
475B MET* 2.9 38.2 + - + +
476B VAL* 3.2 4.0 + - - +
478B ASP* 1.3 76.6 - - - +
480B VAL* 1.3 61.8 + - - +
482B ALA* 3.1 17.8 + - - +
483B THR* 3.6 10.7 + - - +
519B ILE* 4.2 9.6 - - + -
522B LEU* 3.8 20.9 - - + +
523B ARG* 3.8 26.7 - - - +
526B VAL* 3.8 23.6 - - + +
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B ALA* 3.6 34.1 - - + +
411B ILE* 4.3 4.0 - - + -
412B HIS* 4.1 27.1 - - + +
442B GLU* 3.7 18.9 - - - +
445B HIS* 4.3 4.7 - - + -
446B LEU* 3.6 30.7 - - + +
476B VAL* 3.0 21.7 + - + +
479B MET* 1.3 71.7 - - - +
481B LEU* 1.3 63.7 + - - +
483B THR* 2.5 30.6 + - - +
526B VAL* 5.9 0.4 - - + -
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Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B SER* 4.2 9.9 + - - +
442B GLU* 4.2 13.5 - - + -
443B ASN* 4.0 30.1 - - - +
446B LEU* 3.8 18.4 - - + -
477B ILE* 3.0 35.4 + - + +
478B ASP* 4.1 4.7 - - - +
480B VAL* 1.3 76.4 - - - +
482B ALA* 1.3 59.3 + - - +
483B THR 3.2 1.3 + - - -
484B ASP* 3.5 19.3 + - - +
487B LYS* 4.0 9.9 - - - +
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ASP 3.3 12.8 + - - +
479B MET 3.1 13.6 + - - +
481B LEU* 1.3 77.7 - - - +
483B THR* 1.3 56.0 + - - +
484B ASP 3.2 10.5 + - - +
487B LYS* 4.7 4.5 - - - +
491B LEU* 3.8 43.7 - - + +
523B ARG* 3.9 19.5 - - + +
527B HIS* 3.9 12.1 + - - -
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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
------------------------------------------------------------
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