Contacts of the helix formed by residues 479 - 494 (chain B) in PDB entry 1VDV
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 ASN 479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477B PHE* 3.0 32.3 + - - +
478B TRP* 1.3 75.2 - - - +
480B GLU* 1.3 65.3 + - - +
481B LYS* 3.1 14.3 + - - +
482B LEU* 2.9 31.8 + - - +
483B LEU 3.1 9.7 + - - -
520B TYR* 2.8 18.6 + - - -
524B LEU* 5.8 0.2 - - - -
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Residues in contact with GLU 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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479B ASN* 1.3 74.7 - - + +
481B LYS* 1.3 56.7 + - - +
483B LEU* 3.2 27.7 + - - +
484B GLN* 3.0 52.2 + - - +
520B TYR* 3.0 9.7 + - - +
1312B LYS* 5.0 8.2 + - - -
5007B GOL 4.2 15.4 + - - -
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Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ASN* 3.1 12.8 + - - +
480B GLU* 1.3 78.8 - - - +
482B LEU* 1.3 57.0 + - - +
484B GLN* 3.2 19.9 + - + +
485B ASP* 2.8 70.1 + - - +
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Residues in contact with LEU 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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449B VAL* 4.1 8.7 - - + -
452B LEU* 5.5 0.9 - - + -
473B GLN* 3.6 42.2 - - + +
476B LYS* 4.3 4.3 - - + -
477B PHE 3.5 28.3 - - - +
478B TRP* 4.0 29.6 - - + -
479B ASN* 2.9 14.4 + - - +
481B LYS* 1.3 72.7 - - - +
483B LEU* 1.3 64.4 + - - +
485B ASP* 3.8 2.8 - - - +
486B VAL* 2.9 39.5 + - + +
516B PHE* 3.8 26.2 - - + -
520B TYR* 4.4 6.7 - - + -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ASN 3.1 10.7 + - - +
480B GLU* 3.4 29.2 - - - +
482B LEU* 1.3 77.5 - - - +
484B GLN* 1.3 63.4 + - + +
486B VAL* 4.0 0.5 - - - +
487B CYS* 3.1 49.3 + - - -
516B PHE* 3.9 24.0 - - + -
517B PHE* 3.8 35.0 - - + -
520B TYR* 3.8 33.4 - - + -
1312B LYS* 5.3 4.5 - - - +
1313B PHE* 4.8 4.5 - - + -
5007B GOL 5.8 0.4 - - - +
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Residues in contact with GLN 484 (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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480B GLU* 3.0 46.1 + - - +
481B LYS* 3.4 22.1 - - + +
483B LEU* 1.3 76.7 - - + +
485B ASP* 1.3 69.3 + - - +
487B CYS* 3.9 3.9 - - - +
488B ALA* 3.1 24.3 + - - +
1316B LEU* 5.2 2.4 - - - +
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Residues in contact with ASP 485 (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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469B THR* 4.7 1.0 - - - +
473B GLN* 3.1 26.3 + - - +
476B LYS* 5.7 5.0 - - - +
481B LYS* 2.8 56.9 + - - +
482B LEU* 3.8 1.5 - - - +
484B GLN* 1.3 76.3 - - - +
486B VAL* 1.3 53.5 + - - +
488B ALA* 3.2 6.9 + - - +
489B GLY* 2.8 33.3 + - - -
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Residues in contact with VAL 486 (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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452B LEU* 5.0 4.7 - - + -
454B LEU* 4.0 9.4 - - + -
469B THR* 3.6 13.1 - - + +
473B GLN* 3.8 22.0 - - + -
482B LEU* 2.9 29.4 + - + +
483B LEU 4.0 0.2 - - - +
485B ASP* 1.3 76.1 - - - +
487B CYS* 1.3 51.7 + - - +
489B GLY 3.2 0.3 + - - -
490B LEU* 2.8 49.5 + - + +
516B PHE* 3.4 51.8 - - + -
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Residues in contact with CYS 487 (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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483B LEU* 3.1 41.0 + - - +
484B GLN* 3.9 5.4 - - - +
486B VAL* 1.3 79.5 - - - +
488B ALA* 1.3 56.8 + - - +
490B LEU* 4.4 1.3 - - - -
491B ALA* 3.0 30.3 + - - +
513B LEU* 3.4 37.6 - - + +
516B PHE* 4.4 5.4 - - - -
1313B PHE* 3.9 24.2 - - + -
1316B LEU* 4.0 11.0 - - + -
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Residues in contact with ALA 488 (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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484B GLN 3.1 18.3 + - - +
485B ASP* 3.5 6.7 - - - +
487B CYS* 1.3 75.4 - - - +
489B GLY* 1.3 63.8 + - - +
491B ALA* 3.3 7.2 + - - +
492B GLU* 3.1 22.9 + - - +
1316B LEU* 4.3 10.7 - - + +
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Residues in contact with GLY 489 (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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468B LYS* 6.6 0.2 - - - -
469B THR* 3.2 20.2 - - - -
472B LYS* 5.7 6.5 - - - -
485B ASP 2.8 15.3 + - - -
486B VAL 3.6 2.0 - - - -
488B ALA* 1.3 77.0 - - - +
490B LEU* 1.3 51.4 + - - +
492B GLU* 3.1 10.2 + - - +
493B GLU* 2.7 38.3 + - - +
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Residues in contact with LEU 490 (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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454B LEU* 4.2 9.2 - - + -
456B TYR* 3.5 24.0 - - + +
466B ALA* 3.8 28.7 - - + -
469B THR* 3.5 5.3 + - + -
486B VAL* 2.8 39.4 + - + +
487B CYS* 4.5 1.1 - - - -
489B GLY* 1.3 71.6 - - - +
491B ALA* 1.3 58.5 + - - +
493B GLU* 4.4 0.7 - - - +
494B LEU* 2.8 54.9 + - + +
509B ARG* 4.6 0.2 + - - -
512B THR* 3.8 12.5 + - - +
513B LEU* 3.3 22.0 - - + -
516B PHE* 3.9 10.5 - - + -
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Residues in contact with ALA 491 (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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487B CYS 3.0 18.5 + - - +
488B ALA* 3.6 8.3 - - - +
489B GLY 3.3 0.2 - - - -
490B LEU* 1.3 76.6 - - - +
492B GLU* 1.3 59.1 + - - +
495B SER* 4.7 2.6 + - - -
509B ARG* 3.0 36.7 + - - +
513B LEU* 3.8 13.6 - - + +
1316B LEU* 3.7 26.7 - - + +
1317B CYS* 4.8 1.8 - - - -
1322B PRO 6.1 0.7 - - - +
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Residues in contact with GLU 492 (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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468B LYS* 3.9 23.5 - - - -
472B LYS* 4.7 6.1 + - - -
488B ALA 3.1 11.9 + - - +
489B GLY* 3.1 11.4 + - - +
491B ALA* 1.3 79.4 - - - +
493B GLU* 1.3 63.7 + - - +
494B LEU 3.5 0.2 - - - -
495B SER* 4.0 13.7 + - - -
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Residues in contact with GLU 493 (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 4.3 2.3 - - - +
466B ALA* 3.3 23.6 - - - +
467B LEU* 3.6 1.4 + - - +
468B LYS* 3.1 46.1 + - + +
469B THR* 2.6 37.3 + - - +
489B GLY 2.7 18.8 + - - +
490B LEU* 4.4 0.7 - - - +
492B GLU* 1.3 76.6 - - - +
494B LEU* 1.3 65.5 + - + +
495B SER* 3.2 8.6 + - - -
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Residues in contact with LEU 494 (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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456B TYR* 3.7 35.7 - - + -
459B MET* 3.4 28.5 - - + +
464B ILE* 3.9 27.4 - - + -
465B SER 5.7 0.2 - - - +
466B ALA* 4.3 12.6 - - + -
490B LEU* 2.8 34.2 + - + +
493B GLU* 1.3 85.5 - - + +
495B SER* 1.3 62.7 + - - +
509B ARG* 3.1 17.2 + - - +
512B THR* 3.9 23.3 + - + +
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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