Contacts of the helix formed by residues 471 - 488 (chain B) in PDB entry 3VOQ
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 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PRO 4.0 7.8 - - - +
449B SER* 3.6 18.8 + - - +
470B SER* 1.3 87.8 + - - +
472B ALA* 1.3 64.0 + - - +
473B ALA* 3.1 13.2 + - - +
474B THR* 2.7 36.6 + - - -
475B VAL* 3.1 19.1 + - - +
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.8 28.7 - - + +
447B SER 3.7 15.7 - - - +
448B PRO* 2.9 26.3 + - + +
449B SER 4.3 1.0 - - - -
450B HIS 4.3 0.2 - - - +
451B ALA* 3.9 11.2 - - + +
470B SER 3.8 0.8 + - - -
471B ASP* 1.3 72.5 - - - +
473B ALA* 1.3 55.6 + - - +
475B VAL* 3.8 1.4 - - - +
476B ASN* 3.0 30.7 + - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PRO 4.6 1.0 + - - -
471B ASP* 3.1 8.6 + - - +
472B ALA* 1.3 74.6 - - - +
474B THR* 1.3 60.5 + - - +
476B ASN* 3.4 6.3 + - - +
477B GLU* 2.9 30.6 + - - +
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Residues in contact with THR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 4.2 15.5 - - + -
387B LYS 4.8 2.7 - - - +
388B VAL* 4.2 5.8 - - + -
470B SER* 3.5 16.4 - - - +
471B ASP* 2.7 31.9 + - - -
473B ALA* 1.3 77.9 - - - +
475B VAL* 1.3 62.1 + - - +
477B GLU* 3.2 10.7 + - - +
478B ILE* 3.0 46.7 + - + +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B LEU* 3.7 30.5 - - + -
451B ALA* 3.6 30.7 - - + +
452B ILE 4.7 0.7 - - - -
453B PHE* 3.8 35.9 - - + -
470B SER* 3.9 14.6 - - - +
471B ASP 3.1 19.8 + - - +
472B ALA 3.8 4.5 - - - +
474B THR* 1.3 75.0 - - - +
476B ASN* 1.3 59.9 + - - +
478B ILE* 3.2 4.9 + - - +
479B VAL* 2.9 31.2 + - + +
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Residues in contact with ASN 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR 5.7 4.6 - - - +
442B LEU* 6.2 1.9 - - - +
445B GLU* 6.1 0.7 - - - +
472B ALA 3.0 19.2 + - - +
473B ALA* 3.7 6.0 - - - +
475B VAL* 1.3 78.2 - - - +
477B GLU* 1.3 64.0 + - - +
479B VAL* 4.0 6.4 - - - +
480B LEU* 3.0 52.9 + - - +
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS* 2.7 38.0 + - - +
386B PHE* 3.5 24.0 - - + -
473B ALA 2.9 18.2 + - - +
474B THR* 3.2 9.2 + - - +
476B ASN* 1.3 80.0 + - - +
478B ILE* 1.3 56.7 + - - +
480B LEU* 3.8 6.0 - - - +
481B LYS* 3.0 29.3 + - + +
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Residues in contact with ILE 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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386B PHE* 3.7 41.3 - - + -
388B VAL* 3.7 26.7 - - + -
402B LEU* 4.1 5.2 - - + -
404B ILE* 3.6 19.7 - - + -
453B PHE* 3.6 37.7 - - + -
474B THR* 3.0 22.1 + - + +
475B VAL* 3.6 6.3 - - - +
477B GLU* 1.3 74.5 - - - +
479B VAL* 1.4 67.5 + - - +
481B LYS* 3.2 6.2 + - - +
482B VAL* 2.9 29.7 + - + +
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Residues in contact with VAL 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.6 28.0 - - + -
440B CYS* 3.7 17.9 - - - +
442B LEU* 4.3 13.7 - - + +
453B PHE* 3.8 30.7 - - + -
475B VAL* 2.9 26.1 + - + +
476B ASN* 4.0 7.4 - - - +
478B ILE* 1.4 74.7 - - - +
480B LEU* 1.3 66.9 + - + +
482B VAL* 3.5 0.5 + - - +
483B ASN* 3.0 43.9 + - - +
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 5.7 3.1 - - + -
423A PHE* 3.7 27.6 - - + -
476B ASN* 3.0 45.1 + - - +
477B GLU* 3.8 6.1 - - - +
479B VAL* 1.3 80.0 - - + +
481B LYS* 1.4 57.4 + - - +
483B ASN* 3.3 4.1 + - - +
484B TYR* 2.8 34.6 + - + +
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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
----------------------------------------------------------
379B SER 3.4 9.3 + - - -
380B SER* 2.6 41.5 + - - +
382B HIS* 2.7 17.8 + - - +
384B LYS* 4.1 14.2 - - + +
386B PHE* 4.1 22.7 - - + -
404B ILE* 3.2 45.1 - - + -
405B SER* 4.7 0.4 - - - +
477B GLU* 3.0 21.3 + - + +
478B ILE* 3.6 4.7 - - - +
480B LEU* 1.4 76.8 - - - +
482B VAL* 1.4 63.6 + - + +
484B TYR* 3.3 7.4 + - - +
485B ILE* 3.0 27.1 + - + +
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Residues in contact with VAL 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ILE* 3.9 30.5 - - + -
409B VAL* 5.4 3.4 - - + -
437B LEU* 4.5 15.0 - - + -
439B ALA 5.0 0.4 - - - -
440B CYS* 3.4 36.3 - - + -
453B PHE* 6.0 0.2 - - + -
455B LEU* 4.1 16.6 - - + -
478B ILE* 2.9 25.0 + - + +
479B VAL 4.1 0.2 - - - +
481B LYS* 1.4 71.5 - - - +
483B ASN* 1.3 60.2 + - - +
485B ILE* 3.1 10.4 + - - +
486B LEU* 2.8 43.7 + - + +
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Residues in contact with ASN 483 (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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423A PHE* 3.4 48.5 - - + -
439B ALA* 5.4 0.2 - - - -
440B CYS* 2.8 32.0 + - - +
479B VAL* 3.0 27.9 + - - +
480B LEU 3.9 2.7 - - - +
482B VAL* 1.3 72.8 - - - +
484B TYR* 1.3 62.8 + - - +
486B LEU* 3.7 19.9 - - - +
487B GLU* 2.8 41.1 + - - +
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Residues in contact with TYR 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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373B THR* 4.7 2.3 + - - +
376B ASP* 3.3 35.7 + - + +
377B MET* 3.9 20.5 - - + +
380B SER* 3.1 35.2 - - - -
480B LEU* 2.8 20.2 + - + +
481B LYS* 3.6 5.8 - - - +
482B VAL 3.2 0.2 - - - -
483B ASN* 1.3 78.0 - - - +
485B ILE* 1.3 58.7 + - - +
487B GLU* 3.5 10.1 + - + +
488B SER* 2.8 42.5 + - - -
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Residues in contact with ILE 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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380B SER 3.8 19.3 - - - +
381B HIS* 3.8 23.4 + - + +
404B ILE* 3.9 18.6 - - + -
405B SER 3.4 30.5 - - - +
406B GLY* 4.3 18.4 - - - +
434B SER* 4.6 13.2 - - - +
437B LEU* 5.1 9.4 - - + -
481B LYS* 3.0 16.5 + - + +
482B VAL* 3.1 8.3 + - - +
484B TYR* 1.3 74.7 - - - +
486B LEU* 1.4 69.5 + - + +
488B SER* 3.4 9.5 + - - -
489B ARG* 3.8 13.2 + - - +
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Residues in contact with LEU 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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437B LEU* 3.9 25.4 - - + +
438B CYS 3.9 6.3 - - - +
439B ALA* 3.8 26.9 - - - -
440B CYS 4.2 0.2 - - - +
482B VAL* 2.8 33.2 + - + +
483B ASN* 3.7 26.2 - - - +
485B ILE* 1.4 75.7 - - + +
487B GLU* 1.3 65.1 + - + +
488B SER 3.2 1.0 + - - -
489B ARG* 3.3 55.8 + - - +
490B ALA 4.8 0.2 + - - -
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Residues in contact with GLU 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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422A LYS* 4.9 4.0 + - - -
423A PHE* 4.0 26.2 - - - -
483B ASN* 2.8 30.1 + - - +
484B TYR* 4.0 9.3 - - + +
486B LEU* 1.3 73.9 - - + +
488B SER* 1.3 60.7 + - - +
489B ARG 3.2 0.9 + - - -
490B ALA* 3.7 16.2 + - - +
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MET* 3.4 21.1 - - - +
381B HIS* 3.3 34.2 - - - -
484B TYR* 2.8 26.1 + - - -
485B ILE 3.8 2.7 - - - -
486B LEU 3.2 1.0 - - - -
487B GLU* 1.3 75.0 - - - +
489B ARG* 1.3 64.8 + - - +
490B ALA 3.2 8.5 - - - +
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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
------------------------------------------------------------
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