Contacts of the helix formed by residues 458 - 471 (chain B) in PDB entry 2VXO
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 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A ILE* 5.0 3.5 - - + +
391A HIS* 4.3 22.2 - - + +
456B CYS* 3.4 9.2 - - - +
457B LYS* 1.3 77.1 - - - +
459B PHE* 1.3 61.3 + - - +
460B PRO* 3.6 1.3 - - - -
461B GLU* 3.4 12.8 + - - +
462B THR* 2.8 31.5 + - - +
528B TYR* 2.8 31.9 + - - -
556B ASN* 2.8 38.6 + - - +
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Residues in contact with PHE 459 (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 TYR 4.5 1.6 - - - -
455B ILE* 3.7 39.3 - - + -
456B CYS 3.2 16.0 + - - +
458B ASP* 1.3 80.3 + - - +
460B PRO* 1.4 73.0 - - + +
462B THR* 3.9 1.9 - - - -
463B ASN* 3.1 47.6 + - - -
511B LEU* 3.5 45.2 - - + +
513B PRO* 4.7 11.2 - - + -
528B TYR* 3.6 20.0 - + - +
572B PRO 5.4 1.6 - - - -
573B THR* 4.8 17.3 - - + -
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Residues in contact with PRO 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B CYS 4.4 1.3 - - - +
457B LYS 3.5 14.6 - - - +
459B PHE* 1.4 99.2 - - + +
461B GLU* 1.3 64.2 + - - +
463B ASN* 3.4 7.1 + - + +
464B ASN* 3.1 33.7 + - - +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 4.2 17.2 - - - +
391A HIS* 3.6 27.1 + - - -
402A ARG* 5.2 0.3 + - - -
403A GLU* 3.8 16.7 - - - +
457B LYS 5.5 0.9 - - - +
458B ASP* 3.4 13.4 + - - +
459B PHE 3.4 0.4 - - - -
460B PRO* 1.3 79.3 - - - +
462B THR* 1.3 62.7 + - - +
464B ASN* 3.1 11.9 + - + +
465B ILE* 3.0 30.3 + - + +
482B LEU* 5.0 3.3 - - + +
485B ARG* 2.9 36.4 + - - +
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Residues in contact with THR 462 (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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374A ILE* 3.4 13.2 - - - +
458B ASP 2.8 21.7 + - - -
461B GLU* 1.3 77.5 - - - +
463B ASN* 1.3 57.6 + - - +
465B ILE* 3.2 6.0 + - - +
466B LEU* 2.9 38.3 + - + +
511B LEU* 3.7 37.7 - - + -
554B CYS* 4.5 8.1 - - - -
556B ASN* 2.8 34.5 + - - +
557B VAL* 4.2 4.9 - - + -
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Residues in contact with ASN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PHE* 3.1 56.8 + - - +
460B PRO* 3.8 6.8 - - + +
461B GLU 3.3 0.2 - - - -
462B THR* 1.3 73.0 - - - +
464B ASN* 1.3 62.3 + - - +
466B LEU* 3.9 3.9 - - - +
467B LYS* 2.9 29.1 + - - +
509B ALA 4.6 2.8 - - - +
510B PHE* 3.4 11.6 - - + +
511B LEU* 2.8 32.9 + - - +
571B PRO* 6.4 0.7 - - - -
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Residues in contact with ASN 464 (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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460B PRO* 3.1 23.3 + - - +
461B GLU* 3.1 10.5 + - - +
463B ASN* 1.3 75.2 - - - +
465B ILE* 1.3 65.3 + - - +
467B LYS* 3.4 14.9 + - - +
468B ILE* 3.1 27.5 + - - +
482B LEU* 3.5 20.3 - - + +
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Residues in contact with ILE 465 (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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373A LEU* 3.8 39.9 - - + -
374A ILE* 3.6 31.6 - - + -
461B GLU* 3.0 27.4 + - + +
462B THR* 3.2 6.9 + - - +
464B ASN* 1.3 74.4 - - - +
466B LEU* 1.3 59.6 + - + +
468B ILE* 3.2 7.4 + - - +
469B VAL* 3.0 32.7 + - + +
482B LEU* 4.1 21.5 - - + -
485B ARG* 4.8 2.2 - - - +
486B VAL* 4.6 3.1 - - + +
553B MET* 4.1 12.8 - - + -
554B CYS* 3.8 17.7 - - - -
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Residues in contact with LEU 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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462B THR* 2.9 23.4 + - + +
463B ASN* 3.9 4.3 - - - +
464B ASN 3.3 0.4 - - - -
465B ILE* 1.3 75.1 - - + +
467B LYS* 1.3 65.1 + - - +
469B VAL* 3.3 7.8 + - + +
470B ALA* 2.9 26.9 + - - +
509B ALA* 3.7 22.1 - - + +
510B PHE* 3.7 29.8 - - - +
511B LEU* 3.7 24.2 - - + +
530B CYS* 4.1 9.2 - - + -
550B ILE* 3.6 38.4 - - + -
554B CYS* 4.7 12.8 - - - -
557B VAL* 5.3 0.9 - - + -
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Residues in contact with LYS 467 (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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463B ASN 2.9 18.1 + - - +
464B ASN* 3.5 16.4 - - - +
465B ILE 3.3 0.2 - - - -
466B LEU* 1.3 76.5 - - - +
468B ILE* 1.3 58.5 + - + +
470B ALA* 3.5 4.4 + - - +
471B ASP* 3.1 36.1 + - + +
509B ALA 4.0 7.5 + - - +
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Residues in contact with ILE 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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464B ASN 3.1 6.7 + - - +
465B ILE 3.2 7.2 + - - +
467B LYS* 1.3 74.2 - - + +
469B VAL* 1.3 66.0 + - - +
471B ASP* 3.3 1.1 - - - -
472B PHE* 3.0 30.4 + - + +
475B SER* 3.5 20.4 - - - +
482B LEU* 3.5 46.2 - - + +
483B LEU* 3.8 34.3 - - + +
486B VAL* 4.0 19.5 - - + -
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE* 3.0 20.6 + - + +
466B LEU* 3.3 10.7 + - + +
468B ILE* 1.3 77.9 - - - +
470B ALA* 1.3 61.4 - - - +
472B PHE* 3.5 10.7 + - - +
486B VAL* 4.9 5.6 - - + -
498B LEU* 4.0 24.7 - - + +
502B THR* 3.3 17.0 - - - +
509B ALA* 5.8 0.7 - - + -
546B LEU* 4.3 13.6 - - + +
549B LEU* 4.4 4.9 - - + -
550B ILE* 4.3 22.0 - - + -
553B MET* 3.6 32.3 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.8 + - - +
467B LYS* 3.8 5.2 - - - +
469B VAL* 1.3 77.4 - - - +
471B ASP* 1.3 57.8 + - + +
472B PHE 3.5 0.7 - - - -
502B THR* 3.2 22.4 - - - +
505B HIS 5.3 0.2 - - - +
507B LEU* 3.4 43.1 + - + +
508B ASN* 4.0 0.4 - - - -
509B ALA* 3.7 25.1 - - + +
532B ILE* 6.3 0.2 - - + -
546B LEU* 6.0 2.9 - - - -
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Residues in contact with ASP 471 (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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467B LYS* 3.1 21.4 + - + +
468B ILE* 3.3 4.7 - - - -
470B ALA* 1.3 79.3 - - + +
472B PHE* 1.3 50.6 + - - -
473B SER 3.6 1.3 - - - -
474B ALA* 3.4 25.6 + - - +
475B SER* 2.8 40.1 + - - +
502B THR* 4.3 6.2 - - - +
507B LEU 5.3 2.5 - - - +
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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
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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