Contacts of the helix formed by residues 450 - 466 (chain B) in PDB entry 2VGB
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 450 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B SER* 3.2 9.3 + - - +
449B ARG* 1.3 76.3 - - - +
451B PRO* 1.3 73.2 - - - +
452B THR* 3.1 31.4 + - - -
453B GLU* 2.9 26.5 + - + +
454B VAL* 3.1 11.2 + - - +
479B ARG* 4.9 7.6 + - - -
483B LEU* 4.0 9.4 - - - +
563B GLY 5.1 2.9 - - - +
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Residues in contact with PRO 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 5.1 7.9 - - + -
570A VAL* 4.4 18.6 - - + +
449B ARG 3.1 11.2 - - - +
450B ASP* 1.3 89.6 - - - +
452B THR* 1.3 54.8 + - - +
454B VAL* 3.3 11.2 + - + +
455B THR* 2.8 33.8 + - - -
564B TYR* 6.0 0.9 - - - -
565B THR 3.8 13.7 - - - +
566B ASN* 4.3 11.9 - - + -
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Residues in contact with THR 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ASP* 3.0 19.3 + - - -
451B PRO* 1.3 77.7 - - - +
453B GLU* 1.3 62.1 + - - +
455B THR* 3.2 4.9 + - - -
456B ALA* 3.0 21.7 + - + +
479B ARG* 5.2 3.1 - - + -
480B SER* 3.5 31.9 - - - +
483B LEU* 3.5 17.7 - - + -
563B GLY* 4.1 12.6 + - - -
565B THR* 3.6 30.8 + - + +
580B FBP 5.9 1.8 - - - +
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LYS* 4.2 5.3 + - - -
448B SER* 3.7 28.1 + - - +
450B ASP* 2.9 19.9 + - + +
452B THR* 1.3 74.3 - - - +
454B VAL* 1.3 63.2 + - - +
456B ALA* 3.0 16.6 + - - +
457B ILE* 3.0 17.1 + - - +
479B ARG* 5.6 1.9 + - - +
483B LEU* 3.6 32.0 - - + +
486B ARG* 4.4 13.3 + - - -
487B TYR* 2.8 34.8 + - - -
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Residues in contact with VAL 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ALA* 3.4 43.8 - - + +
465A LYS* 4.4 8.5 - - + -
466A CYS* 4.1 16.4 - - + -
551A LEU* 5.3 2.2 - - + -
570A VAL* 4.1 15.9 - - + -
448B SER* 4.0 20.9 - - - +
449B ARG 4.4 2.9 - - - +
450B ASP 3.1 22.0 - - - +
451B PRO* 3.5 9.6 - - + +
453B GLU* 1.3 76.7 - - - +
455B THR* 1.3 61.3 + - - +
457B ILE* 3.5 9.2 - - - +
458B GLY 3.4 14.0 + - - -
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A MET* 4.8 9.2 - - + -
570A VAL* 4.2 5.4 - - - +
451B PRO 2.8 17.6 + - - -
452B THR 3.7 3.6 - - - -
453B GLU 3.2 0.2 - - - -
454B VAL* 1.3 73.3 - - - +
456B ALA* 1.3 54.5 + - - +
458B GLY* 3.2 1.8 + - - +
459B ALA* 2.7 34.0 + - - +
555B VAL* 4.2 11.9 - - + -
565B THR* 4.5 6.1 - - - -
566B ASN* 3.3 22.2 + - - +
567B ILE 3.5 36.8 - - - +
568B MET* 4.0 11.2 - - + +
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Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B THR* 3.0 12.4 + - + +
453B GLU* 3.2 10.5 - - - +
455B THR* 1.3 76.2 - - - +
457B ILE* 1.3 64.8 + - - +
459B ALA* 2.9 4.9 + - - +
460B VAL* 2.8 27.1 + - - +
480B SER 5.3 0.7 - - - +
483B LEU* 3.9 37.2 - - + +
484B LEU* 3.7 17.3 - - + +
487B TYR* 4.6 2.9 - - + -
555B VAL* 5.8 1.7 - - - +
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Residues in contact with ILE 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 3.1 33.7 - - + +
462A ALA* 4.9 0.2 - - - -
465A LYS* 4.1 35.4 - - + +
438B PHE* 4.3 12.1 - - + -
442B ARG* 4.2 17.7 - - + -
453B GLU 3.0 8.3 + - - +
454B VAL 3.5 12.6 - - - +
456B ALA* 1.3 80.2 - - - +
458B GLY* 1.3 60.4 + - - +
460B VAL* 3.3 3.8 + - - +
461B GLU* 2.9 29.1 + - - +
487B TYR* 3.8 39.6 - - + -
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Residues in contact with GLY 458 (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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458A GLY* 3.8 23.7 - - - -
461A GLU* 4.3 6.3 - - - -
462A ALA* 4.6 3.4 - - - -
568A MET* 5.2 2.2 - - - -
454B VAL 3.4 6.3 + - - -
455B THR* 3.2 6.2 + - - -
456B ALA 3.1 0.6 - - - -
457B ILE* 1.3 84.3 - - - +
459B ALA* 1.3 56.8 + - - +
461B GLU* 3.1 3.6 + - - +
462B ALA* 2.9 29.3 + - - +
568B MET* 4.3 8.1 - - - -
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B THR 2.7 16.0 + - - +
456B ALA 3.3 7.9 - - - +
458B GLY* 1.3 73.8 - - - +
460B VAL* 1.3 57.2 + - - +
462B ALA* 3.2 2.8 + - - +
463B ALA* 2.8 29.8 + - - +
471B ILE* 4.4 3.1 - - + -
484B LEU* 3.6 17.7 - - + -
553B ILE* 4.0 9.4 - - + +
555B VAL* 3.7 20.9 - - + -
568B MET* 3.9 18.0 - - + -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 3.8 17.3 - - + -
456B ALA 2.8 19.8 + - - +
457B ILE 3.7 4.9 - - - +
459B ALA* 1.3 74.8 - - - +
461B GLU* 1.3 63.0 + - - +
463B ALA* 3.2 8.0 + - - +
464B PHE* 3.0 47.4 + - + -
471B ILE* 4.3 1.8 - - + -
484B LEU* 3.8 22.9 - - + +
487B TYR* 3.9 20.0 - - + +
489B PRO* 3.7 28.7 - - + -
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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
----------------------------------------------------------
438A PHE* 4.9 0.2 - - - -
442A ARG* 3.4 32.2 + - - +
457A ILE* 3.0 41.8 - - + +
461A GLU* 2.7 44.1 - - + +
438B PHE* 3.9 15.9 - - + -
457B ILE 2.9 17.7 + - - +
458B GLY 3.1 4.2 + - - +
460B VAL* 1.3 78.4 - - - +
462B ALA* 1.3 61.4 + - - +
464B PHE* 3.3 7.6 + - - +
465B LYS* 3.2 19.6 + - - +
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Residues in contact with ALA 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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454A VAL* 3.3 48.7 - - + +
457A ILE* 4.6 4.0 - - - -
458A GLY* 4.6 2.0 - - - -
458B GLY 2.9 16.2 + - - +
459B ALA 3.5 4.5 - - - +
461B GLU* 1.3 73.2 - - - +
463B ALA* 1.3 67.7 + - - +
465B LYS* 3.0 11.3 + - - +
466B CYS* 3.4 4.7 + - - -
553B ILE* 3.9 12.1 - - + -
568B MET* 3.9 15.5 - - + -
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Residues in contact with ALA 463 (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 ALA 2.8 13.7 + - - +
460B VAL* 3.3 10.1 - - - +
462B ALA* 1.3 78.3 - - - +
464B PHE* 1.3 64.1 + - + +
466B CYS 3.3 0.2 + - - -
467B CYS* 3.0 4.9 + - - -
468B ALA* 3.0 45.3 + - + -
471B ILE* 4.1 22.9 - - + -
489B PRO* 5.3 3.1 - - + -
490B ARG 6.1 0.2 - - - +
491B ALA* 4.3 9.6 - - + +
553B ILE* 4.0 4.0 - - + +
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Residues in contact with PHE 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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442A ARG* 6.2 1.1 - - - +
447A LEU* 4.2 12.8 - - - +
434B HIS* 3.9 28.5 - + + -
438B PHE* 3.6 38.8 - + + -
460B VAL* 3.0 38.6 + - + -
461B GLU* 3.6 11.2 - - - +
462B ALA 3.3 0.2 - - - -
463B ALA* 1.3 76.9 - - + +
465B LYS* 1.3 63.8 + - - +
466B CYS 3.2 1.2 + - - -
467B CYS* 3.4 9.7 + - - +
488B ARG 3.9 18.2 - - - -
489B PRO* 4.3 2.7 - - + -
490B ARG* 4.0 25.6 - - + -
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Residues in contact with LYS 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 5.1 2.0 + - - +
445A ALA* 3.4 21.7 + - - +
446A PRO* 2.7 28.6 + - - +
447A LEU* 3.4 11.5 - - + +
448A SER* 2.7 54.3 + - - +
453A GLU* 3.9 8.4 + - - -
454A VAL* 4.7 10.8 - - + +
457A ILE* 3.9 30.5 - - + +
487A TYR* 2.9 28.7 + - - +
461B GLU* 3.2 11.9 + - - +
462B ALA* 3.0 11.1 + - - +
464B PHE* 1.3 77.2 - - - +
466B CYS* 1.3 52.4 + - - +
467B CYS 3.6 0.2 - - - -
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Residues in contact with CYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 5.2 1.6 - - - -
448A SER 3.0 20.6 - - - +
449A ARG* 2.6 31.7 + - - +
454A VAL* 3.8 17.3 - - + -
462B ALA 3.4 15.7 - - - -
463B ALA* 4.3 0.4 - - - -
465B LYS* 1.3 76.7 - - - +
467B CYS* 1.3 65.3 + - - +
468B ALA* 3.1 25.4 + - - -
551B LEU* 3.6 28.4 - - + +
553B ILE* 4.3 4.7 - - - -
570B VAL* 5.6 0.2 - - - -
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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
------------------------------------------------------------
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