Contacts of the helix formed by residues 450 - 467 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C SER* 3.3 8.9 + - - +
449C ARG* 1.3 77.4 - - - +
451C PRO* 1.3 74.7 - - - +
452C THR* 2.8 33.2 + - - -
453C GLU* 2.9 23.5 + - + +
454C VAL* 3.0 10.5 + - - +
479C ARG* 5.0 7.3 + - - -
483C LEU* 4.0 9.7 - - - +
563C GLY 5.1 2.8 - - - +
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Residues in contact with PRO 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C ARG 3.1 10.5 - - - +
450C ASP* 1.3 88.5 - - - +
452C THR* 1.3 52.2 + - - +
454C VAL* 3.3 11.8 + - + +
455C THR* 2.7 38.2 + - - -
564C TYR* 6.4 0.4 - - - -
565C THR 3.9 12.3 - - - +
566C ASN* 4.3 5.8 - - + -
551D LEU* 4.8 7.6 - - + -
570D VAL* 3.9 27.1 - - + +
572D SER* 6.4 1.1 - - - -
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C ASP* 2.8 21.1 + - - -
451C PRO* 1.3 74.6 - - - +
453C GLU* 1.3 64.7 + - - -
455C THR* 3.3 4.5 + - - -
456C ALA* 2.9 22.9 + - - +
479C ARG* 5.2 2.5 - - + -
480C SER* 3.6 33.9 - - - +
483C LEU* 3.6 14.8 - - + -
563C GLY* 4.1 15.9 + - - -
565C THR* 3.8 26.8 + - + +
580C FBP 5.5 3.1 - - - +
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Residues in contact with GLU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C PRO 5.7 0.2 - - - +
448C SER* 3.6 28.8 + - - +
450C ASP* 2.9 19.0 + - + +
452C THR* 1.3 73.9 - - - +
454C VAL* 1.3 64.2 + - - +
456C ALA* 2.9 16.8 + - - +
457C ILE* 3.0 17.4 + - - +
479C ARG* 5.6 2.5 + - - +
483C LEU* 3.6 31.0 - - + +
486C ARG* 4.4 14.5 + - - -
487C TYR* 2.9 33.8 + - - -
465D LYS* 4.2 5.1 + - - -
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Residues in contact with VAL 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C SER 4.0 21.5 - - - +
449C ARG 4.4 2.7 - - - +
450C ASP 3.0 22.2 + - - +
451C PRO* 3.4 9.6 - - + +
453C GLU* 1.3 77.1 - - + +
455C THR* 1.3 61.0 + - - +
457C ILE* 3.4 9.0 - - - +
458C GLY 3.3 15.2 + - - -
462D ALA* 3.5 36.5 - - + +
465D LYS* 4.8 7.0 - - + -
466D CYS* 4.0 16.4 - - + -
551D LEU* 4.9 0.4 - - + -
553D ILE* 4.4 0.4 - - + -
570D VAL* 3.7 24.0 - - + -
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Residues in contact with THR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C PRO 2.7 20.8 + - - -
452C THR 3.8 4.3 - - - -
454C VAL* 1.3 73.9 - - - +
456C ALA* 1.3 60.6 + - - +
458C GLY* 3.3 1.6 + - - -
459C ALA* 2.8 29.6 + - - +
555C VAL* 4.2 12.1 - - + -
565C THR* 4.5 5.6 - - - -
566C ASN* 3.3 21.2 - - - +
567C ILE 3.5 38.8 - - - +
568C MET* 3.9 11.1 - - + +
568D MET* 4.6 9.6 - - + -
570D VAL* 3.9 5.7 - - - +
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Residues in contact with ALA 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C THR 2.9 14.0 + - - +
453C GLU* 2.9 10.7 + - - +
455C THR* 1.3 76.2 - - - +
457C ILE* 1.3 58.7 + - - +
459C ALA* 2.8 19.5 + - - +
460C VAL* 2.9 19.2 + - - +
480C SER 5.3 0.7 - - - +
483C LEU* 3.8 36.3 - - + +
484C LEU* 3.8 17.5 - - + +
487C TYR* 4.7 2.9 - - + -
555C VAL* 5.8 2.0 - - - +
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Residues in contact with ILE 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C PHE* 4.3 14.5 - - + -
442C ARG* 4.2 17.5 - - + -
453C GLU 3.0 7.9 + - - +
454C VAL 3.4 12.8 - - - +
456C ALA* 1.3 78.1 - - - +
458C GLY* 1.3 67.7 + - - +
460C VAL* 3.3 3.3 + - - +
461C GLU* 2.9 23.7 + - - +
487C TYR* 3.9 33.3 - - + -
461D GLU* 3.0 35.9 - - + +
462D ALA* 4.6 1.8 - - - -
465D LYS* 4.0 39.9 - - + -
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Residues in contact with GLY 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454C VAL 3.3 9.3 + - - -
455C THR* 3.3 4.2 + - - -
456C ALA 3.2 0.6 - - - -
457C ILE* 1.3 83.1 - - - +
459C ALA* 1.3 57.8 + - - +
461C GLU* 3.1 4.5 + - - +
462C ALA* 2.9 29.3 + - - +
568C MET* 4.3 6.3 - - - -
458D GLY* 3.8 24.8 - - - -
461D GLU* 4.3 4.9 - - - -
462D ALA* 4.5 3.4 - - - -
568D MET* 5.0 3.8 - - - -
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Residues in contact with ALA 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C THR 2.8 14.1 + - - +
456C ALA 2.8 8.3 + - - +
458C GLY* 1.3 75.5 - - - +
460C VAL* 1.3 59.1 + - - +
462C ALA* 3.2 1.9 + - - +
463C ALA* 2.8 31.1 + - - +
471C ILE* 4.4 4.4 - - + +
484C LEU* 3.7 18.2 - - + -
553C ILE* 4.0 10.1 - - + +
555C VAL* 3.7 20.6 - - + -
568C MET* 4.0 17.2 - - + -
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Residues in contact with VAL 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 3.8 16.6 - - + -
456C ALA 2.9 17.5 + - - +
457C ILE* 3.7 7.6 - - - +
459C ALA* 1.3 76.7 - - - +
461C GLU* 1.3 62.5 + - - +
463C ALA* 3.2 8.4 + - - +
464C PHE* 3.0 51.5 + - + -
471C ILE* 4.4 1.3 - - - -
484C LEU* 3.9 20.6 - - + +
487C TYR* 4.0 19.5 - - + +
489C PRO* 3.6 29.4 - - + -
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Residues in contact with GLU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 3.9 14.8 - - + -
457C ILE 2.9 17.4 + - - +
458C GLY 3.1 4.9 + - - +
460C VAL* 1.3 75.8 - - - +
462C ALA* 1.3 63.7 + - - +
464C PHE* 3.1 7.2 + - - +
465C LYS* 3.1 20.6 + - - +
442D ARG* 3.4 32.9 + - - -
457D ILE* 3.3 42.2 - - + +
461D GLU* 2.6 45.9 - - + +
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Residues in contact with ALA 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C GLY 2.9 15.0 + - - +
459C ALA 3.6 4.0 - - - +
461C GLU* 1.3 76.0 - - - +
463C ALA* 1.3 64.1 + - - +
465C LYS* 3.2 9.7 + - - +
466C CYS* 3.4 15.2 + - - -
553C ILE* 3.9 11.9 - - + -
568C MET* 4.0 15.9 - - + -
454D VAL* 3.4 39.4 - - + +
457D ILE* 4.5 4.9 - - - -
458D GLY* 4.5 1.3 - - - -
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Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C ALA 2.8 17.1 + - - +
460C VAL* 3.4 6.5 - - - +
462C ALA* 1.3 79.3 - - - +
464C PHE* 1.3 62.6 + - + +
467C CYS* 3.1 4.7 + - - -
468C ALA* 3.0 46.4 + - + -
471C ILE* 4.1 23.6 - - + -
489C PRO* 5.3 2.5 - - + -
491C ALA* 4.3 8.5 - - + +
553C ILE* 4.0 4.0 - - + +
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Residues in contact with PHE 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C HIS* 3.9 28.5 - + + -
438C PHE* 3.6 34.1 - + + -
460C VAL* 3.0 42.5 + - + -
461C GLU* 3.1 12.3 + - - +
463C ALA* 1.3 77.4 - - + +
465C LYS* 1.3 61.7 + - - +
466C CYS 3.2 1.0 + - - -
467C CYS* 3.4 11.7 + - - +
488C ARG 3.8 19.3 - - - -
489C PRO* 4.3 1.8 - - + -
490C ARG* 4.0 25.8 - - + -
442D ARG* 6.0 1.6 - - - +
447D LEU* 4.3 11.4 - - - +
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Residues in contact with LYS 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C GLU* 3.1 13.5 + - - +
462C ALA 3.2 9.3 + - - +
464C PHE* 1.3 77.2 - - - +
466C CYS* 1.3 55.1 + - - +
442D ARG* 4.8 2.8 + - - +
445D ALA* 3.3 23.2 + - - +
446D PRO 2.6 29.1 + - - +
447D LEU* 3.3 14.2 - - + +
448D SER* 2.8 45.1 + - - +
453D GLU* 4.2 6.1 + - - -
454D VAL* 4.8 10.3 - - + +
457D ILE* 4.0 30.9 - - + +
487D TYR* 3.1 28.6 + - - -
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Residues in contact with CYS 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C ALA 3.4 16.4 - - - -
463C ALA* 3.8 0.7 - - - -
465C LYS* 1.3 76.4 - - - +
467C CYS* 1.3 66.2 + - - +
468C ALA* 3.1 23.7 + - - -
551C LEU* 3.6 27.3 - - + +
553C ILE* 4.4 4.0 - - - -
570C VAL* 5.6 0.2 - - - -
447D LEU* 5.1 2.5 - - - -
448D SER 2.9 22.4 - - - +
449D ARG* 2.7 30.4 + - - -
454D VAL* 3.9 18.2 - - + -
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Residues in contact with CYS 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 5.3 17.3 - - - -
65C MET* 6.4 1.3 - - - -
463C ALA 3.1 7.8 + - - -
464C PHE* 3.4 6.4 + - - +
466C CYS* 1.3 80.1 - - - +
468C ALA* 1.3 69.1 + - - +
469C ALA* 3.2 2.3 + - - -
551C LEU 5.8 0.2 + - - -
447D LEU* 3.3 37.7 - - - -
449D ARG* 4.4 9.1 + - - +
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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
------------------------------------------------------------
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