Contacts of the helix formed by residues 450 - 466 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D SER* 3.3 10.1 + - - +
449D ARG* 1.3 75.9 - - - +
451D PRO* 1.3 75.2 - - - +
452D THR* 2.9 27.6 + - - -
453D GLU* 2.9 29.3 + - + +
454D VAL* 3.1 11.2 + - - +
479D ARG* 5.0 6.8 + - - -
483D LEU* 4.0 8.5 - - - +
563D GLY 5.2 2.4 - - - +
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Residues in contact with PRO 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C LEU* 4.7 7.6 - - + -
570C VAL* 3.8 34.8 - - + +
572C SER* 6.1 2.2 - - - +
449D ARG 3.2 10.5 - - - +
450D ASP* 1.3 89.8 - - - +
452D THR* 1.3 52.2 + - - +
454D VAL* 3.6 3.7 - - + +
455D THR* 2.6 38.7 + - - -
564D TYR* 6.5 0.2 - - - -
565D THR 3.8 12.6 - - - +
566D ASN* 4.3 6.1 - - + -
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Residues in contact with THR 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D ASP* 2.9 20.0 + - - -
451D PRO* 1.3 75.0 - - - +
453D GLU* 1.3 64.2 + - - -
455D THR* 3.4 4.2 + - - -
456D ALA* 3.1 21.7 + - - +
479D ARG* 5.2 3.1 - - + -
480D SER* 3.5 33.9 - - - +
483D LEU* 3.5 15.5 - - + -
563D GLY* 4.2 13.2 + - - -
565D THR* 3.7 29.6 + - + +
580D FBP 5.8 2.5 - - - +
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Residues in contact with GLU 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LYS* 4.2 4.6 + - - -
448D SER* 3.6 27.6 + - - +
450D ASP* 2.9 20.3 + - + +
452D THR* 1.3 73.8 - - - +
454D VAL* 1.3 57.2 + - - +
456D ALA* 2.8 26.1 + - - +
457D ILE* 3.0 16.1 + - - +
479D ARG* 5.6 1.7 + - - +
483D LEU* 3.5 31.2 - - + +
486D ARG* 4.3 13.5 + - - -
487D TYR* 3.0 34.0 + - - -
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Residues in contact with VAL 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C ALA* 3.4 37.8 - - + +
465C LYS* 4.8 4.9 - - + -
466C CYS* 3.9 17.0 - - + -
551C LEU* 4.8 0.7 - - + -
553C ILE* 4.3 0.7 - - + -
570C VAL* 3.7 22.7 - - + -
448D SER* 4.1 22.4 - - - +
449D ARG 4.4 1.8 - - - -
450D ASP 3.1 22.9 + - - +
451D PRO* 3.6 7.6 - - + +
453D GLU* 1.3 74.3 - - + +
455D THR* 1.3 61.7 + - - +
457D ILE* 3.4 9.6 - - - +
458D GLY 3.3 15.6 + - - -
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Residues in contact with THR 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C MET* 4.6 9.9 - - + -
570C VAL* 4.0 4.5 - - - +
451D PRO 2.6 22.6 + - - -
452D THR 3.7 4.7 - - - -
454D VAL* 1.3 73.0 - - - +
456D ALA* 1.3 55.9 + - - +
458D GLY* 3.1 2.3 + - - -
459D ALA* 2.7 33.4 + - - +
555D VAL* 4.2 13.7 - - + -
565D THR* 4.4 5.6 - - - -
566D ASN* 3.3 21.3 + - - +
567D ILE 3.5 36.3 - - - +
568D MET* 4.0 10.7 - - + +
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Residues in contact with ALA 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D THR 3.1 13.0 + - - +
453D GLU* 2.8 11.8 + - - +
455D THR* 1.3 77.4 - - - +
457D ILE* 1.3 59.0 + - - +
459D ALA* 2.8 19.2 + - - +
460D VAL* 2.8 18.4 + - - +
480D SER 5.3 0.7 - - - +
483D LEU* 3.7 35.7 - - + +
484D LEU* 3.7 18.2 - - + +
487D TYR* 4.6 2.2 - - + -
555D VAL* 5.8 1.3 - - - -
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Residues in contact with ILE 457 (chain D).
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* 3.3 32.5 - - + +
462C ALA* 4.5 2.5 - - - -
465C LYS* 4.0 36.6 - - + -
438D PHE* 4.3 11.4 - - + -
442D ARG* 4.2 16.4 - - + -
453D GLU 3.0 7.7 + - - +
454D VAL 3.4 12.8 - - - +
456D ALA* 1.3 79.1 - - - +
458D GLY* 1.3 67.0 + - - +
460D VAL* 3.4 3.5 + - - +
461D GLU* 2.9 23.9 + - - +
487D TYR* 3.7 40.7 - - + -
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Residues in contact with GLY 458 (chain D).
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* 3.8 24.2 - - - -
461C GLU* 4.5 1.8 - - - -
462C ALA* 4.5 4.0 - - - -
568C MET* 4.9 3.6 - - - -
454D VAL 3.3 6.7 + - - -
455D THR 3.1 6.9 + - - -
456D ALA 3.1 0.6 - - - -
457D ILE* 1.3 84.5 - - - +
459D ALA* 1.3 56.7 + - - +
461D GLU* 3.0 5.7 + - - +
462D ALA* 2.9 28.9 + - - +
568D MET* 4.3 6.5 - - - -
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Residues in contact with ALA 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D THR 2.7 16.4 + - - +
456D ALA 2.8 9.0 + - - +
458D GLY* 1.3 73.3 - - - +
460D VAL* 1.3 55.6 + - - +
462D ALA* 3.2 3.6 + - - +
463D ALA* 2.8 30.6 + - - +
471D ILE* 4.5 4.0 - - + -
484D LEU* 3.7 10.8 - - + -
553D ILE* 3.9 9.6 - - + +
555D VAL* 3.6 28.5 - - + -
568D MET* 3.9 17.9 - - + -
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Residues in contact with VAL 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D PHE* 3.8 16.4 - - + -
456D ALA 2.8 18.9 + - - +
457D ILE* 3.7 5.2 - - - +
459D ALA* 1.3 75.3 - - - +
461D GLU* 1.3 61.9 + - - +
463D ALA* 3.3 7.8 + - - +
464D PHE* 3.0 48.7 + - + -
471D ILE* 4.4 2.0 - - + -
484D LEU* 3.8 21.8 - - + +
487D TYR* 3.9 18.8 - - + +
489D PRO* 3.7 29.2 - - + -
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Residues in contact with GLU 461 (chain D).
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* 4.9 0.2 - - - -
442C ARG* 3.6 27.7 + - - -
457C ILE* 3.0 43.6 - - + +
461C GLU* 2.6 45.6 - - + +
438D PHE* 3.9 15.7 - - + -
457D ILE 2.9 18.3 + - - +
458D GLY 3.4 4.5 - - - +
460D VAL* 1.3 75.9 - - - +
462D ALA* 1.3 63.7 + - - +
464D PHE* 3.2 8.6 + - - +
465D LYS* 3.2 19.4 + - - +
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Residues in contact with ALA 462 (chain D).
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* 3.5 37.4 - - + +
457C ILE* 4.6 1.6 - - - -
458C GLY* 4.5 1.5 - - - -
458D GLY 2.9 12.1 + - - +
459D ALA 3.5 7.9 - - - +
461D GLU* 1.3 76.3 - - - +
463D ALA* 1.3 64.4 + - - +
465D LYS* 3.1 13.3 + - - +
466D CYS* 3.4 15.1 + - - -
553D ILE* 3.8 12.1 - - + -
568D MET* 3.9 15.5 - - + -
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Residues in contact with ALA 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ALA 2.8 13.6 + - - +
460D VAL* 3.4 10.5 - - - +
462D ALA* 1.3 76.1 - - - +
464D PHE* 1.3 63.4 + - + +
465D LYS 3.3 0.3 + - - -
466D CYS 3.3 0.2 + - - -
467D CYS* 3.0 5.0 + - - -
468D ALA* 3.0 46.7 + - + -
471D ILE* 4.1 17.9 - - + -
489D PRO* 5.3 2.7 - - + -
490D ARG 6.1 0.2 - - - +
491D ALA* 4.2 9.6 - - + +
553D ILE* 3.9 8.2 - - + +
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Residues in contact with PHE 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ARG* 6.2 1.3 - - - +
447C LEU* 4.5 11.1 - - - +
434D HIS* 3.9 28.5 - + + -
438D PHE* 3.6 35.0 - + + -
460D VAL* 3.0 42.3 + - + -
461D GLU* 3.2 12.3 + - - +
463D ALA* 1.3 77.1 - - + +
465D LYS* 1.3 63.1 + - - +
466D CYS 3.2 1.0 + - - -
467D CYS* 3.4 10.3 + - - +
488D ARG 3.8 19.7 - - - -
489D PRO* 4.3 2.5 - - + -
490D ARG* 4.0 25.6 - - + -
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Residues in contact with LYS 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ARG* 5.0 3.0 + - - +
445C ALA* 3.4 21.4 + - - +
446C PRO 2.6 29.5 + - - +
447C LEU* 3.5 12.7 - - + +
448C SER* 2.9 48.0 + - - +
453C GLU* 4.2 6.1 + - - -
454C VAL* 4.8 9.6 - - + +
457C ILE* 4.0 33.6 - - + +
487C TYR* 3.1 27.9 + - - -
461D GLU* 3.2 12.0 + - - +
462D ALA* 3.1 10.7 + - - +
464D PHE* 1.3 77.2 - - - +
466D CYS* 1.3 57.5 + - - +
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Residues in contact with CYS 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447C LEU* 5.3 1.6 - - - -
448C SER 3.1 21.5 - - - +
449C ARG* 2.7 26.8 + - - +
454C VAL* 4.0 15.9 - - + -
462D ALA 3.4 16.6 - - - -
463D ALA 3.7 0.9 - - - -
465D LYS* 1.3 75.8 - - - +
467D CYS* 1.3 71.0 + - - +
468D ALA* 3.1 24.2 + - - -
551D LEU* 3.6 29.0 - - + +
553D ILE* 4.3 4.9 - - - -
570D VAL* 5.6 0.4 - - - -
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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