Contacts of the helix formed by residues 469 - 488 (chain A) in PDB entry 2OIV
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 SER 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A TRP* 5.2 14.6 - - - +
339A LEU* 5.8 2.6 - - - +
470A CYS* 1.3 62.5 + - - +
471A GLY* 3.1 5.9 - - - +
472A ASP* 3.1 25.2 + - - +
473A HIS* 2.5 51.0 + - - -
505A ARG* 3.6 28.5 - - - +
509A ARG* 5.9 1.0 - - - +
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Residues in contact with CYS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TRP* 6.3 3.4 - - - -
408A ALA 4.6 3.6 - - - -
409A HIS* 3.5 33.2 - - + +
410A TRP* 3.2 37.8 - - - +
430A SER* 3.9 8.5 - - - +
431A MET 5.6 0.2 - - - +
469A SER* 1.3 81.2 + - - +
471A GLY* 1.3 64.4 + - - +
473A HIS* 3.3 12.6 + - - +
474A VAL* 3.1 25.8 + - - +
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Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.0 19.7 - - - -
344A LEU* 4.9 2.5 - - - +
410A TRP* 3.6 25.8 - - - -
469A SER 3.1 4.3 - - - +
470A CYS* 1.3 84.3 - - - +
472A ASP* 1.3 60.0 + - - +
474A VAL* 3.2 4.8 + - - +
475A LEU* 3.1 26.7 + - - +
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Residues in contact with ASP 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.7 11.4 - - - +
469A SER* 3.1 27.8 + - - +
471A GLY* 1.3 71.7 - - - +
473A HIS* 1.3 61.3 + - - +
475A LEU* 3.3 1.4 + - - +
476A THR* 2.8 35.9 + - - -
503A PRO* 3.9 13.2 - - + -
505A ARG* 3.4 31.6 + - + +
508A ILE* 3.5 22.1 - - + +
509A ARG* 3.0 29.4 + - - -
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Residues in contact with HIS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A SER* 4.1 23.7 + - - +
461A ILE* 3.7 18.3 - - + +
462A ALA* 3.4 36.0 + - + +
469A SER* 2.5 47.1 + - - -
470A CYS* 3.5 11.8 - - - +
472A ASP* 1.3 78.0 - - - +
474A VAL* 1.3 57.6 + - + +
476A THR* 3.3 1.0 + - - -
477A GLY* 2.9 26.9 + - - -
501A ILE* 3.9 3.3 - - + +
503A PRO* 3.5 24.5 - - + +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.9 23.1 - - + -
402A PRO* 4.4 4.5 - - + -
410A TRP* 3.7 14.4 - - + +
411A SER* 3.6 34.8 - - - +
412A LEU* 4.1 20.6 - - + +
428A TYR 5.6 0.2 - - - +
461A ILE* 5.3 1.6 - - + -
470A CYS 3.1 14.5 + - - +
471A GLY 3.2 7.8 + - - +
473A HIS* 1.3 75.3 - - + +
475A LEU* 1.3 59.1 + - - +
477A GLY* 3.1 3.3 + - - -
478A ILE* 2.9 44.6 + - + +
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 4.0 24.7 - - + -
343A HIS 4.7 1.3 - - - +
344A LEU* 3.8 31.4 - - + +
347A TYR* 3.6 60.9 - - + -
348A THR* 4.0 17.9 - - + -
471A GLY 3.1 16.0 + - - +
472A ASP 3.9 3.6 - - - +
474A VAL* 1.3 75.4 - - - +
476A THR* 1.3 61.9 + - - +
478A ILE* 3.5 8.4 + - + +
479A GLU* 3.0 23.2 + - - +
508A ILE* 4.4 13.7 - - + -
512A LEU* 5.4 1.3 - - + -
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 5.5 0.7 - - - -
472A ASP 2.8 23.3 + - - -
475A LEU* 1.3 76.0 - - - +
477A GLY* 1.3 56.7 + - - +
479A GLU* 3.2 7.9 + - + +
480A VAL* 2.9 47.1 + - + +
501A ILE* 3.9 22.9 - - + -
502A GLU 4.3 6.3 - - - +
503A PRO* 3.2 32.2 - - + +
504A ASP 4.2 1.7 + - - +
508A ILE* 3.8 9.2 - - - +
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Residues in contact with GLY 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 4.2 10.1 - - - -
461A ILE* 4.4 0.9 - - - -
473A HIS 2.9 15.8 + - - -
474A VAL 3.5 4.0 - - - -
476A THR* 1.3 75.6 - - - +
478A ILE* 1.3 60.9 + - - +
480A VAL* 4.0 0.3 - - - +
481A LEU* 3.0 30.1 + - - +
498A LEU* 3.7 24.9 - - - -
501A ILE* 3.9 6.1 - - - +
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 6.0 0.7 - - + -
348A THR* 4.1 24.0 - - + -
351A LEU* 3.8 10.8 - - + -
366A PHE* 3.6 33.9 - - + -
400A PHE* 4.1 21.4 - - + +
402A PRO* 4.5 10.5 - - + -
412A LEU* 3.8 28.3 - - + -
474A VAL* 2.9 30.8 + - + +
475A LEU* 3.8 10.1 - - + +
477A GLY* 1.3 74.4 - - - +
479A GLU* 1.3 57.3 + - - +
481A LEU* 4.0 0.5 - - - +
482A ALA* 2.9 34.5 + - - +
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 2.5 29.7 + - - +
351A LEU* 3.4 16.2 - - - +
354A ARG* 2.9 34.8 + - - -
475A LEU 3.0 15.2 + - - +
476A THR* 3.4 12.3 - - + +
478A ILE* 1.3 75.3 - - - +
480A VAL* 1.3 65.9 - - + +
482A ALA* 3.8 0.9 - - - +
483A HIS* 2.8 47.1 + - + +
511A ARG* 3.1 20.6 + - - +
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A THR* 2.9 35.9 + - + +
477A GLY 4.0 2.7 - - - +
479A GLU* 1.3 79.6 - - + +
481A LEU* 1.3 64.8 + - - +
483A HIS* 3.3 5.8 + - - +
484A ARG* 3.1 57.2 + - + +
498A LEU* 3.7 12.8 - - + -
501A ILE* 4.4 12.6 - - + -
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A PHE* 3.6 15.7 - - + -
412A LEU* 4.5 2.5 - - + -
414A VAL* 3.8 27.4 - - + -
428A TYR* 3.6 23.6 - - + +
477A GLY 3.0 18.6 + - - +
480A VAL* 1.3 75.7 - - - +
482A ALA* 1.3 66.0 + - - +
484A ARG* 3.1 10.2 + - - +
485A VAL* 3.0 26.8 + - - +
490A PHE* 4.0 22.5 - - + -
495A GLY 4.0 6.1 - - - +
496A ARG* 4.0 21.8 - - + -
498A LEU* 3.9 24.5 - - + -
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Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 4.3 3.8 - - + -
355A LEU* 3.9 15.5 - - + -
364A LEU* 3.9 29.3 - - + +
366A PHE* 4.0 13.2 - - + -
400A PHE* 4.3 2.3 - - + -
478A ILE 2.9 23.5 + - - +
479A GLU 3.8 3.8 - - - +
481A LEU* 1.3 70.8 - - - +
483A HIS* 1.3 58.4 + - - +
485A VAL* 3.1 6.1 + - - +
486A LEU* 3.0 30.9 + - - +
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Residues in contact with HIS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 4.2 1.8 - - + -
354A ARG* 4.6 3.6 + - - -
355A LEU* 3.8 29.7 - - + +
479A GLU* 2.8 54.4 + - + +
480A VAL* 3.7 6.1 - - - +
481A LEU 3.2 0.2 - - - -
482A ALA* 1.3 78.7 - - - +
484A ARG* 1.3 57.3 + - + +
486A LEU* 3.3 14.7 + - + +
487A ASP* 3.0 31.6 + - - +
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A VAL* 3.1 38.7 + - + +
481A LEU* 3.1 16.2 + - - +
483A HIS* 1.3 73.9 - - + +
485A VAL* 1.3 64.1 + - - +
487A ASP* 2.9 21.5 - - - +
488A GLY 3.0 1.0 + - - -
489A THR* 3.0 30.0 + - - +
490A PHE* 3.1 16.1 + - + +
494A GLY 4.1 4.0 + - - -
495A GLY* 3.1 30.5 + - - -
496A ARG* 4.0 1.8 - - - +
497A ASP 2.8 34.3 + - - +
498A LEU* 4.4 0.6 - - - +
501A ILE* 5.2 4.0 - - - +
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PO4 2.7 39.6 + - - +
360A ASN* 3.1 26.2 + - + +
363A LEU* 4.1 2.9 - - + -
364A LEU* 3.6 31.4 - - + -
398A ILE* 3.9 19.7 - - + -
400A PHE* 4.8 0.7 - - + -
481A LEU 3.0 18.3 + - - +
482A ALA 3.4 7.6 - - - +
484A ARG* 1.3 74.1 - - - +
486A LEU* 1.3 64.7 + - - +
488A GLY 3.1 1.9 + - - -
490A PHE* 3.6 25.6 - - + -
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU* 3.6 29.8 - - + -
358A GLU* 3.6 27.8 - - + +
359A PRO* 3.3 34.2 - - + +
360A ASN* 3.2 17.6 + - - +
361A ALA* 3.8 26.0 - - + +
364A LEU* 4.1 12.1 - - + -
482A ALA 3.0 16.1 + - - +
483A HIS* 3.3 19.2 + - + +
485A VAL* 1.3 75.4 - - - +
487A ASP* 1.3 60.5 + - + +
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Residues in contact with ASP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ASN* 5.1 0.2 - - - -
483A HIS* 3.0 17.6 + - - +
484A ARG* 2.9 9.6 - - - +
486A LEU* 1.3 75.9 - - + +
488A GLY* 1.3 55.3 + - - +
489A THR* 2.7 46.2 + - - +
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PO4 2.8 34.9 + - - -
360A ASN* 4.7 1.3 - - - -
484A ARG 3.0 4.2 + - - -
485A VAL 3.1 4.2 + - - -
486A LEU 3.2 1.6 + - - -
487A ASP* 1.3 76.9 - - - +
489A THR* 1.3 56.7 + - - +
490A PHE 3.2 6.9 + - - -
491A ASP* 3.6 7.8 + - - +
492A TYR* 4.6 8.0 + - - -
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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