Contacts of the helix formed by residues 476 - 496 (chain A) in PDB entry 2BV5
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 ILE 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PHE* 4.1 2.2 - - + -
307A ILE* 3.9 33.2 - - + -
472A SCY 2.8 14.5 + - - +
474A ALA* 4.1 8.3 - - + -
475A GLY* 1.3 81.2 - - - +
477A GLY* 1.3 59.9 + - - +
479A THR 4.2 0.4 - - - -
480A GLY 3.0 16.4 + - - -
511A ARG* 3.6 17.0 - - + +
512A GLY 3.3 19.1 - - - +
513A GLY* 3.6 28.9 - - - +
514A MET* 3.3 7.6 - - - +
515A ILE 2.9 22.1 + - - -
516A GLN* 3.7 32.1 - - + +
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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
----------------------------------------------------------
472A SCY 2.8 16.5 + - - -
476A ILE* 1.3 71.8 - - - +
478A ARG* 1.3 64.7 + - - -
479A THR 3.2 0.2 - - - -
480A GLY* 3.2 2.6 + - - -
481A CYS* 3.0 25.1 + - - -
515A ILE* 4.0 1.9 - - - -
516A GLN* 3.8 13.0 - - - -
520A GLN* 3.3 30.4 - - - +
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Residues in contact with ARG 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 3.3 40.6 + - + +
375A THR* 3.9 3.0 - - - +
376A ASN* 4.1 2.4 - - - +
379A GLU* 2.8 43.3 + - - -
435A TRP* 3.2 62.8 - - + +
472A SCY 3.9 25.4 - - + +
477A GLY* 1.3 73.6 - - - +
479A THR* 1.3 61.7 + - - +
481A CYS* 3.2 2.6 + - - +
482A PHE* 2.9 24.1 + - - +
520A GLN* 3.9 0.4 - - - +
1538A SO4 2.9 37.3 + - - +
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA* 3.7 24.0 - - + -
374A ILE* 4.2 1.3 - - - +
470A VAL* 3.6 35.9 - - + +
471A HIS* 3.3 18.5 - - - -
472A SCY 2.8 27.5 - - - -
475A GLY* 3.7 14.2 - - - +
477A GLY 3.2 0.4 - - - -
478A ARG* 1.3 79.8 - - - +
480A GLY* 1.3 57.7 + - - +
482A PHE* 3.3 3.1 + - - +
483A ILE* 3.0 33.1 + - + +
514A MET* 4.4 1.6 - - + -
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Residues in contact with GLY 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ILE 3.0 23.2 + - - -
477A GLY 3.2 0.6 + - - -
479A THR* 1.3 73.5 - - - +
481A CYS* 1.3 59.8 + - - +
484A ALA* 2.8 34.1 + - - +
507A LEU* 3.9 3.0 - - - +
514A MET* 3.7 19.7 - - - -
515A ILE* 3.6 16.2 - - - +
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Residues in contact with CYS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TRP* 3.8 22.2 - - + -
447A LEU* 4.9 5.4 - - + -
477A GLY 3.0 16.0 + - - -
478A ARG 3.2 7.4 + - - +
480A GLY* 1.3 76.2 - - - +
482A PHE* 1.3 62.0 + - - +
485A THR* 2.8 32.6 + - - -
515A ILE* 3.8 4.2 - - - +
520A GLN* 3.3 50.5 - - - -
523A PHE* 5.3 1.6 - - + -
524A VAL* 3.8 17.5 - - + +
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 4.6 9.4 - + - -
372A VAL* 4.0 12.1 - - + -
374A ILE* 3.6 24.0 - - + -
447A LEU* 4.4 11.1 - - + +
450A LEU* 3.7 35.0 - - + -
451A VAL* 3.7 28.2 - - + +
454A VAL* 3.9 29.2 - - + -
468A ILE* 5.4 0.4 - - + -
470A VAL* 4.0 29.2 - - + -
478A ARG 2.9 6.9 + - - +
479A THR 3.7 3.6 - - - +
481A CYS* 1.3 79.4 - - - +
483A ILE* 1.3 61.4 + - - +
485A THR* 3.8 3.9 - - - -
486A SER* 2.8 49.7 + - - -
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Residues in contact with ILE 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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335A ILE* 4.0 9.0 - - + -
345A TYR* 3.7 53.2 - - + -
347A ALA* 4.5 2.0 - - + -
470A VAL* 4.2 7.2 - - + -
479A THR* 3.0 29.0 + - + +
480A GLY 4.1 1.8 - - - +
482A PHE* 1.3 86.9 - - + +
484A ALA* 1.3 65.1 + - - +
486A SER* 3.1 5.7 + - - -
487A ILE* 2.9 28.6 + - + +
507A LEU* 3.6 25.4 - - + -
514A MET* 3.9 17.7 - - + -
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLY 2.8 18.8 + - - +
481A CYS 4.0 2.5 - - - +
483A ILE* 1.3 78.0 - - - +
485A THR* 1.3 57.4 + - - +
487A ILE* 3.4 1.2 + - - +
488A CYS* 2.9 36.1 + - - -
500A ILE* 5.5 1.6 - - + -
503A THR* 3.9 17.9 - - + -
504A THR* 4.9 2.5 - - - +
507A LEU* 3.7 14.5 - - + +
515A ILE* 3.8 18.2 - - + -
524A VAL* 4.4 10.1 - - + -
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 4.5 9.6 - - + +
448A LEU* 4.8 0.2 - - + -
451A VAL* 3.8 21.3 - - + -
481A CYS 2.8 22.0 + - - -
482A PHE* 3.8 3.8 - - - -
484A ALA* 1.3 73.2 - - - +
486A SER* 1.3 64.9 + - - +
488A CYS* 3.3 0.9 + - - -
489A CYS* 2.9 31.4 + - - -
524A VAL* 3.9 21.6 - - - +
527A VAL* 3.5 29.0 - - + +
528A MET* 3.9 15.6 - - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 3.3 24.9 - - - -
451A VAL* 3.6 22.7 + - - +
455A GLU* 4.4 8.5 - - - +
482A PHE* 2.8 41.4 + - - -
483A ILE* 3.1 4.2 + - - -
485A THR* 1.3 77.1 - - - +
487A ILE* 1.3 63.8 + - - +
489A CYS* 3.5 3.6 + - - +
490A GLN* 3.5 23.3 + - - +
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Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG 3.7 18.8 - - - +
337A GLY* 4.0 7.2 - - - +
338A TYR* 3.8 40.2 - - + +
345A TYR* 4.5 6.1 - - + +
483A ILE* 2.9 38.1 + - + +
484A ALA 3.7 4.0 - - - +
486A SER* 1.3 74.2 - - - +
488A CYS* 1.3 58.5 + - - +
490A GLN* 3.2 7.5 + - - +
491A GLN* 3.0 25.4 + - + +
503A THR* 3.9 32.8 - - + +
506A GLN* 4.3 8.1 - - - +
507A LEU* 4.2 6.5 - - + -
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Residues in contact with CYS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ALA* 2.9 21.9 + - - +
487A ILE* 1.3 75.3 - - - +
489A CYS* 1.3 60.8 + - - +
491A GLN* 3.6 12.1 - - - +
492A LEU* 2.8 31.2 + - - +
498A VAL* 3.9 6.8 - - + +
499A ASP 4.2 2.5 - - - -
500A ILE* 3.8 28.5 - - - -
503A THR* 3.6 26.7 - - - -
528A MET* 3.6 26.0 - - + +
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Residues in contact with CYS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 3.9 20.9 - - - -
451A VAL* 4.1 11.2 - - + -
452A ARG* 5.0 0.9 - - - -
455A GLU* 4.2 7.2 - - - +
485A THR* 2.9 24.1 + - - +
486A SER* 3.7 6.7 - - - +
487A ILE 3.3 0.2 - - - -
488A CYS* 1.3 76.9 - - - +
490A GLN* 1.3 61.5 + - - +
492A LEU* 3.4 1.7 + - - +
493A ARG* 3.1 45.8 + - - +
528A MET* 3.9 13.7 - - - -
531A TYR* 3.6 25.3 - - + -
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Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 3.8 37.5 + - + +
344A VAL* 6.1 0.7 - - - +
345A TYR* 5.0 6.8 + - - -
455A GLU* 3.8 13.4 - - - +
459A GLN* 6.2 1.3 - - - -
486A SER 3.5 8.4 + - - +
487A ILE* 3.2 9.4 + - - +
489A CYS* 1.3 75.9 - - - +
491A GLN* 1.3 58.6 + - - +
493A ARG* 3.3 26.2 + - - +
494A GLN* 2.9 31.5 + - - +
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Residues in contact with GLN 491 (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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260A VAL* 5.5 2.0 - - - +
338A TYR* 3.5 21.2 - - + -
487A ILE* 3.0 13.2 + - + +
488A CYS* 3.3 11.0 + - - +
490A GLN* 1.3 76.5 - - - +
492A LEU* 1.3 54.4 + - - +
495A GLU* 2.7 68.5 + - - +
496A GLY 3.5 0.3 + - - -
497A VAL* 3.5 15.9 - - - +
498A VAL* 3.6 2.3 - - - +
499A ASP* 2.9 47.1 + - - +
502A LYS* 6.3 0.4 - - - +
503A THR* 4.3 6.6 + - - -
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Residues in contact with LEU 492 (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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266A LEU* 5.5 1.6 - - + -
488A CYS 2.8 19.9 + - - +
489A CYS 3.8 4.5 - - - +
490A GLN 3.3 0.2 - - - -
491A GLN* 1.3 72.9 - - - +
493A ARG* 1.3 59.7 + - - +
496A GLY* 2.9 48.1 + - - +
497A VAL* 3.3 12.7 + - - +
498A VAL* 3.8 12.6 - - + -
528A MET* 4.1 11.4 - - + +
531A TYR* 3.8 15.0 - - + -
532A GLU* 3.8 35.4 - - + +
535A LEU* 3.5 28.4 - - + +
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Residues in contact with ARG 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ARG* 4.1 7.6 - - - +
455A GLU* 2.9 43.5 + - - -
456A GLU* 5.4 0.4 + - - -
459A GLN* 5.1 8.9 - - - +
489A CYS* 3.1 29.9 + - - +
490A GLN* 3.5 24.0 - - - +
492A LEU* 1.3 78.9 - - - +
494A GLN* 1.3 60.9 + - - +
496A GLY 4.8 0.2 + - - -
531A TYR* 3.0 34.9 + - + +
535A LEU* 4.2 14.8 - - + -
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Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 3.3 36.2 + - + +
490A GLN 2.9 16.5 + - - +
493A ARG* 1.3 80.1 - - - +
495A GLU* 1.3 67.3 + - + +
496A GLY 3.7 0.2 - - - -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 2.6 32.6 + - - +
491A GLN* 2.7 49.4 + - - +
494A GLN* 1.3 82.4 - - + +
496A GLY* 1.3 59.6 + - - +
497A VAL* 3.4 21.2 + - + +
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Residues in contact with GLY 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLN* 4.1 10.9 - - - +
263A ALA 5.1 2.8 + - - -
491A GLN 3.5 0.2 + - - -
492A LEU* 2.9 31.7 + - - +
493A ARG 4.8 0.4 + - - -
494A GLN 3.7 0.8 - - - -
495A GLU* 1.3 78.5 - - - +
497A VAL* 1.3 62.5 - - - +
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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
------------------------------------------------------------
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