Contacts of the helix formed by residues 482 - 501 (chain A) in PDB entry 6X70
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 THR 482 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A HIS* 3.4 29.1 + - + +
481A ASN* 1.3 83.9 + - - +
483A ASN* 1.3 62.8 + - - +
484A THR* 3.7 7.3 + - - -
485A LEU* 3.2 33.6 + - + +
486A ASN* 2.9 28.0 + - - -
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Residues in contact with ASN 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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482A THR* 1.3 72.5 - - - +
484A THR* 1.3 61.4 + - - +
486A ASN* 3.2 6.2 + - - +
487A ALA* 2.8 34.2 + - - +
531A ILE* 3.9 40.9 + - - +
533A PHE* 5.1 3.4 - - - -
536A ASN* 4.6 12.5 + - - +
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Residues in contact with THR 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A THR* 3.4 6.7 + - - -
483A ASN* 1.3 78.0 - - - +
485A LEU* 1.3 59.6 + - + +
487A ALA* 3.7 6.8 - - + +
488A ARG* 3.0 49.3 + - + +
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ARG* 6.2 2.9 - - - +
480A HIS 5.3 7.9 - - - +
481A ASN* 5.8 1.1 - - - +
482A THR* 3.2 24.7 + - + +
484A THR* 1.3 82.5 - - + +
486A ASN* 1.3 64.0 + - - +
488A ARG* 3.4 24.1 + - + +
489A LEU* 3.2 32.4 + - + +
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Residues in contact with ASN 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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357A ILE* 3.6 17.4 - - - +
359A PHE* 3.8 10.8 - - + -
473A ARG* 5.3 1.4 + - - -
475A ILE* 5.7 0.3 - - - +
481A ASN* 3.2 26.2 + - - +
482A THR 2.9 20.6 + - - -
483A ASN* 3.2 6.6 + - - +
485A LEU* 1.3 78.3 - - - +
487A ALA* 1.3 66.3 + - - +
489A LEU* 3.3 12.7 + - - +
490A CYS* 3.0 27.4 + - - -
510A CYS* 4.1 20.0 - - - -
531A ILE* 3.9 10.3 - - + +
533A PHE* 3.8 13.5 - - - -
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Residues in contact with ALA 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN* 2.8 20.1 + - - +
484A THR* 3.7 9.0 - - + +
486A ASN* 1.3 76.0 - - - +
488A ARG* 1.3 59.1 + - + +
490A CYS* 3.4 2.3 + - - +
491A GLU* 3.1 33.6 + - - +
529A TYR* 3.7 21.8 - - + +
531A ILE* 3.5 17.4 - - + +
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A THR* 3.0 34.7 + - + +
485A LEU* 3.8 22.1 - - + +
486A ASN 3.2 0.4 - - - -
487A ALA* 1.3 75.5 - - + +
489A LEU* 1.3 61.6 + - + +
491A GLU* 3.3 6.1 + - - +
492A GLU* 2.9 29.3 + - - +
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Residues in contact with LEU 489 (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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359A PHE* 4.0 21.1 - - + -
457A ILE* 4.4 20.2 - - + -
458A PHE* 6.5 0.4 - - + -
473A ARG* 3.4 42.8 - - - +
485A LEU* 3.2 20.7 + - + +
486A ASN* 3.3 11.9 + - - +
488A ARG* 1.3 76.1 - - + +
490A CYS* 1.3 58.6 + - - +
492A GLU* 3.1 21.7 + - - +
493A ILE* 2.8 40.2 + - + +
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Residues in contact with CYS 490 (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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359A PHE* 3.7 17.9 - - - -
486A ASN 3.0 24.4 + - - +
487A ALA 3.5 5.4 - - - +
489A LEU* 1.3 75.9 - - - +
491A GLU* 1.3 58.9 + - - +
493A ILE* 3.3 2.3 + - - +
494A ARG* 2.9 35.6 + - - +
508A ILE* 3.5 29.1 - - + +
510A CYS* 4.3 11.0 - - - -
529A TYR* 3.7 34.8 - - + -
531A ILE* 4.5 1.8 - - - -
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Residues in contact with GLU 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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487A ALA 3.1 17.9 + - - +
488A ARG* 3.7 7.2 - - - +
490A CYS* 1.3 75.8 - - - +
492A GLU* 1.3 60.9 + - - +
494A ARG* 3.2 29.7 + - - +
495A GLN* 2.9 31.0 + - - +
529A TYR* 3.8 25.2 + - + +
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Residues in contact with GLU 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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455A LEU* 3.5 26.3 - - + +
457A ILE* 4.5 14.1 - - - +
488A ARG 2.9 16.5 + - - +
489A LEU* 3.5 24.7 - - - +
491A GLU* 1.3 73.7 - - - +
493A ILE* 1.3 66.2 + - - +
495A GLN* 3.2 3.2 + - - +
496A GLU* 2.9 41.7 + - + +
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Residues in contact with ILE 493 (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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359A PHE* 3.9 20.0 - - + -
361A ILE* 3.8 14.4 - - + -
452A LEU* 4.5 4.3 - - + -
455A LEU* 3.8 11.9 - - + -
457A ILE* 3.8 21.1 - - + -
458A PHE* 3.7 24.9 - - + -
489A LEU* 2.8 30.9 + - + +
490A CYS* 3.6 6.5 - - - +
492A GLU* 1.3 72.3 - - - +
494A ARG* 1.3 58.8 + - - +
496A GLU* 3.9 0.5 - - - +
497A ILE* 2.9 52.9 + - + +
508A ILE* 3.7 17.7 - - + -
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Residues in contact with ARG 494 (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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490A CYS 2.9 19.9 + - - +
491A GLU* 3.2 25.0 + - - +
492A GLU 3.2 0.2 - - - -
493A ILE* 1.3 78.3 - - - +
495A GLN* 1.3 57.2 + - - +
497A ILE* 4.1 0.5 - - - +
498A PHE* 3.0 29.1 + - - +
505A THR* 3.8 1.3 + - - -
506A VAL* 2.9 46.0 + - + +
508A ILE* 3.7 15.9 - - + -
527A ASN* 2.6 54.4 + - - +
528A GLY* 3.2 16.0 - - - +
529A TYR* 4.0 15.0 - - - -
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Residues in contact with GLN 495 (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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491A GLU 2.9 17.6 + - - +
492A GLU* 4.0 4.0 - - - +
494A ARG* 1.3 74.8 - - - +
496A GLU* 1.3 69.7 + - + +
498A PHE* 3.4 22.6 + - - +
499A GLN* 3.0 38.4 + - - +
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Residues in contact with GLU 496 (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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451A THR* 3.8 21.2 - - + +
454A ARG* 3.1 24.1 + - - -
455A LEU* 3.8 21.3 - - + +
492A GLU* 2.9 28.7 + - + +
493A ILE 4.0 1.8 - - - +
495A GLN* 1.3 85.5 - - + +
497A ILE* 1.3 57.4 + - - +
499A GLN* 3.9 11.4 - - - +
500A GLY* 2.8 26.3 + - - -
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Residues in contact with ILE 497 (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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361A ILE* 4.2 0.9 - - + -
363A PHE* 4.6 2.0 - - + -
448A PHE* 3.6 35.2 - - + -
451A THR* 3.8 22.9 - - + -
452A LEU* 4.0 7.9 - - + -
493A ILE* 2.9 40.5 + - + +
494A ARG 4.1 2.2 - - - +
496A GLU* 1.3 74.8 - - - +
498A PHE* 1.3 65.2 + - - +
501A THR* 2.8 48.6 + - + +
504A CYS 4.6 4.0 - - - +
506A VAL* 3.7 34.1 - - + -
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Residues in contact with PHE 498 (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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494A ARG 3.0 19.1 + - - +
495A GLN* 3.4 25.5 + - - +
497A ILE* 1.3 77.5 - - - +
499A GLN* 1.3 63.7 + - - +
502A ASN 3.4 0.3 + - - -
503A GLY* 2.9 58.1 + - - -
504A CYS 3.2 26.9 + - - +
505A THR* 4.7 9.6 - - - +
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Residues in contact with GLN 499 (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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454A ARG* 5.8 1.6 + - - -
495A GLN* 3.0 27.8 + - - +
496A GLU* 3.9 13.3 - - - +
498A PHE* 1.3 80.7 - - - +
500A GLY* 1.3 69.0 + - - +
502A ASN* 3.2 14.1 + - - +
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Residues in contact with GLY 500 (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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447A ALA* 3.4 18.2 - - - +
451A THR* 4.3 11.4 - - - -
454A ARG* 6.2 1.3 - - - -
496A GLU 2.8 18.9 + - - -
497A ILE 3.2 1.5 + - - -
499A GLN* 1.3 84.1 + - - +
501A THR* 1.3 60.6 + - - +
502A ASN* 3.4 1.0 + - - +
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Residues in contact with THR 501 (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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363A PHE* 4.1 10.8 - - + -
444A LYS* 3.0 52.6 + - - +
447A ALA* 4.0 9.4 - - + -
448A PHE 4.2 4.0 - - - +
451A THR* 5.8 0.2 - - - +
497A ILE* 2.8 35.6 + - + +
498A PHE 3.6 0.7 + - - -
500A GLY* 1.3 78.1 - - - +
502A ASN* 1.3 66.9 + - - +
503A GLY 3.2 0.3 + - - -
504A CYS* 3.1 37.8 + - - +
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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