Contacts of the helix formed by residues 485 - 507 (chain A) in PDB entry 4XH9
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 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ASN* 3.3 17.8 - - - +
483A ALA* 3.3 1.9 - - - +
484A ASN* 1.3 91.5 - - - +
486A VAL* 1.3 61.3 + - + +
487A PHE* 3.4 5.1 + - + +
488A HIS* 2.8 31.3 + - - +
489A LYS* 3.0 28.1 + - - +
104B LYS* 3.3 34.9 + - - +
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Residues in contact with VAL 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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443A ASP* 5.7 2.2 - - - +
464A ASN* 3.1 22.7 - - - +
485A ASP* 1.3 75.7 - - - +
487A PHE* 1.3 73.3 + - + +
489A LYS* 3.5 11.0 + - + +
490A GLN* 3.2 23.5 + - - +
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ASP* 3.3 7.9 + - + +
486A VAL* 1.3 86.8 - - + +
488A HIS* 1.3 65.6 + - - +
490A GLN* 3.2 7.9 + - + +
491A GLN 3.2 16.3 + - - -
96B PRO* 3.5 48.0 - - + -
100B THR* 3.5 28.5 - - + -
101B PRO* 3.2 21.9 - - + +
104B LYS* 4.0 6.5 - - + -
150B ARG* 3.4 36.3 - - + -
151B ILE* 4.0 11.7 - - + -
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU 4.1 8.1 - - - -
393A LEU* 4.0 10.3 - - + -
483A ALA* 3.4 2.6 - - - +
484A ASN* 3.0 43.7 + - - -
485A ASP* 2.8 32.1 + - - +
487A PHE* 1.3 75.4 - - - +
489A LYS* 1.3 63.8 + - - +
491A GLN* 3.2 10.5 + - + +
492A TRP* 3.3 29.8 + + - -
101B PRO 4.6 1.6 - - - -
104B LYS* 4.0 10.7 - - + +
105B HIS* 3.1 51.1 + - + -
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Residues in contact with LYS 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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440A ASP* 2.7 30.8 + - - -
441A LEU 3.2 8.3 + - - -
443A ASP* 5.3 2.4 + - - -
464A ASN* 3.7 25.6 - - + +
465A ILE 3.0 24.1 + - - +
466A PHE* 4.1 19.7 - - + -
483A ALA* 3.5 16.3 - - + +
485A ASP 3.0 12.5 + - - +
486A VAL* 3.5 14.1 - - + +
488A HIS* 1.3 77.0 - - - +
490A GLN* 1.3 57.6 + - - +
492A TRP* 3.3 5.2 + - - +
493A PHE* 2.7 43.9 + - + +
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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
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486A VAL* 3.2 13.9 + - - +
487A PHE* 3.2 18.3 + - + +
488A HIS 3.1 0.2 - - - -
489A LYS* 1.3 81.9 - - - +
491A GLN* 1.3 61.1 + - - +
493A PHE* 4.3 8.3 - - - +
494A ASN* 2.8 63.5 + - - +
96B PRO 5.4 3.1 - - - +
97B GLU* 5.3 7.8 + - - +
101B PRO* 4.1 11.7 - - + -
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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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388A LEU 5.8 0.6 + - - -
389A CYS* 3.3 28.8 - - - -
487A PHE 3.2 2.6 + - - -
488A HIS* 3.2 11.2 + - + +
490A GLN* 1.3 77.5 - - - +
492A TRP* 1.3 61.8 + - - +
494A ASN* 4.1 2.7 - - - +
495A CYS* 3.1 41.3 + - - -
101B PRO* 3.2 41.4 - - + +
102B GLU* 3.8 14.6 + - - +
105B HIS* 3.7 19.1 + - + +
106B PHE* 4.4 15.0 - - - -
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Residues in contact with TRP 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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389A CYS* 3.7 29.6 - - + -
390A HIS* 3.8 13.5 - - - -
391A GLY* 3.6 28.5 - - - -
392A GLU 4.5 1.2 + - - -
393A LEU* 3.5 33.7 - - + +
403A ILE* 3.5 45.3 - - + -
405A LEU* 4.4 6.5 - - + -
466A PHE* 4.0 15.9 - - + -
483A ALA* 4.9 1.1 - - + -
488A HIS* 3.3 38.8 + + - -
489A LYS 3.3 6.8 + - - +
491A GLN* 1.3 78.3 - - - +
493A PHE* 1.3 65.9 + - - +
495A CYS* 3.3 2.5 + - - +
496A ILE* 3.0 48.9 + - + +
105B HIS* 3.7 6.6 - + - -
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Residues in contact with PHE 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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438A LEU* 3.5 39.9 - - + +
439A GLU 4.1 0.7 - - - -
440A ASP* 3.6 44.9 - - + -
466A PHE* 4.0 20.0 - + + -
489A LYS* 2.7 34.7 + - + +
490A GLN* 4.1 9.4 - - - +
492A TRP* 1.3 72.3 - - - +
494A ASN* 1.3 63.2 + - - +
496A ILE* 4.8 2.5 - - - -
497A ARG* 2.9 50.9 + - + +
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Residues in contact with ASN 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 GLN* 2.8 53.1 + - - +
491A GLN* 4.2 3.1 - - - +
493A PHE* 1.3 81.2 - - - +
495A CYS* 1.3 58.9 - - - +
497A ARG* 3.9 13.3 + - - +
498A ALA* 2.9 33.5 + - - +
97B GLU* 4.6 19.0 + - - -
101B PRO* 5.4 1.6 - - - +
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Residues in contact with CYS 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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388A LEU* 4.3 13.6 - - + +
389A CYS* 3.9 24.0 - - + -
405A LEU* 3.7 15.7 - - + +
491A GLN* 3.1 40.8 + - - +
492A TRP* 3.7 3.6 - - + +
494A ASN* 1.3 77.1 - - - +
496A ILE* 1.3 59.4 + - - +
498A ALA* 3.8 4.2 - - - +
499A ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 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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403A ILE* 6.1 0.4 - - + -
405A LEU* 3.8 19.1 - - + -
410A LEU* 4.2 13.0 - - + -
436A LEU* 3.7 26.0 - - + -
438A LEU* 3.8 20.6 - - + -
466A PHE* 3.8 28.0 - - + -
468A ILE* 4.2 11.9 - - + -
481A LEU* 6.0 0.4 - - + -
492A TRP* 3.0 38.3 + - + +
493A PHE 3.9 2.2 - - - +
495A CYS* 1.3 75.4 - - - +
497A ARG* 1.3 64.0 + - - +
499A ALA* 3.2 2.9 + - - +
500A ILE* 3.0 29.9 + - + +
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Residues in contact with ARG 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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438A LEU* 3.8 12.3 - - + +
493A PHE* 2.9 37.2 + - - +
494A ASN* 3.9 12.3 + - - +
496A ILE* 1.3 76.4 - - - +
498A ALA* 1.3 57.9 + - - +
500A ILE* 3.5 8.3 + - - +
501A ALA* 3.0 29.7 + - + +
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Residues in contact with ALA 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 ASN 2.9 19.2 + - - +
495A CYS* 3.8 4.9 - - - +
497A ARG* 1.3 74.3 - - - +
499A ALA* 1.3 56.2 + - - +
501A ALA* 3.7 5.8 - - - +
502A HIS* 2.7 36.4 + - - +
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Residues in contact with ALA 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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388A LEU* 3.7 22.9 - - + +
405A LEU* 4.2 14.1 - - + -
407A GLN* 4.4 11.4 + - - +
433A VAL* 3.4 19.3 - - + +
436A LEU* 5.9 0.2 - - + -
495A CYS 2.9 17.4 + - - +
496A ILE* 3.5 5.8 - - - +
498A ALA* 1.3 77.2 - - - +
500A ILE* 1.3 62.2 + - + +
502A HIS* 3.2 8.0 + - - +
503A HIS* 3.1 18.5 + - - +
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Residues in contact with ILE 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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433A VAL* 3.7 13.7 - - + +
436A LEU* 3.6 46.9 - - + +
438A LEU* 3.8 31.0 - - + +
496A ILE* 3.0 23.1 + - + +
497A ARG* 3.8 6.1 - - - +
499A ALA* 1.3 74.1 - - - +
501A ALA* 1.3 63.6 + - - +
503A HIS* 3.3 3.1 + - - +
504A HIS* 3.1 49.7 + - + +
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Residues in contact with ALA 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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497A ARG* 3.0 19.9 + - + +
498A ALA* 3.7 7.4 - - - +
500A ILE* 1.3 74.2 - - - +
502A HIS* 1.3 64.5 + - - +
504A HIS* 3.5 5.9 + - - +
505A HIS* 3.0 24.9 + - - +
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Residues in contact with HIS 502 (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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407A GLN* 3.2 39.9 + - + +
408A ASP* 5.7 1.3 - - - -
498A ALA 2.7 23.4 + - - +
499A ALA 3.4 6.1 - - - +
501A ALA* 1.3 73.6 - - - +
503A HIS* 1.3 66.8 + - + +
505A HIS* 3.3 10.9 + - - +
506A HIS* 3.3 44.3 + + + -
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Residues in contact with HIS 503 (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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407A GLN 5.9 0.9 - - - +
408A ASP* 5.8 1.2 + - - -
433A VAL* 4.0 13.2 - - + -
434A GLN* 3.3 58.9 + - + +
499A ALA 3.1 13.3 + - - +
500A ILE 3.5 7.6 - - - +
501A ALA 3.2 0.2 - - - -
502A HIS* 1.3 80.0 - - - +
504A HIS* 1.3 72.1 + + - +
506A HIS* 2.7 8.0 + - - +
507A HIS* 2.3 69.7 + - - +
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Residues in contact with HIS 504 (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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433A VAL 5.0 1.4 + - - -
434A GLN 4.5 11.9 + - - -
436A LEU 5.5 1.4 + - - -
500A ILE* 3.1 43.1 + - + +
501A ALA* 3.8 5.2 - - - +
503A HIS* 1.3 95.7 + + - +
505A HIS* 1.3 57.2 - - - +
506A HIS 3.3 0.2 - - - -
507A HIS* 2.9 35.2 + - - +
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Residues in contact with HIS 505 (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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501A ALA 3.0 17.5 + - - +
502A HIS* 3.4 9.4 - - - +
503A HIS 3.0 0.4 + - - -
504A HIS* 1.3 78.8 - - - +
506A HIS* 1.3 86.5 + + + +
507A HIS* 4.5 5.6 + - - -
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Residues in contact with HIS 506 (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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502A HIS* 3.3 48.0 + + + +
503A HIS* 2.7 5.8 + - - +
505A HIS* 1.3 107.8 + + - +
507A HIS* 1.3 77.0 + - - +
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Residues in contact with HIS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLN* 5.2 3.1 - - - -
503A HIS* 2.3 58.7 + - - +
504A HIS* 2.9 35.2 + - + +
505A HIS 4.6 5.6 + - - -
506A HIS* 1.3 82.3 - - - +
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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
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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