Contacts of the helix formed by residues 494 - 509 (chain J) in PDB entry 5A31
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 ASN 494 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489J HIS* 3.0 17.8 + - + +
492J MET* 3.8 30.5 - - - +
493J GLY* 1.3 81.7 - - - +
495J PHE* 1.3 64.0 + - - +
496J GLU 3.3 2.5 - - - -
497J ASN* 3.3 32.2 + - + +
498J ALA* 3.1 22.6 + - - +
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Residues in contact with PHE 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 3.9 14.8 - + - -
22G ILE* 6.4 0.9 - - + -
490J SER 3.4 19.5 - - - -
493J GLY* 3.5 29.8 + - - -
494J ASN* 1.3 70.0 - - - +
496J GLU* 1.3 59.9 + - - +
498J ALA* 3.6 0.7 - - - +
499J VAL* 3.0 34.8 + - - +
522J CYS* 3.4 34.1 - - - +
525J MET* 3.0 58.3 - - + -
526J TYR* 4.4 16.4 - - + -
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Residues in contact with GLU 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494J ASN 3.3 0.6 - - - -
495J PHE* 1.3 76.4 - - - +
497J ASN* 1.3 70.9 + - - +
499J VAL* 3.4 11.4 + - - +
500J ASP* 3.5 10.4 + - - +
526J TYR* 3.1 45.7 + - + +
420P TYR* 4.8 10.7 + - - +
424P ARG* 5.2 7.4 + - - +
427P GLN* 3.3 23.9 + - - -
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Residues in contact with ASN 497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489J HIS* 4.1 23.3 + - + +
494J ASN* 3.3 39.8 + - - +
496J GLU* 1.3 81.0 - - - +
498J ALA* 1.3 67.3 + - - +
500J ASP* 3.2 21.7 - - - +
501J TYR* 3.3 17.1 - - + -
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Residues in contact with ALA 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486J GLY* 3.5 24.5 - - - +
489J HIS* 3.8 10.9 - - + +
490J SER 3.8 3.6 - - - +
494J ASN 3.1 14.0 + - - +
495J PHE 3.6 0.7 - - - +
496J GLU 3.3 0.2 - - - -
497J ASN* 1.3 79.7 - - - +
499J VAL* 1.3 63.9 + - - +
501J TYR* 2.9 13.0 + - - +
502J PHE* 2.9 20.8 + - + -
522J CYS* 3.4 27.4 - - - -
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Residues in contact with VAL 499 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495J PHE 3.0 23.8 + - - +
496J GLU* 3.4 4.7 + - - +
497J ASN 3.3 0.6 - - - -
498J ALA* 1.3 75.7 - - - +
500J ASP* 1.3 63.0 + - - +
502J PHE* 3.4 3.0 + - - +
503J HIS* 3.1 32.6 + - + +
519J LEU* 3.8 19.7 - - + +
522J CYS* 3.8 25.4 - - + +
523J ILE* 4.2 22.2 - - + +
526J TYR* 5.0 2.5 - - + -
420P TYR* 3.8 33.4 - - + +
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Residues in contact with ASP 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496J GLU 3.5 7.0 + - - +
497J ASN* 3.2 15.1 + - - +
499J VAL* 1.3 81.1 - - - +
501J TYR* 1.3 78.6 + - - +
503J HIS* 3.2 8.8 + - - +
504J THR* 3.1 31.2 + - - +
396P LYS* 4.1 24.5 + - - +
420P TYR* 5.1 3.4 + - - -
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Residues in contact with TYR 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469J ARG* 6.0 3.3 - - - +
472J LEU* 5.4 1.4 - - + +
482J TYR* 3.7 29.5 - + - +
485J ILE* 3.2 34.5 - - + +
486J GLY* 3.6 19.7 - - - -
489J HIS* 3.6 32.5 + + - -
497J ASN* 3.3 23.5 + - + -
498J ALA 2.9 3.7 + - - +
500J ASP* 1.3 93.3 - - - +
502J PHE* 1.3 62.3 + - - +
504J THR* 3.2 10.2 + - + -
505J ALA* 3.1 23.6 + - - +
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Residues in contact with PHE 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483J SER* 3.8 17.3 - - - -
486J GLY* 3.4 20.0 - - - -
487J TYR* 3.3 26.0 - - + -
490J SER* 4.6 0.4 - - - -
498J ALA* 2.9 35.9 + - + +
499J VAL* 4.6 1.3 - - - -
501J TYR* 1.3 71.7 - - - +
503J HIS* 1.3 66.2 + - - +
505J ALA* 3.5 3.9 + - - +
506J LEU* 3.1 28.2 + - - +
514J PHE* 4.1 9.2 - + - -
515J SER* 3.7 25.3 - - - +
518J MET* 3.8 44.0 - - + -
519J LEU* 3.9 28.0 - - + +
522J CYS* 4.8 2.5 - - + -
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Residues in contact with HIS 503 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 4.8 6.8 - - + +
499J VAL* 3.1 37.8 + - + +
500J ASP* 3.4 11.9 - - - +
502J PHE* 1.3 76.5 - - - +
504J THR* 1.3 64.3 + - + +
506J LEU* 3.0 6.5 + - - +
507J GLY* 3.0 18.9 + - - -
519J LEU* 3.9 23.3 - - + +
523J ILE* 5.0 1.4 - - - +
389P ARG* 3.3 21.9 + - - -
392P ILE* 5.6 5.4 - - + -
402P TRP* 5.1 8.1 - + - -
417P TYR* 5.3 2.0 - + - -
420P TYR* 4.3 10.5 - + - -
421P TYR* 3.2 39.7 - + - -
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Residues in contact with THR 504 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482J TYR* 3.2 34.3 - - + -
500J ASP* 3.1 32.9 + - - +
501J TYR* 3.2 11.9 + - + -
503J HIS* 1.3 75.7 - - + +
505J ALA* 1.3 65.3 + - - +
507J GLY* 3.1 3.6 + - - -
508J LEU* 3.1 28.5 + - - +
393P GLU* 6.0 4.0 - - - -
396P LYS* 5.7 5.2 - - - +
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Residues in contact with ALA 505 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479J ALA* 3.8 22.5 - - + +
482J TYR* 3.9 10.3 - - + -
483J SER* 3.9 19.1 - - - +
501J TYR 3.1 12.7 + - - +
502J PHE* 3.7 5.8 - - - +
504J THR* 1.3 82.6 + - - +
506J LEU* 1.3 58.5 + - - +
508J LEU* 3.3 7.4 + - - +
509J ARG* 3.0 29.1 + - - +
512J ASP* 5.6 0.6 - - - +
515J SER* 4.2 9.5 + - - +
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Residues in contact with LEU 506 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.4 51.4 - - + -
502J PHE 3.1 7.6 + - - +
503J HIS* 3.0 9.5 + - - +
505J ALA* 1.3 79.2 - - - +
507J GLY* 1.3 63.1 + - - +
509J ARG 3.7 8.1 - - - +
510J ARG* 3.3 34.5 + - - +
512J ASP 3.8 7.9 - - - +
515J SER* 3.0 36.1 - - - +
516J VAL* 3.7 26.7 - - + +
519J LEU* 4.3 12.8 - - + -
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Residues in contact with GLY 507 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 5.6 1.5 - - - +
503J HIS 3.0 12.2 + - - -
504J THR* 3.1 5.5 + - - -
506J LEU* 1.3 79.8 - - - +
508J LEU* 1.3 65.5 + - - +
509J ARG* 4.7 0.2 - - - -
510J ARG* 4.7 3.5 + - - +
389P ARG* 5.8 5.2 - - - -
393P GLU* 3.6 22.6 - - - +
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Residues in contact with LEU 508 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477J GLN* 2.8 46.9 - - + +
479J ALA* 4.1 14.4 - - + +
482J TYR* 3.8 27.6 - - + -
504J THR* 3.1 14.2 + - - +
505J ALA 3.3 5.6 + - - +
507J GLY* 1.3 81.3 - - - +
509J ARG* 1.3 57.6 + - - +
510J ARG 4.1 0.2 - - - -
183P ASP* 5.9 0.9 - - - +
393P GLU* 5.4 5.8 - - - +
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Residues in contact with ARG 509 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLU* 4.9 12.5 + - - -
478J ASN* 5.0 5.1 + - - -
479J ALA* 3.8 23.1 - - + +
480J SER* 4.3 22.2 - - - +
505J ALA 3.0 10.7 + - - +
506J LEU* 3.3 12.5 - - - +
508J LEU* 1.3 77.6 - - - +
510J ARG* 1.3 64.6 + - - +
511J ASP* 3.2 14.7 + - + -
512J ASP* 3.4 49.8 + - + +
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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
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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