Contacts of the helix formed by residues 501 - 518 (chain A) in PDB entry 2IO2
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 GLY 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A ARG* 4.5 1.3 - - - -
493A TYR* 3.5 19.3 - - - -
500A LYS* 1.3 84.2 - - - +
502A HIS* 1.3 62.2 + - - -
503A ARG 3.7 1.1 - - - -
504A ILE* 3.8 22.5 - - - +
505A CYS* 3.6 20.4 - - - -
533A SER* 3.5 10.3 + - - -
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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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500A LYS* 4.0 23.3 - - + +
501A GLY* 1.3 71.3 - - - +
503A ARG* 1.3 63.5 + - - +
504A ILE 3.0 5.4 + - - -
505A CYS* 3.2 6.3 + - - +
506A GLU* 3.0 27.9 + - - +
531A HIS* 4.5 16.5 + + - +
532A HIS* 5.5 1.1 - - - -
533A SER* 3.5 28.8 + - - -
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Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 3.0 50.3 + - - +
502A HIS* 1.3 78.9 - - - +
504A ILE* 1.3 64.6 + - + +
506A GLU* 4.0 24.7 - - + +
507A ILE* 3.1 50.9 + - + +
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Residues in contact with ILE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A TYR* 3.2 37.8 + - + +
447A LYS* 3.7 14.4 - - - +
473A ILE* 3.3 32.5 - - + -
475A ARG* 4.5 26.2 - - - +
482A VAL* 4.2 8.7 - - + -
493A TYR* 5.0 4.7 - - + -
501A GLY* 3.8 24.5 - - - +
502A HIS 3.0 1.2 - - - -
503A ARG* 1.3 77.9 - - + +
505A CYS* 1.3 63.0 + - - +
507A ILE* 3.2 5.0 + - - +
508A LEU* 2.9 29.9 + - + +
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Residues in contact with CYS 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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482A VAL* 4.8 9.6 - - - -
491A LEU* 4.5 9.9 - - + +
492A LYS 5.1 0.7 - - - -
493A TYR* 3.8 27.4 - - - -
501A GLY 3.6 16.4 - - - -
502A HIS* 3.2 2.6 + - - +
504A ILE* 1.3 75.6 - - - +
506A GLU* 1.3 70.0 + - - +
507A ILE 2.9 0.5 + - - -
508A LEU* 2.9 9.0 + - - +
509A LEU* 2.8 28.9 + - - +
531A HIS* 3.5 40.4 - - + -
532A HIS 4.8 4.9 - - - -
533A SER* 5.4 0.4 - - - -
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Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A HIS* 3.0 15.7 + - - +
503A ARG* 3.9 26.8 + - + +
505A CYS* 1.3 78.9 - - - +
507A ILE* 1.3 64.3 + - + +
509A LEU* 3.7 8.3 - - - +
510A GLN* 3.4 18.4 + - - +
531A HIS* 4.5 15.4 + - + +
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Residues in contact with ILE 507 (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 TYR* 3.6 27.6 - - + +
446A LEU* 4.6 16.6 - - + +
447A LYS* 3.9 12.3 - - + +
503A ARG* 3.1 62.5 + - + +
504A ILE 3.4 4.0 - - - +
505A CYS 2.9 1.2 + - - -
506A GLU* 1.3 77.3 - - + +
508A LEU* 1.3 67.6 + - - +
510A GLN* 3.0 21.7 + - - +
511A TYR* 3.3 5.9 + - - +
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 4.0 16.2 - - + -
443A TYR* 4.6 13.0 - - + -
446A LEU* 3.8 24.2 - - + -
471A VAL* 3.9 24.5 - - + -
473A ILE* 5.1 0.9 - - + -
482A VAL* 3.7 35.4 - - + -
484A ILE* 4.9 4.7 - - + -
491A LEU* 4.6 6.7 - - + -
504A ILE* 2.9 17.8 + - + +
505A CYS* 2.9 9.2 + - - +
507A ILE* 1.3 73.8 - - - +
509A LEU* 1.3 60.7 + - - +
511A TYR* 2.7 36.3 + - + +
512A LEU* 3.3 8.2 + - - +
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Residues in contact with LEU 509 (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 LEU* 3.8 23.9 - - + +
505A CYS 2.8 20.4 + - - +
506A GLU* 3.7 8.3 - - - +
508A LEU* 1.3 71.2 - - - +
510A GLN* 1.3 53.8 + - - +
511A TYR 2.7 1.2 + - - -
512A LEU* 2.7 48.5 + - + +
513A GLN* 3.1 11.6 + - - +
524A LEU* 6.0 2.0 - - + -
526A LEU* 4.5 27.4 - - + +
529A TRP* 4.1 33.7 - - + +
530A THR 5.1 0.7 - - - +
531A HIS* 4.8 16.4 - - + +
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Residues in contact with GLN 510 (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 TYR* 5.5 1.2 - - - +
506A GLU 3.4 10.8 + - - +
507A ILE* 3.0 16.5 + - - +
509A LEU* 1.3 78.1 - - - +
511A TYR* 1.3 58.2 + - - +
513A GLN* 3.2 28.1 - - - +
514A ASP* 3.6 22.5 + - - +
526A LEU* 6.4 0.6 - - - +
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Residues in contact with TYR 511 (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 PHE* 3.1 29.4 - + - -
442A PHE* 3.8 12.3 - + - -
446A LEU* 3.6 35.7 - - + -
451A TYR* 3.5 26.0 - + - -
454A VAL* 4.1 15.0 + - + +
458A THR* 2.8 34.7 - - - +
463A LEU* 4.0 9.9 - - + -
507A ILE 3.3 2.9 + - - +
508A LEU* 2.7 26.0 + - + +
510A GLN* 1.3 71.0 - - - +
512A LEU* 1.3 61.3 - - + +
514A ASP* 3.3 4.9 + - - +
515A GLU* 2.6 57.5 + - + +
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Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 3.9 26.7 - - + -
464A PHE* 3.8 18.5 - - + -
469A ILE* 5.2 4.3 - - + -
484A ILE* 4.4 11.7 - - + -
491A LEU* 4.1 14.8 - - + -
508A LEU 3.7 5.8 - - - +
509A LEU* 2.7 38.1 + - + +
511A TYR* 1.3 80.9 - - + +
513A GLN* 1.3 61.0 + - - +
515A GLU* 2.4 29.6 + - - +
516A SER* 2.7 12.1 + - - -
524A LEU* 4.3 6.7 - - + -
529A TRP* 4.3 18.6 - - + -
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Residues in contact with GLN 513 (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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509A LEU 3.1 7.4 + - - +
510A GLN* 3.2 28.7 - - - +
512A LEU* 1.3 78.3 - - - +
514A ASP* 1.3 63.2 + - - +
516A SER* 3.7 1.6 - - - -
517A LYS* 2.9 41.9 + - - +
523A ASP* 3.5 16.9 + - - +
524A LEU* 3.4 41.0 - - + +
526A LEU* 4.0 23.2 - - + +
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Residues in contact with ASP 514 (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 TYR* 3.4 30.2 - - + +
510A GLN* 3.6 23.7 + - - +
511A TYR 3.3 7.8 + - - +
512A LEU 2.7 1.2 + - - -
513A GLN* 1.3 89.6 + - - +
515A GLU* 1.3 59.1 + - - +
516A SER 2.8 10.6 + - - -
517A LYS* 4.4 4.3 - - - +
518A THR* 2.9 37.3 + - - +
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Residues in contact with GLU 515 (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 TYR* 2.5 29.2 + - + -
458A THR* 2.6 29.0 + - - +
461A VAL 5.3 1.2 - - - +
463A LEU* 4.0 23.7 + - + +
464A PHE* 4.1 11.6 - - + -
511A TYR* 2.6 52.7 + - + +
512A LEU* 2.4 25.4 + - - +
514A ASP* 1.3 67.6 - - - +
516A SER* 1.3 55.7 + - - -
519A LYS* 3.2 27.6 - - - +
520A ARG* 5.0 1.6 - - - +
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Residues in contact with SER 516 (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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464A PHE* 3.7 13.7 - - - -
512A LEU 2.7 10.0 + - - -
513A GLN 3.7 4.0 - - - -
514A ASP 2.8 0.6 - - - -
515A GLU* 1.3 79.8 - - - +
517A LYS* 1.3 53.7 + - - -
518A THR 2.5 17.6 + - - -
519A LYS 2.8 11.1 + - - -
520A ARG* 2.6 52.1 + - - +
521A ASN 3.4 0.3 + - - -
522A SER 2.7 17.7 + - - -
523A ASP 3.4 4.0 + - - -
524A LEU* 4.2 8.3 - - - -
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Residues in contact with LYS 517 (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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513A GLN* 2.9 29.8 + - - +
514A ASP* 5.0 2.9 - - - +
516A SER* 1.3 74.1 + - - +
518A THR* 1.3 61.8 + - - +
521A ASN* 3.9 29.0 - - - +
522A SER 3.2 8.9 + - - -
523A ASP* 2.8 36.4 + - - +
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Residues in contact with THR 518 (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 TYR* 3.6 22.6 - - + -
455A LYS* 4.0 22.4 - - - +
514A ASP* 2.9 25.0 + - - +
516A SER 2.5 7.3 + - - -
517A LYS* 1.3 78.9 + - - +
519A LYS* 1.3 56.0 + - + +
520A ARG 3.4 4.4 + - - -
521A ASN* 4.3 3.0 + - - +
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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