Contacts of the helix formed by residues 460 - 481 (chain A) in PDB entry 5I35
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 SER 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A LEU* 1.3 79.6 - - - +
461A GLN* 1.3 58.9 + - - +
462A GLU* 3.6 16.1 + - - +
463A ILE* 3.0 30.9 + - - +
464A ARG* 3.0 29.4 + - - +
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Residues in contact with GLN 461 (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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460A SER* 1.3 73.2 - - - +
462A GLU* 1.3 69.2 + - - +
464A ARG* 3.0 29.9 + - - +
465A ASN* 2.8 63.6 + - - +
624A LYS* 2.8 27.7 + - - +
625A ALA* 4.0 1.4 - - - +
626A ARG* 4.1 8.3 - - + +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A SER* 3.2 17.2 + - - +
461A GLN* 1.3 92.7 + - - +
463A ILE* 1.3 59.4 + - + +
465A ASN* 3.6 8.7 + - - +
466A GLU* 3.1 31.5 + - - +
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LEU* 3.8 19.3 - - + -
460A SER* 3.0 28.4 + - - +
462A GLU* 1.3 77.4 - - + +
464A ARG* 1.3 63.0 + - - +
466A GLU* 3.3 9.5 + - - +
467A ILE* 2.8 55.1 + - + +
496A TYR* 3.8 24.5 - - + +
501A HIS* 4.3 13.5 - - + +
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Residues in contact with ARG 464 (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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456A ALA* 3.4 25.6 - - + +
457A GLU* 3.5 15.8 + - - +
459A LEU* 3.1 35.2 + - + -
460A SER* 3.0 10.4 + - - +
461A GLN* 3.0 47.8 + - - +
463A ILE* 1.3 76.8 - - - +
465A ASN* 1.3 64.5 + - - +
467A ILE* 3.3 7.5 + - + +
468A CYS* 3.0 30.8 + - - +
623A LEU* 2.8 45.5 + - + +
624A LYS* 3.4 17.8 - - - +
625A ALA* 4.6 2.0 - - + -
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Residues in contact with ASN 465 (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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461A GLN* 2.8 50.2 + - - +
462A GLU* 3.7 8.8 + - - +
463A ILE 3.3 0.2 - - - -
464A ARG* 1.3 75.9 - - - +
466A GLU* 1.3 56.9 + - - +
468A CYS 3.8 0.2 - - - -
469A TYR* 2.8 32.5 + - - +
625A ALA* 3.4 7.9 - - - -
626A ARG* 3.0 43.4 + - - +
627A PHE* 3.8 8.1 - - + -
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Residues in contact with GLU 466 (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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427A PHE* 4.9 0.7 - - - -
462A GLU* 3.1 18.1 + - - +
463A ILE* 3.6 11.7 - - - +
464A ARG 3.2 0.2 - - - -
465A ASN* 1.3 78.4 - - - +
467A ILE* 1.3 61.0 + - - +
469A TYR* 3.9 5.5 - - + +
470A ASN* 2.7 46.1 + - - +
501A HIS* 3.0 36.3 + - + +
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Residues in contact with ILE 467 (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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427A PHE* 4.1 19.6 - - + -
453A LEU* 3.7 36.1 - - + -
456A ALA* 5.9 0.4 - - + -
459A LEU* 4.3 6.3 - - + -
463A ILE* 2.8 42.0 + - + +
464A ARG* 3.3 9.6 + - + +
466A GLU* 1.3 78.2 - - + +
468A CYS* 1.3 62.4 + - - +
470A ASN* 3.3 2.9 + - - +
471A ILE* 2.9 34.0 + - + +
496A TYR* 3.9 29.2 - - + -
501A HIS* 5.4 1.1 - - + -
503A VAL* 4.4 10.1 - - + -
623A LEU* 5.0 2.7 - - + -
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Residues in contact with CYS 468 (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 ARG 3.0 18.5 + - - +
467A ILE* 1.3 77.3 - - - +
469A TYR* 1.3 66.5 + - - +
471A ILE* 3.6 8.0 - - - +
472A LEU* 2.8 26.5 + - - +
619A ILE* 4.1 5.6 - - - -
620A CYS* 3.6 32.9 - - - -
623A LEU* 3.5 41.7 - - - -
625A ALA* 3.7 15.5 - - + -
627A PHE* 3.6 4.6 - - + -
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Residues in contact with TYR 469 (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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465A ASN 2.8 23.4 + - - +
466A GLU* 3.9 7.6 - - + +
468A CYS* 1.3 71.7 - - - +
470A ASN* 1.3 74.3 + - - +
472A LEU* 3.3 0.9 + - - -
473A VAL* 3.1 44.3 + - + +
627A PHE* 3.4 31.7 - + + -
628A PRO* 4.1 12.8 - - + -
631A ALA* 5.6 3.1 - - - +
632A MSE 3.4 35.7 + - + +
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Residues in contact with ASN 470 (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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425A HIS* 5.5 3.1 - - - -
427A PHE* 3.7 48.4 - - + +
428A PHE* 3.3 16.5 - - + -
466A GLU* 2.7 33.9 + - - +
467A ILE 3.6 4.5 - - - +
469A TYR* 1.3 90.2 - - - +
471A ILE* 1.3 60.5 + - - +
473A VAL* 3.5 6.1 + - - +
474A LEU 3.1 17.8 + - - -
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Residues in contact with ILE 471 (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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428A PHE* 3.9 14.6 - - + -
453A LEU* 3.7 29.4 - - + -
467A ILE* 2.9 27.7 + - + +
468A CYS* 3.1 8.5 + - - +
470A ASN* 1.3 74.7 - - - +
472A LEU* 1.3 60.9 + - - +
474A LEU* 3.2 5.6 + - + +
475A CYS* 2.9 26.0 + - + +
489A PRO* 6.3 0.2 - - + -
494A PHE* 3.8 38.1 - - + -
616A SER* 4.9 15.3 - - - +
619A ILE* 4.2 26.9 - - + -
620A CYS* 5.6 1.8 - - - -
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Residues in contact with LEU 472 (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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468A CYS 2.8 16.0 + - - +
469A TYR 4.0 2.7 - - - +
471A ILE* 1.3 78.6 - - - +
473A VAL* 1.3 63.0 + - - +
475A CYS* 3.2 11.9 + - + +
476A LEU* 2.9 25.2 + - + +
570A PHE* 4.7 7.4 - - + -
578A PHE* 4.0 31.0 - - + -
613A MSE 4.7 4.5 - - - -
616A SER* 3.9 26.5 - - - +
617A PHE* 4.1 23.8 - - + -
620A CYS* 4.7 4.7 - - - -
627A PHE* 4.0 8.3 - - + -
629A CYS* 4.2 7.2 - - - -
632A MSE 3.8 21.8 - - - -
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Residues in contact with VAL 473 (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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469A TYR* 3.1 43.3 + - + +
470A ASN* 3.8 8.3 - - - +
472A LEU* 1.3 74.5 - - - +
474A LEU* 1.3 63.1 + - - +
476A LEU* 3.1 9.1 + - + +
477A ARG* 3.0 42.4 + - + +
632A MSE 3.7 24.7 - - + -
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Residues in contact with LEU 474 (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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418A PHE* 5.1 2.2 - - + -
422A LEU* 4.3 19.5 - - + -
425A HIS* 5.7 1.3 - - - +
428A PHE* 3.8 31.0 - - + -
470A ASN 3.1 17.3 + - - +
471A ILE* 3.2 5.8 + - + +
473A VAL* 1.3 75.7 - - - +
475A CYS* 1.3 57.8 + - - +
477A ARG* 3.1 13.9 + - + +
478A GLU* 2.8 45.4 + - + +
482A PHE* 4.1 24.2 - - + -
494A PHE* 5.1 7.9 - - + -
505A LEU* 4.2 23.8 - - + -
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Residues in contact with CYS 475 (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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471A ILE* 2.9 13.7 + - + +
472A LEU* 3.2 13.4 + - - +
474A LEU* 1.3 76.0 - - - +
476A LEU* 1.3 64.3 + - - +
478A GLU* 3.1 13.3 + - - +
479A LEU* 2.9 39.5 + - - +
612A LYS* 3.8 29.2 - - - +
613A MSE 4.2 13.5 - - - -
616A SER* 3.4 30.7 - - - +
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Residues in contact with LEU 476 (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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472A LEU* 2.9 17.8 + - + +
473A VAL* 3.1 8.3 + - + +
475A CYS* 1.3 73.0 - - + +
477A ARG* 1.3 57.5 + - + +
479A LEU* 3.4 1.5 + - + -
480A PHE* 2.9 57.8 + - + +
570A PHE* 4.3 14.1 - - + -
613A MSE 4.2 22.0 - - + -
632A MSE 4.0 50.5 - - + +
633A PHE* 4.2 13.9 - - + +
636A ALA* 4.2 15.0 - - + -
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Residues in contact with ARG 477 (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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421A LEU 5.3 3.4 + - - -
422A LEU* 4.9 3.0 - - - +
425A HIS* 4.0 27.1 + - - -
473A VAL* 3.0 32.9 + - + +
474A LEU* 3.4 12.6 - - - +
476A LEU* 1.3 75.0 - - + +
478A GLU* 1.3 56.6 + - - +
481A GLU* 2.7 57.1 + - - +
482A PHE* 2.8 61.9 + - + -
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Residues in contact with GLU 478 (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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418A PHE* 3.7 16.8 - - + -
474A LEU* 2.8 40.1 + - + +
475A CYS* 3.6 9.6 + - - +
477A ARG* 1.3 73.5 - - - +
479A LEU* 1.3 62.2 + - - +
482A PHE* 3.8 21.3 - - + +
484A PHE 3.6 27.2 - - - +
485A MSE 3.4 17.0 - - + +
486A GLN* 2.6 39.1 + - - +
612A LYS* 2.9 27.7 + - - -
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Residues in contact with LEU 479 (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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475A CYS* 2.9 37.3 + - - +
476A LEU* 3.8 3.6 - - - +
478A GLU* 1.3 79.0 - - - +
480A PHE* 1.3 86.4 + - + +
481A GLU 3.8 0.4 + - - -
482A PHE 4.8 3.3 - - - +
485A MSE 3.9 11.3 - - + +
519A THR* 3.9 21.3 - - - +
522A TYR* 4.5 7.6 - - + -
609A LEU* 3.7 33.2 - - + +
612A LYS* 3.9 22.0 - - + -
613A MSE 4.0 27.1 - - + -
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Residues in contact with PHE 480 (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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476A LEU* 2.9 48.0 + - + +
479A LEU* 1.3 100.6 - - + +
481A GLU* 1.3 58.0 + - - +
482A PHE 5.2 0.2 - - - -
519A THR* 3.9 12.3 - - + -
522A TYR* 3.9 24.0 - + + -
523A ILE* 3.2 57.0 - - + -
526A ILE* 4.5 4.9 - - + -
613A MSE 4.6 3.4 - - + -
633A PHE* 4.7 6.5 - + - -
636A ALA* 4.7 13.9 - - + +
640A TYR* 3.6 23.2 - + + +
643A ARG* 2.8 19.6 + - - -
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Residues in contact with GLU 481 (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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477A ARG* 2.7 64.0 + - - +
479A LEU 3.8 0.4 + - - -
480A PHE* 1.3 74.8 - - + +
482A PHE* 1.3 81.0 + - + +
483A HIS* 5.2 4.5 - - - -
643A ARG* 3.8 32.7 + - - +
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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