Contacts of the helix formed by residues 463 - 476 (chain A) in PDB entry 1YI1
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 PRO 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A PHE* 3.9 16.4 - - + -
456A LYS 4.2 6.5 - - - +
457A THR* 3.7 35.4 - - + +
458A PHE 5.2 0.4 - - - +
461A ALA 3.3 7.6 - - - +
462A ILE* 1.3 88.4 - - + +
464A PRO* 1.3 71.7 - - + +
465A GLN* 3.2 5.2 - - - +
466A TYR* 3.1 19.8 + - + -
467A ALA 3.0 17.5 + - - -
618A LYS* 3.8 15.5 - - + -
642A PRO* 5.3 1.1 - - + -
645A GLU* 5.6 3.1 - - - +
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Residues in contact with PRO 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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462A ILE 3.4 7.5 - - - +
463A PRO* 1.3 80.2 - - + +
465A GLN* 1.3 77.8 - - - +
467A ALA* 3.1 9.3 + - + +
468A ILE* 3.0 27.7 + - - +
491A TRP* 3.6 39.0 - - + -
563A LEU* 3.8 17.2 - - + +
641A CYS* 3.9 27.4 - - + -
642A PRO* 4.9 0.2 - - + -
645A GLU* 4.1 16.8 - - + -
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Residues in contact with GLN 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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454A SER 5.4 1.0 + - - -
455A PHE* 3.6 29.1 - - + +
463A PRO* 3.6 4.9 - - - +
464A PRO* 1.3 90.2 - - - +
466A TYR* 1.3 59.0 + - - +
468A ILE* 3.2 7.5 + - - +
469A LYS* 2.9 27.8 + - - +
491A TRP* 3.7 29.0 - - + +
495A PHE* 3.3 54.4 - - + +
645A GLU* 3.7 17.8 + - - +
646A HIS 4.8 4.2 + - - -
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Residues in contact with TYR 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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455A PHE* 3.9 24.2 - + + -
463A PRO* 3.1 23.3 + - + +
465A GLN* 1.3 78.3 - - - +
467A ALA* 1.3 64.5 + - - +
469A LYS* 3.0 14.6 + - + +
470A VAL* 2.8 48.6 + - + +
618A LYS* 3.6 47.2 + - + -
621A LEU* 3.9 16.8 - - + -
622A ARG* 5.3 10.7 + - + +
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Residues in contact with ALA 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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462A ILE* 4.3 6.5 - - + -
463A PRO 3.0 10.7 + - - +
464A PRO* 3.3 14.1 - - + +
466A TYR* 1.3 76.6 - - - +
468A ILE* 1.3 62.0 - - - +
470A VAL* 3.0 6.4 + - - +
471A LEU* 3.0 19.3 + - - +
561A LEU* 4.9 5.2 - - + -
563A LEU* 4.4 15.9 - - + -
621A LEU* 3.7 26.2 - - + +
625A ILE* 3.6 10.0 - - + +
639A VAL* 4.5 6.1 - - + -
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Residues in contact with ILE 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 PRO 3.0 12.2 + - - +
465A GLN* 3.5 7.0 - - - +
467A ALA* 1.3 75.5 - - + +
469A LYS* 1.3 57.4 + - - +
471A LEU* 3.1 9.8 + - - +
472A ASP* 2.8 26.3 + - - +
488A HIS 4.3 0.4 - - - +
491A TRP* 3.4 19.3 - - + +
492A ALA* 3.3 37.2 - - + +
495A PHE* 3.5 26.0 - - + +
496A TYR* 4.2 13.1 - - + -
535A ILE* 4.2 19.1 - - + -
561A LEU* 4.7 5.1 - - + +
563A LEU* 4.1 20.0 - - + -
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Residues in contact with LYS 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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453A LEU 5.8 1.6 + - - -
455A PHE* 4.0 26.6 - - + -
465A GLN 2.9 11.8 + - - +
466A TYR* 3.0 15.7 + - + +
468A ILE* 1.3 77.7 - - - +
470A VAL* 1.3 57.6 + - + +
472A ASP* 3.3 5.9 + - + +
473A GLU* 3.0 27.5 + - - +
495A PHE* 3.8 39.2 - - + +
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Residues in contact with VAL 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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466A TYR* 2.8 54.2 + - + +
467A ALA* 3.0 7.6 + - - +
469A LYS* 1.3 73.9 - - + +
471A LEU* 1.3 61.9 + - - +
473A GLU* 3.2 7.2 + - - +
474A LEU* 2.8 51.2 + - + +
621A LEU* 4.4 4.3 - - + -
622A ARG* 3.9 33.2 - - + +
625A ILE* 3.8 12.8 - - + -
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Residues in contact with LEU 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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467A ALA 3.0 11.5 + - - +
468A ILE* 3.3 9.0 - - - +
470A VAL* 1.3 75.7 - - - +
472A ASP* 1.3 56.9 + - - +
474A LEU* 3.9 0.8 - - - -
475A THR* 2.5 54.1 + - + +
481A ILE* 4.2 10.1 - - + -
496A TYR* 4.2 8.7 - - + -
533A VAL* 3.8 26.7 - - + -
535A ILE* 3.7 20.6 - - + -
561A LEU* 3.6 25.4 - - + -
625A ILE* 4.1 24.8 - - + +
628A MET* 4.2 9.9 - - + -
629A LEU* 4.5 1.3 - - + -
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Residues in contact with ASP 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 ILE 2.8 13.1 + - - +
469A LYS* 3.3 13.7 - - + +
471A LEU* 1.3 77.9 - - - +
473A GLU* 1.3 58.7 + - - +
476A ASP* 2.8 26.9 + - - -
477A GLY* 3.0 18.0 + - - -
495A PHE 4.0 3.4 - - - +
496A TYR* 3.4 23.7 - - + -
497A ASN* 2.8 48.8 + - - +
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Residues in contact with GLU 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 LYS 3.0 8.7 + - - +
470A VAL* 3.5 11.4 - - - +
472A ASP* 1.3 80.1 - - - +
474A LEU* 1.3 72.1 + - + +
476A ASP* 3.0 15.6 + - - +
622A ARG* 2.4 37.6 + - - +
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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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470A VAL* 2.8 29.3 + - + +
471A LEU 4.2 1.3 - - - +
473A GLU* 1.3 78.5 - - + +
475A THR* 1.3 58.7 + - - +
476A ASP* 3.4 0.6 + - - +
622A ARG* 3.5 52.9 - - + +
625A ILE* 3.7 16.4 - - + -
626A GLN* 3.6 39.7 + - - +
629A LEU* 3.8 18.0 - - + +
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Residues in contact with THR 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 LEU* 2.5 35.4 + - + +
472A ASP 3.3 1.7 + - - -
474A LEU* 1.3 75.1 - - - +
476A ASP* 1.3 71.6 + - - +
477A GLY 3.2 0.7 + - - -
478A LYS* 3.2 15.1 + - - +
479A ALA* 4.0 17.0 - - + -
496A TYR* 2.8 25.0 + - - -
531A ILE* 4.2 21.4 - - + +
533A VAL* 5.0 0.2 - - + -
629A LEU* 3.6 31.4 - - + -
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Residues in contact with ASP 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 ASP* 2.8 9.1 + - - -
473A GLU* 3.0 10.7 + - - +
474A LEU 5.2 0.7 - - - +
475A THR* 1.3 82.5 - - - +
477A GLY* 1.3 63.3 + - - +
478A LYS* 3.1 28.4 + - + +
499A LYS* 3.1 21.7 + - - -
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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