Contacts of the helix formed by residues 488 - 499 (chain A) in PDB entry 1Y57
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 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LEU* 3.5 33.9 - - + -
483A CYS* 4.2 0.7 - - - -
486A GLU 3.6 7.2 - - - +
487A CYS* 1.3 90.8 - - - +
489A GLU* 1.3 66.7 + - - +
490A SER* 3.9 5.4 - - - +
491A LEU* 3.0 15.7 + - + +
492A HIS 3.2 8.1 + - - -
519A TYR* 3.3 20.4 - - - +
524A GLU* 4.0 17.7 - - + +
527A TYR* 5.0 8.3 - - + -
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Residues in contact with GLU 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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483A CYS* 4.4 16.4 - - + -
487A CYS 3.5 1.6 + - - +
488A PRO* 1.3 72.5 - - - +
490A SER* 1.3 56.4 + - - +
492A HIS* 3.3 3.6 + - - +
493A ASP* 2.8 39.6 + - - +
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Residues in contact with SER 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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488A PRO* 3.9 0.7 - - - +
489A GLU* 1.3 78.2 - - - +
491A LEU* 1.3 58.2 + - - +
493A ASP* 3.6 13.1 + - - +
494A LEU* 3.3 18.7 + - - +
515A PHE* 4.1 9.2 - - - -
519A TYR* 2.7 25.9 + - - -
523A THR* 3.6 18.6 - - - +
524A GLU* 2.6 29.9 + - - +
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Residues in contact with LEU 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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360A LEU* 3.9 21.1 - - + -
364A VAL* 4.2 11.9 - - + -
452A LEU* 4.8 12.1 - - + -
456A THR* 3.9 27.6 - - + -
487A CYS* 3.9 8.7 - - - -
488A PRO* 3.0 10.7 + - + +
490A SER* 1.3 77.4 + - - +
492A HIS* 1.3 65.9 + - - +
494A LEU* 3.2 17.6 + - + +
495A MET* 3.1 28.0 + - + +
516A LEU* 4.1 25.1 - - + -
519A TYR* 3.6 23.6 - - + +
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Residues in contact with HIS 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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480A ARG* 6.2 0.2 - - + -
481A MET 2.9 25.4 + - - -
482A PRO* 3.4 8.7 - - + -
483A CYS* 3.5 52.2 - - + +
487A CYS* 4.3 2.9 - - - -
488A PRO 3.2 4.4 + - - -
489A GLU* 3.3 7.1 + - - +
491A LEU* 1.3 78.6 - - - +
493A ASP* 1.3 60.2 + - - +
495A MET* 3.2 25.1 + - + +
496A CYS* 2.9 50.3 + - - -
499A TRP* 4.5 2.2 - + - -
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Residues in contact with ASP 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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489A GLU* 2.8 32.8 + - - +
490A SER* 3.6 10.9 - - - +
491A LEU 3.3 0.2 - - - -
492A HIS* 1.3 76.6 + - - +
494A LEU* 1.3 63.0 + - - +
496A CYS* 3.3 8.8 + - - +
497A GLN* 3.1 36.2 + - - +
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Residues in contact with LEU 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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452A LEU* 4.1 15.0 - - + -
490A SER 3.3 9.6 + - - +
491A LEU* 3.2 13.1 + - + +
492A HIS 3.2 0.4 - - - -
493A ASP* 1.3 77.1 - - - +
495A MET* 1.3 64.6 + - - +
497A GLN* 3.3 18.4 + - - +
498A CYS* 3.2 22.2 + - - -
507A PRO* 5.3 0.9 - - + -
511A TYR* 4.0 15.3 - - + +
512A LEU* 3.7 32.5 - - + -
515A PHE* 3.6 44.2 - - + -
516A LEU* 4.0 19.5 - - + -
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Residues in contact with MET 495 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A GLY* 4.0 3.4 - - - +
452A LEU* 4.0 34.8 - - + +
453A THR* 3.9 20.2 - - - -
456A THR* 3.7 26.5 - - + +
482A PRO 5.6 0.2 - - - +
484A PRO* 4.5 6.1 - - + -
487A CYS* 4.1 19.5 - - - -
491A LEU* 3.1 19.8 + - + +
492A HIS* 3.2 25.5 + - - +
494A LEU* 1.3 75.5 - - - +
496A CYS* 1.3 58.9 + - - +
498A CYS* 3.1 24.6 + - - +
499A TRP* 3.2 36.1 + - + -
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Residues in contact with CYS 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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480A ARG* 5.0 11.2 - - + -
492A HIS* 2.9 49.3 + - - +
493A ASP* 3.7 8.3 - - - +
494A LEU 3.2 0.4 - - - -
495A MET* 1.3 73.3 - - - +
497A GLN* 1.3 65.0 + - - +
499A TRP* 3.2 26.4 + - - +
500A ARG* 3.5 13.4 + - - +
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Residues in contact with GLN 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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493A ASP* 3.1 30.7 + - - +
494A LEU* 3.3 24.1 + - - +
496A CYS* 1.3 73.6 - - - +
498A CYS* 1.3 64.7 + - - +
499A TRP 3.3 0.9 + - - -
500A ARG* 3.4 51.0 + - - +
506A ARG* 3.6 4.9 - - - +
507A PRO* 3.4 27.6 - - + +
511A TYR* 4.3 16.8 + - - -
515A PHE* 6.2 1.0 - - - -
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Residues in contact with CYS 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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445A VAL* 3.5 39.3 - - - +
446A TRP* 3.4 13.0 - - - -
448A PHE* 4.5 2.9 - - - -
449A GLY* 3.8 20.6 - - - -
452A LEU* 5.0 2.0 - - - -
494A LEU 3.2 17.8 + - - -
495A MET* 3.1 11.3 + - - +
497A GLN* 1.3 77.1 - - - +
499A TRP* 1.3 57.8 + - + +
500A ARG 3.4 0.2 - - - -
506A ARG* 3.2 21.7 + - - -
507A PRO* 4.1 2.2 - - - -
512A LEU* 3.9 27.1 - - - -
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Residues in contact with TRP 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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446A TRP* 3.3 54.0 + + + -
449A GLY* 3.3 24.3 - - - -
450A ILE* 3.4 23.0 - - + +
453A THR* 3.6 21.8 - - + -
463A TYR* 5.6 2.5 - - - -
480A ARG* 2.9 57.4 + - + +
481A MET* 3.9 33.4 - - + -
492A HIS* 4.5 2.0 - + - -
495A MET* 3.2 38.7 + - + -
496A CYS* 3.2 18.6 + - - +
497A GLN 3.1 1.0 - - - -
498A CYS* 1.3 81.2 - - - +
500A ARG* 1.3 60.2 + - - +
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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