Contacts of the helix formed by residues 507 - 519 (chain A) in PDB entry 1YGY
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 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A ALA* 5.2 5.4 - - + +
480A VAL* 4.9 8.3 - - + -
504A GLN* 6.5 0.2 - - - -
505A ASP 3.7 9.2 - - - +
506A VAL* 1.3 88.4 - - + +
508A ASP* 1.3 60.7 + - - +
509A ASP* 3.4 11.9 - - - +
510A VAL* 2.9 46.3 - - + +
511A ARG* 2.9 9.7 + - - +
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Residues in contact with ASP 508 (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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506A VAL 3.6 0.4 + - - -
507A PRO* 1.3 70.1 - - - +
509A ASP* 1.3 68.4 + - - +
511A ARG* 3.2 24.1 + - - +
512A THR* 3.0 27.4 + - - +
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Residues in contact with ASP 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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507A PRO* 4.4 7.3 - - - +
508A ASP* 1.3 78.7 + - - +
510A VAL* 1.3 73.1 + - - +
512A THR* 3.1 8.7 + - - -
513A ALA* 2.8 27.8 + - - +
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Residues in contact with VAL 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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474A LEU* 5.1 8.7 - - + +
475A LEU* 5.3 1.3 - - + -
478A ALA* 3.9 26.0 - - + -
506A VAL* 2.8 39.0 - - + -
507A PRO* 2.9 30.1 - - + +
509A ASP* 1.3 84.7 - - - +
511A ARG* 1.3 64.3 + - - +
513A ALA* 3.2 7.6 + - - +
514A ILE* 2.9 33.8 + - + +
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Residues in contact with ARG 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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505A ASP* 2.9 31.5 + - - -
506A VAL* 2.8 26.4 + - + +
507A PRO 2.9 18.8 + - - +
508A ASP* 3.2 22.5 + - - +
510A VAL* 1.3 76.2 - - - +
512A THR* 1.3 58.2 + - - +
514A ILE* 3.2 7.5 + - - +
515A ALA* 3.0 29.2 + - - +
523A LEU* 4.0 33.4 + - + +
524A GLU* 5.0 0.8 - - - +
525A VAL* 3.5 35.6 + - - +
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Residues in contact with THR 512 (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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508A ASP* 3.0 14.6 + - - +
509A ASP* 3.4 11.8 - - - -
511A ARG* 1.3 73.0 - - - +
513A ALA* 1.3 67.5 + - - +
515A ALA* 3.3 6.8 + - - +
516A ALA* 3.0 26.9 + - + +
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Residues in contact with ALA 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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474A LEU* 4.0 23.1 - - + -
509A ASP 2.8 14.4 + - - +
510A VAL* 3.5 12.6 - - + +
512A THR* 1.3 77.6 - - - +
514A ILE* 1.3 61.9 + - - +
516A ALA* 3.4 5.4 + - - +
517A ALA* 2.9 26.3 + - - +
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Residues in contact with ILE 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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457A LEU* 4.1 13.0 - - + -
459A ILE* 3.7 26.7 - - + -
471A ILE* 4.2 22.2 - - + +
474A LEU* 3.8 27.1 - - + -
475A LEU* 3.7 34.3 - - + -
506A VAL* 4.8 4.3 - - + -
510A VAL* 2.9 24.2 + - + +
511A ARG* 3.2 6.0 + - - +
513A ALA* 1.3 75.8 - - - +
515A ALA* 1.3 64.0 - - - +
517A ALA* 3.1 1.8 + - - +
518A VAL* 3.0 32.2 + - + +
523A LEU* 4.1 7.0 - - + -
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Residues in contact with ALA 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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511A ARG 3.0 16.5 + - - +
512A THR* 3.6 7.6 - - + +
514A ILE* 1.3 77.9 - - - +
516A ALA* 1.3 53.3 + - - +
519A ASP* 2.7 32.4 + - - -
520A ALA* 2.9 32.9 + - + +
523A LEU* 4.7 10.7 - - + +
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Residues in contact with ALA 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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512A THR* 3.0 19.5 + - + +
513A ALA* 3.8 6.1 - - - +
515A ALA* 1.3 77.4 - - - +
517A ALA* 1.3 62.5 + - - +
519A ASP* 3.5 10.3 + - - +
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Residues in contact with ALA 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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463A ASP* 3.8 12.8 - - - +
470A LYS* 3.8 32.5 + - + +
474A LEU* 4.1 17.3 - - + -
513A ALA 2.9 18.1 + - - +
514A ILE 3.1 3.3 + - - +
516A ALA* 1.3 80.4 - - - +
518A VAL* 1.3 61.3 + - + +
519A ASP* 3.7 0.3 + - - +
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Residues in contact with VAL 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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459A ILE* 4.1 14.1 - - + -
461A TYR* 3.4 31.8 - - + +
463A ASP* 3.0 25.6 + - - +
467A ALA* 3.7 25.4 - - + +
470A LYS* 4.6 7.6 - - + -
471A ILE* 3.6 27.6 - - + -
514A ILE* 3.0 26.0 + - + +
517A ALA* 1.3 76.8 - - + +
519A ASP* 1.3 70.8 + - - +
520A ALA* 4.1 4.7 - - + +
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Residues in contact with ASP 519 (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 VAL* 3.2 35.4 + - - +
463A ASP* 3.8 15.8 - - + +
515A ALA 2.7 13.0 + - - -
516A ALA* 3.5 7.8 + - - +
517A ALA 3.3 2.8 - - - +
518A VAL* 1.3 81.2 - - - +
520A ALA* 1.3 65.1 + - - +
521A TYR* 4.8 0.2 - - - -
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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