Contacts of the helix formed by residues 453 - 469 (chain A) in PDB entry 2YD0
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ARG 3.1 8.9 - - - +
452A LEU* 1.3 79.5 - - - +
454A ALA* 1.3 63.7 + - - +
455A ASP* 3.4 14.4 - - - -
456A ALA* 3.9 15.8 - - - +
457A PHE* 3.3 15.8 + - - +
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Residues in contact with ALA 454 (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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296A TYR* 4.7 3.5 + - - -
449A ARG* 4.1 37.1 + - + +
453A SER* 1.3 70.9 - - - +
455A ASP* 1.3 63.5 + - - +
457A PHE* 3.5 2.9 + - - +
458A LYS* 3.0 29.2 + - - +
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Residues in contact with ASP 455 (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 SER* 3.4 7.4 - - - -
454A ALA* 1.3 78.3 - - - +
456A ALA* 1.3 65.5 + - - +
458A LYS* 3.2 17.5 + - - +
459A SER* 2.9 26.7 + - - -
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Residues in contact with ALA 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 3.9 10.8 - - + -
453A SER* 3.8 24.5 + - - +
454A ALA 3.4 0.2 - - - -
455A ASP* 1.3 77.6 - - - +
457A PHE* 1.3 64.1 + - - +
459A SER* 3.1 5.9 + - - -
460A GLY 3.1 17.7 + - - -
485A ILE* 3.3 31.4 - - + +
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Residues in contact with PHE 457 (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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296A TYR* 4.5 5.8 - - - -
378A PHE* 4.2 12.6 - + - -
381A PHE* 3.8 30.1 - + - -
382A MET* 5.8 1.8 - - - -
385A VAL* 6.0 0.2 - - + -
445A LEU* 3.9 22.4 - - + -
448A LEU* 4.4 19.3 - - + -
449A ARG* 3.7 36.1 - - + -
452A LEU* 4.4 12.4 - - + +
453A SER 3.3 16.9 + - - +
454A ALA 3.6 4.7 - - - +
455A ASP 3.3 0.2 - - - -
456A ALA* 1.3 78.2 - - - +
458A LYS* 1.3 63.6 - - - +
460A GLY* 3.2 3.8 + - - -
461A ILE* 3.0 52.7 + - + +
482A MET* 4.1 14.7 - - + +
485A ILE* 4.8 0.9 - - - -
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Residues in contact with LYS 458 (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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295A ASP* 5.1 4.6 + - - -
296A TYR* 3.7 65.5 + - + +
454A ALA 3.0 15.2 + - - +
455A ASP* 3.2 17.7 + - - +
457A PHE* 1.3 79.4 - - - +
459A SER* 1.3 63.8 + - - +
461A ILE* 3.3 11.8 + - - +
462A VAL* 3.0 32.2 + - + +
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Residues in contact with SER 459 (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 ASP 2.9 14.5 + - - -
456A ALA* 3.5 9.6 - - - -
458A LYS* 1.3 77.1 - - - +
460A GLY* 1.3 62.1 + - - +
462A VAL* 3.3 7.1 + - - +
463A GLN* 3.0 25.2 + - - +
485A ILE* 4.3 13.7 - - - -
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Residues in contact with GLY 460 (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 3.1 9.7 + - - -
457A PHE 3.2 4.2 + - - -
459A SER* 1.3 75.6 - - - +
461A ILE* 1.3 63.0 + - - +
462A VAL 3.3 0.2 + - - -
463A GLN* 3.4 4.7 + - - +
464A TYR* 3.0 23.7 + - - +
481A SER* 4.1 10.6 - - - -
482A MET* 3.9 11.7 - - - -
485A ILE* 3.7 25.0 - - - +
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Residues in contact with ILE 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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296A TYR* 3.9 27.1 - - + -
297A PHE* 4.5 16.8 - - + -
360A PHE* 4.1 17.5 - - + -
378A PHE* 3.8 22.0 - - + -
382A MET* 4.9 3.8 - - - -
457A PHE* 3.0 34.9 + - + +
458A LYS* 3.4 11.9 - - - +
460A GLY* 1.3 75.7 - - - +
462A VAL* 1.3 62.5 + - + +
464A TYR* 3.3 5.8 + - + +
465A LEU* 2.8 33.8 + - - +
478A LEU* 5.3 0.2 - - + -
482A MET* 3.1 26.0 - - + -
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR 4.1 7.6 - - - +
297A PHE* 3.5 37.9 - - - +
298A SER* 4.5 10.3 - - - +
299A ILE* 4.7 0.2 - - - +
458A LYS* 3.0 26.2 + - + +
459A SER* 3.7 6.7 - - - +
460A GLY 3.2 0.4 - - - -
461A ILE* 1.3 76.5 - - + +
463A GLN* 1.3 60.3 + - - +
465A LEU* 3.4 5.8 + - - +
466A GLN* 2.8 52.8 + - + +
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Residues in contact with GLN 463 (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 SER 3.0 16.4 + - - +
460A GLY* 3.8 4.7 - - - +
462A VAL* 1.3 76.1 - - - +
464A TYR* 1.3 57.2 + - - +
466A GLN* 3.8 13.7 - - - +
467A LYS* 2.8 57.3 + - - +
481A SER* 2.9 36.8 + - - +
484A SER* 4.5 14.1 + - - +
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Residues in contact with TYR 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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360A PHE* 3.8 32.0 - + - -
364A VAL* 3.6 16.0 - - + +
374A LEU* 4.1 17.7 + - + +
378A PHE* 5.3 1.3 - + - -
460A GLY 3.0 17.5 + - - +
461A ILE* 3.4 7.6 - - - +
463A GLN* 1.3 83.2 + - - +
465A LEU* 1.3 67.9 + - + +
468A HIS* 3.1 42.4 + + - +
473A THR* 2.7 43.1 + - + -
477A ASP 4.2 0.2 - - - -
478A LEU* 3.8 43.1 - - + -
481A SER* 3.6 17.5 - - - +
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Residues in contact with LEU 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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297A PHE* 3.7 42.0 - - + -
299A ILE* 3.6 14.4 - - + -
359A TRP* 4.0 28.5 - - + +
360A PHE* 3.8 31.9 - - + -
363A LEU* 4.9 2.7 - - + -
364A VAL* 3.8 22.9 - - + +
461A ILE 2.8 25.5 + - - +
462A VAL* 3.9 2.5 - - - +
464A TYR* 1.3 75.9 - - + +
466A GLN* 1.3 55.9 + - - +
469A SER* 2.7 36.1 + - - -
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Residues in contact with GLN 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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298A SER* 5.0 8.1 + - - -
299A ILE* 4.1 17.5 - - + -
462A VAL* 2.8 41.1 + - + +
463A GLN* 3.8 13.7 - - - +
465A LEU* 1.3 75.2 - - - +
467A LYS* 1.3 63.6 - - - +
468A HIS 3.3 0.2 + - - -
469A SER* 3.5 15.5 + - - -
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Residues in contact with LYS 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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463A GLN* 2.8 45.3 + - - +
466A GLN* 1.3 75.6 - - - +
468A HIS* 1.3 89.2 + - + +
469A SER 3.4 0.9 + - - +
471A LYS* 4.2 14.2 + - - +
481A SER* 5.6 0.9 - - - +
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Residues in contact with HIS 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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364A VAL* 3.4 17.4 - - + +
464A TYR* 3.1 38.8 + + - +
467A LYS* 1.3 106.1 + - + +
469A SER* 1.3 67.0 + - - +
470A TYR 3.2 0.7 + - - -
471A LYS* 2.9 30.6 + - + +
472A ASN 4.5 5.1 + - - -
473A THR* 3.3 33.8 - - + +
477A ASP* 4.1 25.8 + - - +
481A SER* 4.4 6.5 + - - -
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Residues in contact with SER 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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299A ILE* 4.5 3.6 - - - +
363A LEU* 3.6 19.2 - - - +
364A VAL* 4.1 5.2 - - - -
465A LEU 2.7 21.9 + - - -
466A GLN* 3.7 12.5 + - - -
467A LYS 3.4 2.0 - - - -
468A HIS* 1.3 77.4 - - - +
470A TYR* 1.3 83.3 + - - +
471A LYS* 3.2 15.6 + - - +
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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