Contacts of the helix formed by residues 455 - 465 (chain B) in PDB entry 5OY0
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 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B ILE 3.5 2.6 - - - +
454B GLU* 1.3 86.2 - - + +
456B VAL* 1.3 64.7 + - - +
457B PHE* 3.2 4.1 + - - -
458B ALA* 3.6 5.4 + - + -
459B GLN* 3.1 39.2 + - - +
509B ILE* 3.9 21.1 - - + -
510B GLY 3.3 33.7 - - - +
513B ASP* 5.4 0.7 - - + -
514B PHE* 4.1 26.2 - - + +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B GLU* 2.9 32.7 + - + +
455B PRO* 1.3 71.9 - - - +
457B PHE* 1.3 69.4 + - + +
459B GLN* 3.9 7.4 - - - +
460B TRP* 2.8 29.7 + - + +
472B PHE* 3.5 28.0 - - + -
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Residues in contact with PHE 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B PRO 3.2 0.8 - - - -
456B VAL* 1.3 88.8 - - + +
458B ALA* 1.3 59.2 + - - +
460B TRP* 3.2 9.5 + - + +
461B ILE* 2.9 34.2 + - + +
514B PHE* 6.6 0.4 - + - -
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B PRO* 3.6 7.1 + - + +
457B PHE* 1.3 79.1 - - - +
459B GLN* 1.3 58.6 + - - +
461B ILE* 3.2 13.0 + - + +
462B GLN* 2.9 34.4 + - - +
509B ILE* 3.6 21.5 - - + -
517B HIS* 6.1 4.0 - - + +
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Residues in contact with GLN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B GLU* 2.7 41.9 + - - +
455B PRO* 3.1 25.0 + - - +
456B VAL* 3.8 6.3 - - - +
458B ALA* 1.3 77.8 - - - +
460B TRP* 1.3 57.7 + - - +
462B GLN* 3.3 1.8 + - - +
463B ALA* 2.9 24.4 + - - +
470B TYR* 3.4 53.7 - - + +
472B PHE* 3.7 15.5 - - + -
509B ILE* 2.9 33.7 + - + -
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Residues in contact with TRP 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B VAL* 2.8 20.6 + - + +
457B PHE* 3.5 5.8 - - - +
459B GLN* 1.3 74.8 - - - +
461B ILE* 1.3 72.0 + - + +
463B ALA* 3.2 4.0 + - - +
464B THR* 2.9 46.4 + - + +
472B PHE* 3.6 31.5 - + + -
474B VAL* 3.3 45.9 - - + +
475B LEU* 4.9 4.9 - - + -
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Residues in contact with ILE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B PHE* 2.9 21.9 + - + +
458B ALA* 3.5 14.4 - - - +
459B GLN 3.2 0.2 - - - -
460B TRP* 1.3 88.7 - - + +
462B GLN* 1.3 67.1 + - + +
464B THR* 2.2 34.0 + - - +
465B SER* 3.5 6.4 + - - +
506B PHE* 5.1 11.4 - - + -
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Residues in contact with GLN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ALA* 2.9 18.7 + - - +
459B GLN 3.5 6.5 - - - +
461B ILE* 1.3 74.5 - - + +
463B ALA* 1.3 63.3 + - - +
465B SER* 3.0 16.2 + - - -
466B GLY 3.5 0.5 + - - -
467B LYS* 2.7 45.6 + - + +
470B TYR* 2.6 29.4 + - + -
498B ILE* 4.1 0.7 - - - +
506B PHE* 3.5 40.8 - - + +
507B LEU 3.0 22.9 + - - -
509B ILE* 4.1 15.6 - - - +
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B GLN 2.9 14.2 + - - +
460B TRP 3.3 9.4 - - - +
461B ILE 3.2 0.2 - - - -
462B GLN* 1.3 76.3 - - - +
464B THR* 1.3 61.4 + - - +
465B SER 3.0 1.1 + - - -
466B GLY 3.2 4.5 + - - -
467B LYS* 3.3 21.5 - - - +
470B TYR* 4.9 0.7 - - + -
472B PHE* 3.8 33.0 - - + +
474B VAL* 3.1 4.1 - - + +
477B SER* 2.8 31.9 + - - +
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Residues in contact with THR 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B TRP* 2.9 46.7 + - + +
461B ILE* 2.2 33.7 + - - +
463B ALA* 1.3 75.1 - - - +
465B SER* 1.3 60.8 + - - +
466B GLY 3.5 0.4 - - - -
474B VAL* 3.6 14.8 - - + -
475B LEU* 3.6 28.7 - - + +
476B LEU* 3.1 22.8 + - - +
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Residues in contact with SER 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ILE* 3.9 8.1 + - - +
462B GLN 3.0 9.6 + - - -
464B THR* 1.3 81.6 + - - +
466B GLY* 1.3 57.4 + - - +
467B LYS 3.6 2.2 - - - -
476B LEU* 3.6 13.0 - - - -
494B TRP* 2.6 51.0 + - - -
498B ILE* 3.2 11.7 - - - +
506B PHE* 4.5 12.1 - - - -
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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