Contacts of the helix formed by residues 451 - 461 (chain O) in PDB entry 6FF7
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 LEU 451 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447O ASP* 5.3 5.6 - - + -
450O GLU* 1.3 72.3 - - + +
452O PHE* 1.3 54.2 + - - +
454O ASN* 3.3 9.8 + - + +
455O TYR* 2.8 27.9 + - - +
87p ASN* 2.4 24.3 + - - +
89p PRO* 2.8 8.7 - - - -
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Residues in contact with PHE 452 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447O ASP* 4.6 11.4 - - + -
448O ALA 4.0 4.3 - - - +
451O LEU* 1.3 65.3 - - - +
453O LYS* 1.3 49.4 - - - +
455O TYR* 3.1 10.6 + - - +
456O THR* 3.0 22.2 + - - -
87p ASN 3.3 1.4 + - - -
88p ASP* 2.5 22.4 - - + +
89p PRO* 1.6 34.3 - - - +
90p TYR 4.8 0.2 - - - +
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Residues in contact with LYS 453 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452O PHE* 1.3 33.1 - - - +
454O ASN* 1.3 55.9 + - - -
456O THR* 3.5 10.0 - - - -
457O ILE* 2.9 29.8 + - - +
89p PRO* 1.1 93.7 - - - +
90p TYR* 1.5 66.0 - - + +
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Residues in contact with ASN 454 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450O GLU 4.5 4.0 - - - +
451O LEU* 3.5 20.2 - - + +
453O LYS 1.3 64.7 - - - -
455O TYR* 1.3 59.6 + - - +
457O ILE* 3.8 3.5 - - - +
458O PHE* 2.8 30.5 + - - +
89p PRO* 1.7 28.4 - - + +
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Residues in contact with TYR 455 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435O ILE* 5.7 9.6 - - + -
451O LEU 2.8 16.5 + - - +
452O PHE* 3.1 12.8 + - - +
454O ASN* 1.3 74.9 - - - +
456O THR* 1.3 56.4 - - - +
458O PHE* 3.2 7.6 + - - +
459O GLU* 2.9 29.1 + - - +
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Residues in contact with THR 456 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452O PHE 3.0 12.1 + - - -
453O LYS* 3.2 13.4 + - - -
455O TYR* 1.3 77.2 - - - +
457O ILE* 1.3 58.1 + - - +
459O GLU* 3.1 8.5 + - - +
460O LYS* 2.9 26.6 + - - +
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Residues in contact with ILE 457 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453O LYS 2.9 16.3 + - - +
454O ASN* 4.4 3.4 - - - +
456O THR* 1.3 73.6 - - - +
458O PHE* 1.3 64.1 + - - +
459O GLU 3.3 0.2 - - - -
460O LYS* 3.6 15.1 + - + +
461O LYS* 3.8 14.6 + - - +
462O PHE* 6.0 0.2 - - - +
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Residues in contact with PHE 458 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424O GLU* 5.3 7.8 - - - +
454O ASN 2.8 20.3 + - - +
455O TYR* 3.3 10.5 - - - +
456O THR 3.2 0.2 - - - -
457O ILE* 1.3 79.3 - - - +
459O GLU* 1.3 58.6 + - - +
462O PHE* 4.4 15.4 - - - +
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Residues in contact with GLU 459 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455O TYR 2.9 12.9 + - - +
456O THR* 3.1 9.4 + - - +
458O PHE* 1.3 77.8 - - - +
460O LYS* 1.3 63.6 + - - +
462O PHE* 4.3 8.3 + - - +
463O GLY* 5.0 1.6 + - - -
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Residues in contact with LYS 460 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545M ILE* 5.2 8.3 - - + +
546M SER* 3.2 26.2 + - - -
456O THR 2.9 15.7 + - - +
457O ILE* 4.1 10.1 - - + +
458O PHE 3.6 0.8 - - - -
459O GLU* 1.3 79.7 - - - +
461O LYS* 1.3 62.6 + - + +
462O PHE 3.3 2.5 + - - -
463O GLY* 4.1 0.7 + - - -
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Residues in contact with LYS 461 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545M ILE 4.2 9.4 - - - +
546M SER* 3.8 19.2 - - - +
549M LYS* 5.0 17.9 - - + +
457O ILE 3.8 11.0 + - - +
460O LYS* 1.3 78.5 - - + +
462O PHE* 1.3 59.1 + - - +
463O GLY 3.7 2.2 - - - -
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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