Contacts of the helix formed by residues 459 - 467 (chain A) in PDB entry 1BFD
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 GLY 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A SER* 4.1 10.0 - - - -
455A ASN* 4.8 3.1 - - - -
457A THR* 3.0 15.6 + - - -
458A TYR* 1.3 73.4 - - - +
460A ALA* 1.3 60.9 + - - +
462A ARG* 3.2 7.1 + - - +
463A TRP* 3.0 22.2 + - - +
530A TPP 2.8 21.5 + - - -
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Residues in contact with ALA 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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377A THR* 3.5 24.5 - - - +
378A SER* 3.7 14.1 - - - +
459A GLY* 1.3 70.8 - - - -
461A LEU* 1.3 58.0 + - - +
463A TRP* 3.3 8.4 + - - +
464A PHE* 2.9 46.0 + - + -
530A TPP 2.7 29.9 + - - +
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Residues in contact with LEU 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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458A TYR* 3.1 20.3 + - + +
460A ALA* 1.3 74.6 - - - +
462A ARG* 1.3 55.7 + - - +
463A TRP 3.0 1.6 - - - -
464A PHE* 3.2 17.8 + - + +
465A ALA* 2.7 36.1 + - - +
475A GLY 5.7 0.2 - - - +
476A LEU* 3.8 25.7 - - + +
530A TPP 3.9 54.0 - - + +
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Residues in contact with ARG 462 (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 THR* 2.9 35.7 + - - +
458A TYR 3.0 9.7 + - - +
459A GLY* 3.2 8.5 + - - +
461A LEU* 1.3 75.0 - - - +
463A TRP* 1.3 58.7 + - - +
465A ALA* 3.4 9.5 + - - +
466A GLY* 2.9 23.9 + - - -
476A LEU* 3.9 27.3 - - + +
477A ASP* 2.7 34.8 + - - -
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Residues in contact with TRP 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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282A GLN* 6.0 8.3 - - + -
378A SER* 6.0 1.6 - - - -
459A GLY 3.0 12.0 + - - +
460A ALA* 3.3 11.7 - - - +
461A LEU 3.0 0.4 - - - -
462A ARG* 1.3 75.0 - - - +
464A PHE* 1.3 112.4 + + - +
466A GLY* 2.8 17.1 + - - -
467A VAL* 3.0 35.3 + - + +
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Residues in contact with PHE 464 (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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281A HIS* 3.6 37.7 - + - -
282A GLN* 5.1 15.5 - - + -
460A ALA* 2.9 44.7 + - + -
461A LEU* 3.9 18.6 - - + +
463A TRP* 1.3 101.8 - + - +
465A ALA* 1.3 65.0 + - - +
466A GLY 2.8 1.4 + - - -
467A VAL* 2.9 22.3 + - + +
468A LEU* 3.0 26.7 + - + +
530A TPP 6.0 2.5 - - - -
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Residues in contact with ALA 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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461A LEU 2.7 22.3 + - - +
462A ARG* 3.4 11.2 - - - +
464A PHE* 1.3 72.4 - - - +
466A GLY* 1.3 57.4 + - - +
468A LEU* 4.6 4.0 - - - -
469A GLU* 3.4 0.3 + - - -
470A ALA* 2.8 53.4 + - + +
473A VAL* 4.7 7.9 - - + -
476A LEU* 4.2 16.2 - - + -
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Residues in contact with GLY 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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462A ARG 2.9 10.1 + - - -
463A TRP* 2.8 10.1 + - - -
465A ALA* 1.3 77.4 - - - +
467A VAL* 1.3 66.8 + - - +
469A GLU* 3.0 12.9 + - - +
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Residues in contact with VAL 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 TRP* 3.0 50.6 + - + +
464A PHE* 2.9 18.2 + - + +
466A GLY* 1.3 73.0 - - - +
468A LEU* 1.3 78.4 + - + +
469A GLU* 2.6 20.0 + - - +
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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