Contacts of the helix formed by residues 447 - 455 (chain A) in PDB entry 3BNF
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 THR 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LYS 5.9 0.2 - - - -
81A PRO* 3.4 7.4 - - - -
446A GLU* 1.3 99.9 - - + +
448A LYS* 1.3 64.2 + - - +
449A GLU* 3.5 17.1 + - - +
450A LYS* 3.1 29.5 + - + +
451A ALA* 2.9 24.8 + - - +
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Residues in contact with LYS 448 (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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75A ASP* 2.5 32.2 + - - +
77A LEU* 3.4 36.5 - - + +
78A LYS* 4.0 21.7 + - + +
81A PRO* 3.3 15.5 - - - +
84A VAL* 4.5 0.9 - - + -
94A LYS 4.7 2.0 + - - -
95A ASP* 6.0 0.6 + - - +
447A THR* 1.3 71.6 - - - +
449A GLU* 1.3 69.7 + - - +
451A ALA* 3.6 1.9 - - - -
452A GLN* 2.7 75.0 + - + +
459A MET* 3.9 21.9 - - + +
500A SER* 5.1 7.5 + - - -
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Residues in contact with GLU 449 (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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78A LYS* 5.2 8.8 + - - +
447A THR* 3.1 19.9 - - - +
448A LYS* 1.3 94.4 + - + +
450A LYS* 1.3 60.8 + - + +
452A GLN* 3.3 7.6 + - - +
453A LYS* 3.0 29.3 + - - +
459A MET* 5.9 2.5 - - + +
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Residues in contact with LYS 450 (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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444A ASP* 3.8 29.5 + - - +
445A PHE* 4.6 1.3 - - - -
446A GLU* 2.8 43.6 + - - +
447A THR* 3.1 23.2 + - + +
449A GLU* 1.3 79.9 - - + +
451A ALA* 1.3 63.7 + - - +
453A LYS* 3.3 13.7 + - + +
454A LEU* 3.2 27.3 + - - +
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Residues in contact with ALA 451 (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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81A PRO* 3.3 27.6 - - + +
84A VAL* 3.5 19.3 - - + +
85A VAL* 4.3 4.1 - - + +
445A PHE* 4.0 22.4 - - + +
447A THR 2.9 16.3 + - - +
448A LYS 3.8 2.0 - - - +
450A LYS* 1.3 77.4 - - - +
452A GLN* 1.3 62.5 + - - +
454A LEU* 3.1 7.7 + - - +
455A ALA* 3.0 18.7 + - - +
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Residues in contact with GLN 452 (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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77A LEU* 4.1 1.2 - - - +
84A VAL* 3.7 23.6 - - + -
93A SER 3.0 20.0 - - - +
94A LYS 3.6 6.1 - - - +
448A LYS* 2.7 44.2 + - + +
449A GLU* 4.0 6.3 - - - +
451A ALA* 1.3 68.8 - - - +
453A LYS* 1.3 60.9 + - - +
455A ALA* 3.4 1.7 + - - -
456A LYS 2.9 22.9 + - - -
457A VAL* 2.9 28.5 + - + +
459A MET* 3.1 51.5 - - - +
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Residues in contact with LYS 453 (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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449A GLU 3.0 12.9 + - - +
450A LYS* 3.4 15.3 - - + +
451A ALA 3.3 0.2 - - - -
452A GLN* 1.3 76.8 - - - +
454A LEU* 1.3 63.7 + - + +
456A LYS* 3.1 18.7 + - - +
457A VAL 5.6 0.4 - - - -
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Residues in contact with LEU 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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85A VAL* 4.3 7.0 - - + -
267A ILE* 3.7 19.3 - - + +
364A LEU* 4.2 21.9 - - + +
443A PRO* 3.6 33.0 - - + -
444A ASP 3.7 23.1 - - - +
445A PHE* 3.8 18.2 - - + -
450A LYS 3.2 11.0 + - - +
451A ALA* 3.1 7.2 + - - +
453A LYS* 1.3 81.5 - - + +
455A ALA* 1.3 60.6 + - - +
456A LYS* 3.2 12.9 + - - +
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Residues in contact with ALA 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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84A VAL* 3.6 23.1 - - + +
85A VAL* 5.1 0.9 - - - -
88A ALA* 3.8 30.6 - - + +
89A GLY 4.7 8.5 + - - -
93A SER* 4.7 0.2 - - - -
267A ILE* 4.4 2.9 - - + -
451A ALA 3.0 15.2 + - - +
452A GLN 3.4 3.8 + - - +
454A LEU* 1.3 75.5 - - - +
456A LYS* 1.3 70.7 + - - +
457A VAL* 3.3 13.4 + - + +
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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