Contacts of the helix formed by residues 81 - 87 (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 PRO 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU 3.1 12.3 - - - +
78A LYS 3.9 6.5 - - - +
79A GLU 3.5 9.2 - - - +
80A LYS* 1.3 88.2 - - - +
82A ALA* 1.3 63.5 + - - +
83A LEU 3.1 0.2 - - - -
84A VAL* 2.9 25.0 + - + +
85A VAL 3.7 0.3 + - - -
445A PHE 3.6 8.3 - - - +
446A GLU* 3.6 29.2 - - - +
447A THR* 3.4 11.0 - - - +
448A LYS* 3.3 25.1 - - - +
451A ALA* 3.3 6.5 - - + +
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Residues in contact with ALA 82 (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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80A LYS* 4.6 3.8 - - + +
81A PRO* 1.3 80.1 - - + +
83A LEU* 1.3 57.3 + - + +
85A VAL* 3.1 7.4 + - - +
86A ALA* 3.0 24.7 + - - +
353A ASP 6.0 0.2 - - - +
356A PHE* 4.0 30.0 - - + +
357A ASP* 4.9 0.9 - - - +
360A GLY* 5.4 1.0 - - - -
445A PHE* 3.7 34.1 + - + -
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Residues in contact with LEU 83 (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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76A MET* 4.1 11.7 - - + +
77A LEU* 4.3 4.5 - - + -
80A LYS* 3.0 36.2 + - + +
82A ALA* 1.3 75.0 - - + +
84A VAL* 1.3 60.5 + - - +
86A ALA* 3.6 4.3 - - - -
87A TRP* 2.9 69.1 + - + -
96A TYR* 4.0 16.4 - - + -
352A GLN* 5.0 2.5 - - - +
356A PHE* 3.7 25.1 - - + -
397A ILE* 3.6 30.7 - - + -
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Residues in contact with VAL 84 (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* 4.0 31.4 - - + +
81A PRO* 2.9 19.6 + - + +
83A LEU* 1.3 74.3 - - - +
85A VAL* 1.3 67.9 + - - +
87A TRP 3.2 1.9 + - - -
88A ALA* 3.0 23.2 + - - +
93A SER* 3.8 15.3 - - - +
448A LYS* 4.5 2.2 - - + -
451A ALA* 3.5 35.9 - - + +
452A GLN* 3.6 25.6 - - + +
455A ALA* 3.6 11.4 - - + -
457A VAL* 5.1 0.2 - - + -
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Residues in contact with VAL 85 (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 3.7 0.4 + - - +
82A ALA 3.1 7.6 + - - +
84A VAL* 1.3 76.2 - - - +
86A ALA* 1.3 58.3 + - - +
87A TRP 3.2 0.7 + - - -
88A ALA* 3.2 8.3 + - - +
265A HIS* 2.8 29.5 + - - -
267A ILE* 4.2 11.4 - - + -
360A GLY* 3.8 33.9 - - - +
363A HIS* 4.3 6.1 - - + -
364A LEU* 4.2 12.6 - - + -
445A PHE* 3.7 37.5 - - + -
451A ALA* 4.3 12.8 - - + +
454A LEU* 4.3 13.0 - - + -
455A ALA* 5.1 1.1 - - - -
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Residues in contact with ALA 86 (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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82A ALA 3.0 13.5 + - - +
83A LEU* 3.5 14.8 - - - +
84A VAL 3.2 0.2 - - - -
85A VAL* 1.3 77.9 - - - +
87A TRP* 1.3 63.0 - - + +
263A TRP* 3.5 1.2 - - - -
265A HIS* 3.0 19.8 + - - -
356A PHE* 4.0 19.3 - - + -
359A ILE* 4.8 2.7 - - + -
360A GLY* 5.5 0.9 - - - -
363A HIS* 4.2 5.6 - - - -
390A GLN* 3.0 41.5 + - - +
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Residues in contact with TRP 87 (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* 4.3 2.2 - - + -
83A LEU* 2.9 61.1 + - + +
84A VAL 3.5 2.9 - - - -
85A VAL 3.2 0.2 - - - -
86A ALA* 1.3 77.6 - - + +
88A ALA* 1.3 66.3 + - - +
90A TYR* 2.9 30.0 + + + +
92A PHE* 3.5 29.6 - + + -
93A SER* 3.3 16.2 - - - +
96A TYR* 3.6 38.4 - + - -
263A TRP* 3.7 16.2 - + - -
274A LYS* 3.3 29.4 - - + +
356A PHE* 5.5 0.8 - + - -
390A GLN* 3.5 23.0 - - - +
394A ASP* 3.5 27.6 + - - -
397A ILE* 5.1 1.8 - - + -
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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