Contacts of the helix formed by residues 80 - 84 (chain D) in PDB entry 3BXB
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 PHE 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D LYS* 3.5 45.3 - - + +
68D THR* 4.2 2.9 - - - +
70D ILE* 4.4 5.8 - - + -
72D HIS* 4.1 8.1 - + - -
78D ASP* 3.8 10.5 - - - +
79D PHE* 1.3 88.0 - + + +
81D LYS* 1.3 64.9 + - - +
83D SER* 3.1 16.0 + - - -
84D PHE* 3.1 19.2 - - - -
88D PHE* 3.8 29.1 - + + -
147D LEU* 4.1 17.9 - - + -
154D LEU* 4.3 9.6 - - + -
178D TYR* 3.5 36.8 - + + -
193D TYR* 3.8 20.2 - - - -
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.3 19.0 - - + +
34D PRO* 3.3 24.3 + - - -
35D TYR* 3.7 40.4 - - + +
67D LYS 5.2 0.2 + - - -
68D THR* 2.7 34.0 + - + +
70D ILE 3.0 24.9 + - - -
72D HIS 5.1 0.4 - - - +
78D ASP* 2.9 32.9 + - + +
80D PHE* 1.3 75.4 - - - +
82D GLN* 1.3 59.4 + - + +
83D SER 3.1 4.3 + - - -
84D PHE* 3.5 21.4 + - - +
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PRO* 3.8 5.1 - - - +
78D ASP* 2.9 39.9 + - + +
79D PHE* 4.1 5.8 - - - +
81D LYS* 1.3 73.5 - - - +
83D SER* 1.3 57.6 + - - +
84D PHE 3.3 2.7 - - - +
182D LYS* 2.9 27.5 - - - +
186D ASN 4.2 4.5 - - - +
187D LEU* 3.7 11.6 - - + -
188D LYS* 2.8 55.2 + - - +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 2.6 19.6 + - - -
80D PHE* 3.2 14.0 - - - -
81D LYS 3.0 2.0 - - - -
82D GLN* 1.3 77.5 - - - +
84D PHE* 1.3 63.7 + - - +
86D GLU* 3.3 10.6 + - - +
87D GLY 3.1 30.5 + - - +
88D PHE* 4.2 9.3 - - - +
180D SER* 2.8 31.9 + - - -
182D LYS* 3.6 8.6 - - - +
187D LEU* 4.0 2.1 - - - +
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Residues in contact with PHE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.0 11.8 - - + +
5D ILE* 3.8 19.7 - - + -
68D THR* 3.5 28.9 - - + -
80D PHE 3.1 23.1 - - - -
81D LYS 3.5 12.2 + - - +
82D GLN 3.3 3.6 - - - +
83D SER* 1.3 80.6 - - - +
85D PRO* 1.3 69.4 - - + +
86D GLU 3.3 0.4 - - - -
87D GLY* 4.2 17.9 - - - -
88D PHE* 3.6 15.3 - + - -
108D THR* 3.9 9.2 - - + -
110D LEU* 3.8 33.4 - - + -
115D LEU* 3.6 25.1 - - + -
182D LYS* 3.0 17.0 + - - -
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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