Contacts of the helix formed by residues 87 - 96 (chain D) in PDB entry 1BI8
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D GLY 2.8 11.5 + - - +
86D PHE* 1.3 70.4 - - - +
88D ASP* 1.3 71.4 + - - +
90D LEU* 2.8 20.8 + - + -
91D LYS* 2.7 60.2 + - + +
121D ALA* 3.7 36.3 - - + +
122D VAL* 4.3 10.3 - - + -
125D PHE* 3.6 24.0 - - + -
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Residues in contact with ASP 88 (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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111C LYS* 3.5 26.0 + - + +
52D GLY 4.0 1.4 - - - +
54D THR* 2.7 27.3 + - + +
85D GLY 4.6 0.3 - - - +
86D PHE* 3.4 16.7 - - - +
87D LEU* 1.3 86.2 + - - +
89D THR* 1.3 64.0 + - - -
91D LYS* 3.3 10.1 - - - +
92D VAL* 3.1 26.7 + - - +
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Residues in contact with THR 89 (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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49D MET* 3.9 13.9 - - + -
51D PHE* 2.8 32.7 + - + +
54D THR* 3.2 24.0 + - - +
57D ALA* 3.9 23.1 - - + -
81D ALA* 4.6 2.0 - - + -
86D PHE* 3.1 8.2 + - - -
87D LEU 3.0 0.8 - - - -
88D ASP* 1.3 76.5 + - - +
90D LEU* 1.3 60.8 + - - +
91D LYS 3.1 1.8 - - - -
92D VAL* 3.4 8.3 - - - +
93D LEU* 2.8 37.7 + - + +
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Residues in contact with LEU 90 (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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78D VAL* 3.8 36.1 - - + +
81D ALA* 3.9 14.8 - - + -
82D ALA* 4.1 8.3 - - + +
86D PHE 2.9 8.2 + - - +
87D LEU* 3.2 21.3 - - + +
89D THR* 1.3 77.3 - - - +
91D LYS* 1.3 61.9 + - - +
93D LEU* 3.5 4.6 - - - +
94D VAL* 3.0 29.8 + - + +
100D VAL* 6.1 0.2 - - + -
110D PRO* 5.7 0.2 - - + -
122D VAL* 3.4 27.8 - - + -
125D PHE* 3.4 33.4 - - + -
126D LEU* 3.9 11.2 - - + -
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Residues in contact with LYS 91 (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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87D LEU* 2.7 47.9 + - + +
88D ASP* 3.3 11.9 - - - +
90D LEU* 1.3 72.8 - - - +
92D VAL* 1.3 55.5 + - + +
94D VAL* 2.6 29.0 + - - -
95D GLU* 2.6 39.8 + - - +
125D PHE* 3.4 28.1 - - + -
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Residues in contact with VAL 92 (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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54D THR* 3.4 24.2 - - + -
57D ALA* 4.4 3.1 - - + -
58D LEU* 3.8 40.8 - - + +
61D LEU* 3.6 18.8 - - + -
88D ASP 3.1 16.8 - - - +
89D THR* 3.4 7.6 - - - +
91D LYS* 1.3 78.6 - - + +
93D LEU* 1.3 63.0 + - - +
95D GLU* 3.4 8.6 + - - +
96D HIS* 2.7 33.4 + - - +
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Residues in contact with LEU 93 (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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46D LEU* 4.0 19.5 - - + -
49D MET* 4.9 2.2 - - + -
51D PHE* 4.9 2.7 - - + -
57D ALA* 5.6 0.2 - - + -
61D LEU* 3.9 19.7 - - + -
67D PRO* 4.4 2.8 - - + +
77D PRO* 3.5 53.4 - - + +
78D VAL* 3.7 8.7 - - + +
81D ALA* 4.0 11.4 - - + -
89D THR* 2.8 30.7 + - + +
90D LEU* 3.5 5.6 - - - +
92D VAL* 1.3 72.0 - - + +
94D VAL* 1.3 63.5 + - - +
96D HIS* 3.0 13.5 + - - +
98D ALA* 3.0 31.3 + - + +
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Residues in contact with VAL 94 (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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78D VAL* 4.8 4.7 - - + -
90D LEU* 3.0 15.1 + - + +
91D LYS 2.6 13.2 + - - +
93D LEU* 1.3 69.6 - - - +
95D GLU* 1.3 61.2 + - - +
96D HIS 2.6 16.5 + - - -
97D GLY* 2.6 18.7 + - - -
98D ALA* 3.5 16.3 + - + +
100D VAL* 3.5 30.1 - - + -
125D PHE* 4.0 24.9 - - + -
129D GLU* 4.5 12.8 - - - +
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Residues in contact with GLU 95 (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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91D LYS* 2.6 63.8 + - + +
92D VAL* 3.5 9.9 - - - +
94D VAL* 1.3 79.2 - - - +
96D HIS* 1.3 67.3 + - + +
97D GLY 3.4 1.5 + - - -
125D PHE* 4.6 3.1 - - - -
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Residues in contact with HIS 96 (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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58D LEU* 3.7 29.2 - - + +
61D LEU* 3.8 43.5 - - + +
62D LYS* 4.4 10.1 - - - +
67D PRO* 3.4 18.0 - - - +
92D VAL* 2.7 29.9 + - + +
93D LEU 3.0 6.2 + - - +
94D VAL 2.6 6.3 + - - -
95D GLU* 1.3 84.0 - - + +
97D GLY* 1.3 56.8 + - - +
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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