Contacts of the helix formed by residues 87 - 96 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLY 2.8 12.2 + - - +
86B PHE* 1.3 69.1 - - - +
88B ASP* 1.3 71.7 + - - +
90B LEU* 3.5 21.1 - - + -
91B LYS* 2.7 61.0 + - + +
121B ALA* 3.7 36.3 - - + +
122B VAL* 4.3 10.1 - - + +
125B PHE* 3.6 23.1 - - + -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.5 25.7 + - + +
52B GLY 4.0 1.4 - - - +
54B THR* 2.7 29.0 + - + +
85B GLY 4.6 0.3 - - - +
86B PHE* 3.4 15.8 - - - +
87B LEU* 1.3 86.8 + - - +
89B THR* 1.3 63.8 + - - -
91B LYS* 3.3 9.8 - - - +
92B VAL* 3.1 25.9 + - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B MET* 3.9 14.6 - - + -
51B PHE* 2.8 31.9 + - + +
53B SER 5.5 0.2 - - - +
54B THR* 3.2 23.6 + - - -
57B ALA* 3.9 23.1 - - + -
81B ALA* 4.6 2.2 - - + -
86B PHE* 3.1 8.8 + - - +
87B LEU 3.0 0.4 - - - -
88B ASP* 1.3 77.3 + - - +
90B LEU* 1.3 61.1 + - - +
91B LYS 3.1 1.8 - - - -
92B VAL* 3.3 8.6 + - - +
93B LEU* 2.8 37.5 + - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 3.8 36.8 - - + +
81B ALA* 3.9 14.8 - - + -
82B ALA* 4.1 8.7 - - + +
86B PHE 2.9 7.9 + - - +
87B LEU* 3.2 21.8 - - + +
89B THR* 1.3 77.0 - - - +
91B LYS* 1.3 62.5 + - - +
93B LEU* 3.5 4.8 - - - +
94B VAL* 3.0 29.4 + - + +
110B PRO* 5.7 0.2 - - + -
122B VAL* 3.4 28.3 - - + -
125B PHE* 3.4 33.4 - - + -
126B LEU* 3.9 11.7 - - + -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 2.7 48.5 + - + +
88B ASP* 3.3 12.1 - - - +
90B LEU* 1.3 72.5 - - - +
92B VAL* 1.3 54.3 + - + +
94B VAL* 2.6 28.8 + - - -
95B GLU* 2.6 40.0 + - + +
125B PHE* 3.4 28.1 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 3.4 24.9 - - + -
57B ALA* 4.4 3.4 - - + -
58B LEU* 3.8 40.2 - - + +
61B LEU* 3.6 19.7 - - + -
88B ASP 3.1 17.7 - - - +
89B THR* 3.4 7.6 - - - +
91B LYS* 1.3 79.2 - - + +
93B LEU* 1.3 62.9 + - - +
95B GLU* 3.4 9.0 + - - +
96B HIS* 2.7 33.1 + - + +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 4.0 18.8 - - + -
49B MET* 4.9 2.2 - - + -
51B PHE* 4.9 2.7 - - + -
57B ALA* 5.6 0.4 - - + -
61B LEU* 3.9 20.6 - - + -
67B PRO* 4.4 3.0 - - + +
77B PRO* 3.5 52.7 - - + +
78B VAL* 3.7 8.7 - - + +
81B ALA* 4.0 11.9 - - + -
89B THR* 2.8 31.7 + - + +
90B LEU* 3.5 5.8 - - - +
92B VAL* 1.3 71.9 - - - +
94B VAL* 1.3 63.7 + - - +
96B HIS* 3.0 13.0 + - - +
98B ALA* 3.0 31.4 + - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 4.8 4.9 - - + -
90B LEU* 3.0 15.6 + - + +
91B LYS 2.6 12.3 + - - +
93B LEU* 1.3 70.3 - - - +
95B GLU* 1.3 61.8 + - - +
96B HIS 2.6 16.6 + - - -
97B GLY* 2.6 18.7 + - - -
98B ALA* 3.5 17.4 + - + +
100B VAL* 3.5 30.1 - - + -
125B PHE* 4.0 25.1 - - + -
129B GLU* 4.5 12.6 - - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LYS* 2.6 64.0 + - + +
92B VAL* 3.5 9.9 - - - +
94B VAL* 1.3 79.8 - - - +
96B HIS* 1.3 67.9 + - + +
97B GLY 3.4 1.2 + - - -
125B PHE* 4.6 2.6 - - - -
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 3.7 30.1 - - + +
61B LEU* 3.8 42.6 - - + +
62B LYS* 4.4 10.3 - - + +
67B PRO* 3.4 18.0 - - - +
92B VAL* 2.7 29.0 + - + +
93B LEU 3.0 7.5 + - - +
94B VAL 2.6 5.9 + - - -
95B GLU* 1.3 84.9 - - + +
97B GLY* 1.3 57.2 + - - +
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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