Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1BO1
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 ARG 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B LYS* 3.6 23.7 - - - +
79B VAL 2.9 5.2 - - - -
80B ASP* 3.0 30.8 + - + +
81B ASN 6.1 0.2 - - - -
90B PRO* 3.4 11.6 - - - +
91B SER* 1.3 88.0 - - - +
93B PHE* 1.3 67.3 - - - +
191B VAL* 4.8 5.0 - - - +
192B ASP 5.5 1.2 + - - -
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Residues in contact with PHE 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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45B VAL* 3.6 30.7 - - + -
48B TRP* 3.8 37.9 - + - -
77B ILE 5.7 0.2 - - - -
78B LYS* 3.7 3.6 - - - +
79B VAL* 2.9 70.2 + - + +
80B ASP* 4.7 0.2 + - - -
81B ASN* 5.1 1.1 - - - -
89B LEU* 4.0 23.6 - - + -
90B PRO* 3.3 37.5 - - + -
92B ARG* 1.3 73.6 - - - +
94B LYS* 1.3 71.5 + - - +
190B THR* 3.5 15.7 - - - +
191B VAL* 4.9 1.8 - - + +
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Residues in contact with LYS 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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45B VAL* 4.0 6.2 - - - +
76B LYS* 5.9 7.4 - - + -
77B ILE 3.1 9.4 - - - +
78B LYS* 3.1 51.0 - - + +
93B PHE* 1.3 83.4 - - - +
95B PHE* 1.3 62.2 + - - +
188B ARG* 4.7 10.8 - - - +
189B LEU* 3.6 2.6 - - - -
190B THR* 3.0 54.3 + - + +
195B GLU* 5.7 1.1 - - - +
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Residues in contact with PHE 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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45B VAL* 3.6 22.7 - - + -
46B LEU* 4.1 8.1 - - + -
48B TRP* 4.2 14.6 - + + -
49B GLY* 3.3 38.8 - - - -
50B VAL 3.8 2.5 - - - -
53B THR* 3.6 17.5 - - + -
76B LYS* 3.5 2.3 - - - +
77B ILE* 2.9 46.7 + - + +
93B PHE* 5.2 0.7 - - + -
94B LYS* 1.3 74.0 - - - +
96B LYS* 1.3 65.5 + - - +
187B TYR* 3.4 42.8 - + + -
188B ARG 3.9 1.8 - - - -
189B LEU* 3.7 31.4 - - + -
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Residues in contact with LYS 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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74B TYR* 3.2 43.3 - - + -
75B SER 3.2 14.1 - - - +
76B LYS* 3.9 13.1 - - + +
95B PHE* 1.3 80.2 - - - +
97B GLU* 1.3 61.6 + - - +
98B TYR* 3.1 38.4 + - + -
187B TYR* 3.2 7.8 - - - +
188B ARG* 2.9 78.8 + - + +
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Residues in contact with GLU 97 (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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84A PHE* 5.2 1.0 - - - -
53B THR* 3.4 35.3 + - + +
54B ILE* 5.5 1.6 - - - +
57B LEU* 4.3 5.6 - - - +
74B TYR* 3.3 6.9 - - - -
75B SER* 2.9 41.5 + - - +
95B PHE* 4.9 0.2 - - - -
96B LYS* 1.3 74.0 - - - +
98B TYR* 1.3 69.2 + - - +
100B PRO* 3.2 36.5 - - + +
103B PHE* 5.6 2.4 - - + +
107B ARG* 4.0 16.5 + - - -
186B MET 3.9 5.8 - - - +
187B TYR* 4.0 25.5 + - + -
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Residues in contact with TYR 98 (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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74B TYR* 4.3 5.2 - + + -
96B LYS* 3.1 38.2 + - + -
97B GLU* 1.3 74.2 - - - +
99B CYS* 1.3 70.2 + - - +
100B PRO* 3.3 1.6 - - - +
103B PHE* 3.2 19.1 - - + -
157B VAL* 3.5 21.1 - - + +
161B HIS* 3.5 30.3 - + + +
186B MET* 3.1 49.2 + - + +
187B TYR* 4.1 6.1 - - - -
188B ARG* 3.5 28.9 + - + +
197B TYR* 3.0 27.8 + + - -
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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