Contacts of the helix formed by residues 88 - 94 (chain B) in PDB entry 3BRW
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B CYS* 4.0 28.8 - - - +
84B ASN 5.2 4.5 + - - -
85B PRO* 3.4 12.0 + - - +
86B THR 3.2 0.6 - - - -
87B ALA* 1.3 78.2 - - + +
89B ILE* 1.3 65.2 + - - +
90B TYR 3.5 1.3 - - - -
91B ARG* 3.9 7.0 + - + +
92B LYS* 3.5 21.1 + - + +
186B GLU* 4.2 15.9 - - + +
189B ILE* 3.8 41.8 - - + +
191B ASN* 3.9 12.3 + - - +
262B LYS* 4.7 10.0 - - - +
374B TYR* 5.8 0.4 + - - -
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Residues in contact with ILE 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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85B PRO* 3.5 19.5 - - + +
86B THR* 3.2 26.0 + - + +
88B ARG* 1.3 76.5 - - + +
90B TYR* 1.3 69.3 + - - +
92B LYS* 3.0 5.4 + - - +
93B HIS* 2.9 42.6 + - + +
94B PHE* 4.3 9.9 - - + -
128B ARG* 4.1 4.0 - - - +
130B LEU* 4.6 4.7 - - + -
139B HIS* 3.4 55.0 - - + +
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Residues in contact with TYR 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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86B THR 4.4 1.4 + - - -
87B ALA 5.5 0.4 - - - +
88B ARG* 3.5 0.6 - - - +
89B ILE* 1.3 77.3 - - - +
91B ARG* 1.3 59.6 + - - +
94B PHE* 2.8 60.7 + + + -
95B LEU* 3.1 17.9 + - + -
99B HIS* 2.6 27.9 + - - -
101B ASN* 3.6 8.1 + - - -
115B SER* 3.5 19.5 - - - -
130B LEU* 4.0 3.7 - - + +
132B ARG* 3.8 16.4 - - - -
178B SER* 3.4 36.2 - - - -
181B ILE* 3.8 16.8 - - + +
182B VAL* 3.8 22.7 - - + -
185B ASP* 3.4 24.8 + - + +
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Residues in contact with ARG 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 ALA 5.6 0.2 + - - -
88B ARG* 3.9 9.3 + - + +
89B ILE 3.3 0.6 - - - -
90B TYR* 1.3 78.7 - - - +
92B LYS* 1.3 64.0 + - + +
95B LEU* 3.7 46.7 + - - +
97B LYS* 5.2 0.5 + - - -
182B VAL* 3.9 24.6 - - + +
183B THR* 5.7 3.4 - - - +
186B GLU* 2.8 45.2 + - - +
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Residues in contact with LYS 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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88B ARG* 3.5 13.3 + - + +
89B ILE* 3.0 9.2 + - - +
91B ARG* 1.3 82.8 - - + +
93B HIS* 1.3 96.4 + - + +
97B LYS* 3.2 19.3 + - - -
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Residues in contact with HIS 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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89B ILE* 2.9 25.2 + - + +
92B LYS* 1.3 115.3 + - + +
94B PHE* 1.3 62.0 + - + +
95B LEU 3.9 0.2 - - - -
97B LYS* 3.8 9.2 - - - +
117B LYS* 3.1 35.5 + - - +
128B ARG* 3.4 58.6 + - - +
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Residues in contact with PHE 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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89B ILE* 4.3 4.0 - - + -
90B TYR* 2.8 53.0 + + + +
93B HIS* 1.3 76.3 - - + +
95B LEU* 1.3 67.2 + - - +
97B LYS* 3.1 15.9 + - - +
99B HIS* 3.1 43.2 + + + -
115B SER* 4.0 12.8 - - - -
116B LEU* 3.6 19.1 - - - -
117B LYS* 3.5 23.1 - - + -
128B ARG* 3.4 43.1 - - + -
130B LEU* 3.8 23.1 - - + -
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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