Contacts of the helix formed by residues 88 - 94 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS* 3.2 50.2 - - - +
81A LEU* 3.4 21.4 + - - +
82A GLU* 5.3 0.6 - - - +
83A CYS* 2.8 39.3 + - - -
84A ASN 4.9 1.1 - - - +
85A PRO* 3.4 22.0 - - + +
87A ALA* 1.3 75.5 - - - +
89A ILE* 1.3 65.5 + - - +
90A TYR 3.5 0.4 - - - -
91A ARG* 3.3 17.6 - - + +
92A LYS* 3.4 15.7 + - - +
186A GLU* 3.8 20.6 - - - +
189A ILE* 4.5 7.5 - - + +
122D ASP* 3.5 20.6 + - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR* 3.4 37.5 - - - +
87A ALA 3.1 1.2 + - - -
88A ARG* 1.3 75.4 - - - +
90A TYR* 1.3 70.8 + - - +
92A LYS* 2.8 15.1 + - - -
93A HIS* 3.1 32.4 + - + +
94A PHE* 4.4 4.0 - - + -
128A ARG* 4.2 7.9 - - - +
130A LEU* 4.0 15.7 - - + -
139A HIS* 3.6 46.2 - - + +
121D GLU* 4.5 2.2 - - + -
122D ASP* 3.7 27.8 - - + -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 4.0 4.5 + - - +
88A ARG 3.5 0.2 - - - -
89A ILE* 1.3 77.7 - - - +
91A ARG* 1.3 65.6 + - - +
94A PHE* 3.0 49.4 + + + +
95A LEU* 3.1 20.8 + - + -
99A HIS* 2.9 30.0 + + - -
101A ASN* 3.7 4.6 + - - -
115A SER* 3.4 22.0 - - - -
130A LEU* 3.9 10.3 - - + +
132A ARG* 3.8 14.8 - - - -
178A SER* 3.5 34.2 - - - -
181A ILE* 3.5 13.2 - - + +
182A VAL* 3.8 23.3 - - + -
185A ASP* 3.6 21.8 - - + +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 4.8 0.4 + - - -
88A ARG* 3.3 16.5 + - + +
90A TYR* 1.3 81.2 - - - +
92A LYS* 1.3 66.2 + - + +
93A HIS 3.8 0.2 + - - -
95A LEU* 3.4 43.2 + - - +
182A VAL* 3.9 21.2 - - + +
186A GLU* 2.8 45.1 + - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 5.1 8.1 - - - +
88A ARG* 3.7 16.8 - - + +
89A ILE* 2.8 7.8 + - - -
91A ARG* 1.3 81.7 - - + +
93A HIS* 1.3 82.3 + - + +
97A LYS* 4.0 17.3 + - - -
122D ASP* 3.2 39.5 + - + +
123D GLU* 4.4 12.6 - - - +
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 3.1 25.5 + - + +
92A LYS* 1.3 103.9 + - + +
94A PHE* 1.3 76.3 + - + +
95A LEU 3.8 0.4 - - - -
97A LYS* 3.4 12.6 - - - +
117A LYS* 2.9 38.2 + - + +
128A ARG* 3.3 43.7 + - - +
122D ASP 2.9 27.5 + - - -
123D GLU* 5.6 2.2 - - - -
125D VAL* 6.1 2.2 - - + -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 4.4 3.6 - - + -
90A TYR* 3.0 39.6 + + + +
93A HIS* 1.3 85.5 - - + +
95A LEU* 1.3 65.3 + - - +
97A LYS* 3.2 13.1 + - - +
99A HIS* 2.8 49.2 + + + +
115A SER* 3.8 11.9 - - - -
116A LEU 3.6 13.0 - - - -
117A LYS* 3.6 26.5 - - + -
128A ARG* 3.6 45.3 - - + -
130A LEU* 4.1 26.5 - - + -
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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