Contacts of the strand formed by residues 165 - 171 (chain A) in PDB entry 1BJW
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 THR 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.7 13.2 + - - +
119A ILE* 4.1 16.9 - - + +
160A ALA 4.2 2.1 + - - -
161A ILE* 3.5 11.2 - - + -
162A THR* 2.9 34.9 + - - +
163A PRO 3.4 0.2 - - - -
164A ARG* 1.3 74.9 - - - +
166A LYS* 1.3 61.1 + - - +
167A ALA 4.1 15.7 - - - +
196A HIS 5.3 0.2 - - - +
198A PHE* 3.4 37.8 - - + +
1B MET 3.4 21.1 + - - -
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Residues in contact with LYS 166 (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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111A ILE* 2.8 27.5 + - + +
112A LEU* 4.1 9.2 - - + -
113A ASP* 4.5 8.9 + - - -
116A ASP* 3.0 37.0 + - + +
117A GLU 2.8 11.0 + - - +
164A ARG 3.3 1.9 + - - +
165A THR* 1.3 73.0 - - - +
167A ALA* 1.3 63.7 - - - +
198A PHE* 3.4 6.8 - - - +
199A TYR* 2.9 41.1 + - + -
1B MET* 3.3 24.2 - - + +
2B ARG 3.9 8.5 - - - -
3B GLY 3.2 25.2 + - - +
4B LEU 4.9 1.8 + - - -
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Residues in contact with ALA 167 (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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108A PHE* 4.9 1.3 - - + -
111A ILE* 4.4 11.7 - - + -
117A GLU 3.4 3.3 + - - +
118A VAL* 3.2 23.2 - - + -
119A ILE* 2.7 32.2 + - - +
165A THR* 3.7 5.8 - - - +
166A LYS* 1.3 83.8 - - + +
168A LEU* 1.3 56.0 + - - +
198A PHE* 4.3 4.9 - - - -
199A TYR* 3.1 16.4 - - + +
201A VAL* 4.3 17.3 - - + -
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Residues in contact with LEU 168 (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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119A ILE* 3.4 32.5 - - + +
121A LEU* 4.3 12.8 - - + -
157A VAL* 4.0 24.7 - - + -
167A ALA* 1.3 75.9 - - - +
169A VAL* 1.3 71.4 + - - +
170A VAL* 3.9 9.9 - - + -
189A LEU* 4.3 25.1 - - + +
192A LEU* 5.5 0.9 - - + -
198A PHE* 3.9 22.7 - - + -
199A TYR 3.1 4.6 + - - -
200A LEU* 3.4 25.5 - - + +
201A VAL* 2.9 24.3 + - - +
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Residues in contact with VAL 169 (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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104A LEU* 5.3 1.3 - - + -
108A PHE* 4.1 17.3 - - + -
118A VAL* 3.7 26.7 - - + -
119A ILE 2.9 10.4 + - - +
120A VAL* 4.3 13.2 - - + -
121A LEU* 3.9 22.7 + - - +
128A TYR* 3.8 43.5 - - + +
132A VAL* 5.5 0.4 - - + -
168A LEU* 1.3 75.5 - - - +
170A VAL* 1.3 69.3 + - - +
171A ASN* 5.8 0.2 - - - -
201A VAL* 3.5 19.5 - - + +
203A ASP* 5.3 2.0 - - + -
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Residues in contact with VAL 170 (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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121A LEU* 4.7 4.7 - - + -
168A LEU* 3.9 11.7 - - + -
169A VAL* 1.3 80.9 - - - +
171A ASN* 1.3 63.4 + - - +
172A SER* 4.1 1.9 + - - +
181A TYR* 3.7 28.7 - - + -
186A LEU* 4.1 11.4 - - + -
189A LEU* 4.1 23.8 - - + -
200A LEU* 3.5 29.4 - - + -
201A VAL 2.8 9.9 + - - +
202A SER* 3.4 9.6 + - - +
203A ASP* 2.8 27.2 + - - +
218A PRO* 5.8 2.0 - - + -
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Residues in contact with ASN 171 (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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121A LEU* 5.6 0.6 - - - +
128A TYR* 3.3 31.1 + - + +
169A VAL 4.3 0.4 + - - -
170A VAL* 1.3 76.0 - - - +
172A SER* 1.3 61.7 + - - +
173A PRO 3.4 13.3 + - - -
174A ASN* 3.1 34.4 + - - +
175A ASN 3.2 28.8 + - - +
181A TYR* 4.0 8.2 - - - -
203A ASP* 2.9 30.5 + - - +
205A ILE* 4.2 3.6 - - - +
234A LLP 3.5 16.7 - - - +
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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