Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 3BFR
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 LYS 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLN* 3.6 22.0 - - + +
146A LYS* 3.8 1.1 - - - -
147A ASN* 2.9 29.3 + - - +
150A ASN* 3.3 44.5 + - - +
151A GLY* 4.0 14.9 + - - +
152A GLY* 1.3 78.2 - - - +
154A LEU* 1.3 65.5 + - - +
155A ASP* 3.8 0.7 + - - +
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Residues in contact with LEU 154 (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 LEU* 3.7 4.9 - - + -
114A ALA* 3.7 13.9 - - + +
115A ILE* 3.6 46.4 - - + +
118A GLN* 2.8 30.9 - - - +
119A PHE* 3.6 23.0 - - + -
125A LEU* 4.9 2.5 - - + -
144A ILE* 4.9 5.6 - - + -
145A VAL 3.3 6.3 - - - +
146A LYS* 4.6 0.4 - - - -
153A LYS* 1.3 74.8 - - - +
155A ASP* 1.3 65.7 + - - +
172A LEU* 3.5 32.3 - - + -
210A PHE* 3.7 19.3 - - + -
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Residues in contact with ASP 155 (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 PHE* 4.6 6.6 - - - -
128A LEU* 5.3 5.2 - - - +
132A LYS* 5.0 2.6 + - - -
144A ILE* 3.5 5.9 - - - +
145A VAL* 2.9 42.7 + - + +
147A ASN* 5.8 3.4 - - + -
153A LYS 3.8 2.4 + - - +
154A LEU* 1.3 75.9 - - - +
156A VAL* 1.3 85.0 + - - +
157A VAL* 4.4 8.4 - - + +
169A LEU* 6.2 0.9 - - + -
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Residues in contact with VAL 156 (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 PHE* 5.0 0.2 - - + -
125A LEU* 3.6 30.3 - - + -
128A LEU* 3.9 19.6 - - + +
129A THR* 3.6 31.0 - - + +
132A LYS* 3.2 49.8 + - + -
142A ALA* 4.5 2.0 - - + -
143A PHE 3.3 10.3 - - - +
144A ILE* 4.1 4.9 - - + -
155A ASP* 1.3 89.2 + - - +
157A VAL* 1.3 69.1 - - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LYS* 5.0 1.8 - - - +
142A ALA* 3.3 4.3 - - - +
143A PHE* 2.8 48.2 + - + +
145A VAL* 4.0 18.6 - - + -
155A ASP* 4.4 11.4 - - - +
156A VAL* 1.3 81.7 - - - +
158A GLN* 1.3 67.3 + - - +
159A THR* 5.1 0.9 - - + -
165A VAL* 3.6 30.3 - - + -
169A LEU* 4.5 12.8 - - + -
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Residues in contact with GLN 158 (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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132A LYS* 2.6 56.3 + - + +
135A GLY* 3.3 27.4 + - - +
136A VAL* 4.1 11.2 - - + -
141A TRP 3.3 7.4 - - - +
142A ALA* 5.2 0.4 - - + -
157A VAL* 1.3 78.0 - - - +
159A THR* 1.3 69.3 + - - +
160A TYR* 4.3 17.0 + - + -
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Residues in contact with THR 159 (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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136A VAL* 4.4 3.1 - - - +
140A GLY* 3.2 2.8 - - - -
141A TRP* 2.9 39.5 + - - +
143A PHE* 3.5 30.1 - - + -
157A VAL* 4.2 1.1 + - + -
158A GLN* 1.3 80.2 - - - +
160A TYR* 1.3 67.5 + - - +
163A ASP* 2.7 38.0 + - + +
164A THR 4.1 12.3 - - - +
165A VAL* 4.6 6.1 - - + +
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Residues in contact with TYR 160 (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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135A GLY 3.7 7.4 + - - -
136A VAL* 4.0 9.0 - - + -
137A GLN* 2.9 59.5 + - + +
138A GLY* 4.8 2.5 - - - -
139A SER 3.4 15.0 - - - -
158A GLN* 4.3 18.2 + - + -
159A THR* 1.3 81.6 - - - +
161A ASN* 1.3 77.6 + - - +
163A ASP* 3.0 37.8 + - - +
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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