Contacts of the strand formed by residues 125 - 132 (chain B) in PDB entry 1BT8
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 GLY 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.8 12.2 - - - +
123B GLY 3.9 1.2 + - - -
124B SER* 1.3 77.2 - - - +
126B TRP* 1.3 68.3 + - - -
143B PHE 3.0 13.5 - - - -
145B ASP 3.5 10.5 - - - -
162B MET* 2.9 29.6 + - - +
163B TRP* 3.5 7.5 - - - -
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Residues in contact with TRP 126 (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 ASN* 3.4 53.8 - - + +
75B HIS* 3.5 32.3 - + - -
78B PHE* 4.0 11.4 - + + -
121B ILE* 3.7 9.4 - - - +
125B GLY* 1.3 76.3 - - - -
127B ALA* 1.3 63.7 + - - +
128B SER* 5.3 0.4 - - - -
142B GLN* 3.4 5.7 - - - -
143B PHE* 2.9 48.1 + + + +
145B ASP 3.0 22.1 + - - -
146B HIS* 2.9 22.8 - + - -
159B GLN* 4.0 17.3 - - + -
160B LEU 3.4 8.1 - - - -
161B ASP* 3.5 48.5 - - + -
162B MET* 4.4 0.4 - - - +
163B TRP* 3.5 4.0 - - - +
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Residues in contact with ALA 127 (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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114B PHE* 3.5 26.4 - - + +
117B ALA* 4.6 4.9 - - + -
118B ALA* 3.6 39.3 - - + +
121B ILE* 4.6 0.2 - - - +
126B TRP* 1.3 74.0 - - - +
128B SER* 1.3 60.1 + - - +
141B LEU 3.7 4.9 - - - -
142B GLN* 4.9 0.9 - - - +
159B GLN* 3.4 4.3 - - - +
160B LEU* 2.9 32.8 + - + +
162B MET* 4.7 0.6 - - - +
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.9 6.3 - - - -
126B TRP* 5.3 0.2 - - - -
127B ALA* 1.3 76.1 - - - +
129B LEU* 1.3 63.0 + - - +
130B VAL* 3.3 18.1 - - - +
139B ASN 3.8 0.2 - - - +
140B THR* 3.1 7.6 - - - -
141B LEU* 2.8 41.8 + - - -
143B PHE* 3.8 21.3 - - - -
156B PRO* 4.6 0.2 - - - +
158B LEU 3.4 4.0 + - - -
159B GLN* 3.0 32.8 + - - +
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Residues in contact with LEU 129 (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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96B LEU* 5.7 1.3 - - + -
100B ILE* 4.9 11.0 - - + -
104B PHE* 3.8 10.5 - - + -
110B MET* 4.2 26.5 - - + -
114B PHE* 4.3 7.0 - - + -
128B SER* 1.3 71.7 + - - +
130B VAL* 1.3 60.7 + - - +
138B ILE* 3.6 29.2 - - + -
139B ASN 3.5 1.6 - - - +
140B THR* 3.8 25.1 - - + -
157B LEU* 2.8 35.2 + - + +
158B LEU* 2.8 39.2 + - + +
188B TRP* 5.0 4.5 - - + -
191B VAL* 5.0 3.8 - - + -
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Residues in contact with VAL 130 (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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128B SER* 3.3 26.2 - - - +
129B LEU* 1.3 73.8 - - - +
131B TRP* 1.3 63.9 + - - +
132B ASP* 5.0 2.2 - - + +
138B ILE* 3.3 6.1 - - - +
139B ASN* 2.9 46.7 + - + +
141B LEU* 3.7 33.2 - - + -
143B PHE* 4.5 5.6 - - + -
154B SER* 4.4 13.2 - - - +
155B ILE 3.3 20.2 - - - +
156B PRO* 3.9 9.2 - - + -
157B LEU* 4.1 5.8 - - - -
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Residues in contact with TRP 131 (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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103B PHE* 4.5 6.5 - + - -
130B VAL* 1.3 73.4 - - - +
132B ASP* 1.3 61.3 + - - +
133B PRO* 3.1 36.6 - - + +
136B LYS* 3.5 36.7 - - + +
137B ARG* 3.4 29.8 - - - -
138B ILE* 3.8 7.4 - - + -
154B SER* 4.1 2.9 - - - -
155B ILE* 2.9 32.1 + - + +
157B LEU* 4.0 8.4 - - + +
195B PHE* 3.6 30.7 - + - -
198B ALA* 3.4 46.8 + - + -
199B ARG* 4.1 23.8 + - + +
201B ALA* 5.5 1.6 + - - +
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Residues in contact with ASP 132 (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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130B VAL* 3.8 3.7 + - + -
131B TRP* 1.3 73.0 + - - +
133B PRO* 1.3 57.2 - - - +
134B LEU* 3.2 17.5 + - - +
135B GLY* 3.1 23.4 + - - -
136B LYS* 2.6 36.9 + - - -
137B ARG* 2.8 23.0 + - + +
139B ASN* 3.6 27.4 + - + +
154B SER* 5.8 1.1 - - - +
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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