Contacts of the helix formed by residues 137 - 153 (chain A) in PDB entry 1BG7
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 GLN 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 4.8 1.0 - - - +
57A GLU* 5.7 0.5 - - - +
58A GLU* 4.4 6.4 - - - +
61A HIS* 4.5 12.6 + - - -
103A GLU* 3.2 50.6 + - - +
106A VAL* 4.0 18.0 - - - +
107A ASN* 3.5 25.5 - - - +
110A LEU* 3.8 24.6 - - + +
134A PRO* 2.9 14.4 + - + +
136A GLU* 1.3 78.8 - - - +
138A VAL* 1.3 57.9 + - - +
140A SER* 3.4 4.4 + - - -
141A ILE* 3.0 34.1 + - - +
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Residues in contact with VAL 138 (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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107A ASN* 4.9 13.5 - - - +
134A PRO* 3.1 19.8 + - + +
135A GLU* 3.6 15.9 - - - +
137A GLN* 1.3 73.1 - - + +
139A LYS* 1.3 63.9 + - - +
141A ILE* 3.8 9.2 - - + +
142A LYS* 3.1 28.8 + - - +
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Residues in contact with LYS 139 (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 GLU 3.6 14.9 + - - +
136A GLU* 3.6 33.5 - - - +
137A GLN 3.2 0.2 - - - -
138A VAL* 1.3 78.5 - - + +
140A SER* 1.3 60.2 + - - +
142A LYS* 3.4 6.2 + - - +
143A GLN* 2.9 30.5 + - - +
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Residues in contact with SER 140 (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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54A GLN* 4.0 13.5 + - - -
57A GLU* 4.4 8.1 + - - -
103A GLU* 3.3 28.7 + - - +
136A GLU* 3.2 14.7 + - - -
137A GLN* 3.5 7.0 - - - -
139A LYS* 1.3 81.5 - - - +
141A ILE* 1.3 57.2 + - - +
143A GLN* 3.3 17.3 + - - +
144A LEU* 3.0 34.0 + - - +
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Residues in contact with ILE 141 (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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100A LEU* 3.8 22.4 - - + +
103A GLU* 3.8 38.1 - - + +
104A LYS* 4.3 18.8 - - + +
107A ASN* 3.8 28.0 - - + +
137A GLN* 3.0 19.4 + - - +
138A VAL* 4.1 6.7 - - + +
139A LYS 3.3 0.2 - - - -
140A SER* 1.3 73.1 - - - +
142A LYS* 1.3 65.5 + - - +
144A LEU* 3.3 5.5 + - - +
145A GLY* 3.0 19.6 + - - -
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Residues in contact with LYS 142 (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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138A VAL 3.1 19.8 + - - +
139A LYS* 3.7 5.8 - - - +
141A ILE* 1.3 76.0 - - - +
143A GLN* 1.4 58.2 + - - +
145A GLY* 3.3 3.0 + - - -
146A ASP* 2.7 65.0 + - - +
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Residues in contact with GLN 143 (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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50A PHE* 4.2 19.1 - - - -
54A GLN* 5.0 5.1 + - - +
139A LYS 2.9 14.2 + - - +
140A SER* 3.4 20.6 + - - +
142A LYS* 1.4 75.0 - - - +
144A LEU* 1.3 57.6 + - - +
146A ASP* 3.3 11.3 + - + +
147A TYR* 3.0 68.5 + - + -
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Residues in contact with LEU 144 (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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30A TYR* 4.4 2.7 - - + +
50A PHE* 4.3 20.6 - - + -
54A GLN* 6.5 0.2 - - + -
96A MET* 3.7 30.3 - - - +
99A ALA* 3.8 30.5 - - + +
100A LEU* 3.9 18.2 - - + +
103A GLU* 3.7 31.2 - - + -
140A SER* 3.0 16.4 + - - +
141A ILE* 3.7 5.6 - - - +
143A GLN* 1.3 76.2 - - + +
145A GLY* 1.3 56.5 + - - +
147A TYR* 3.3 6.5 + - + +
148A ILE* 3.0 35.4 + - - +
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Residues in contact with GLY 145 (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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100A LEU* 4.6 7.3 - - - +
141A ILE 3.0 14.6 + - - -
142A LYS* 3.3 4.2 + - - -
144A LEU* 1.3 71.5 - - - +
146A ASP* 1.3 66.5 + - - +
148A ILE* 3.3 10.2 + - - +
149A THR* 3.0 28.2 + - - -
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Residues in contact with ASP 146 (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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142A LYS* 2.7 54.4 + - - +
143A GLN* 3.4 12.0 - - - +
145A GLY* 1.3 75.7 - - - +
147A TYR* 1.3 67.9 + - + +
149A THR* 3.3 5.5 + - - -
150A ASN* 3.1 34.0 + - - +
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Residues in contact with TYR 147 (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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50A PHE* 3.9 26.6 - + - -
96A MET* 3.9 30.3 - - + -
143A GLN* 3.0 49.6 + - + +
144A LEU* 3.5 12.8 - - + +
145A GLY 3.3 0.2 - - - -
146A ASP* 1.3 81.1 - - + +
148A ILE* 1.3 56.9 + - - +
150A ASN* 3.3 6.3 + - + +
151A LEU* 2.9 34.2 + - - +
166A PHE* 3.9 14.4 - + + -
170A THR* 3.5 31.2 + - + +
171A MET* 4.0 17.7 - - - -
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Residues in contact with ILE 148 (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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93A LEU* 3.8 17.3 - - + -
96A MET* 3.8 37.5 - - + +
97A GLN* 3.8 19.3 - - + +
100A LEU* 3.8 28.9 - - + -
144A LEU 3.0 21.0 + - - +
145A GLY* 3.8 5.8 - - - +
147A TYR* 1.3 74.4 - - - +
149A THR* 1.3 63.2 + - - +
151A LEU* 3.3 8.0 + - - +
152A LYS* 3.0 43.1 + - + +
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Residues in contact with THR 149 (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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145A GLY 3.0 14.3 + - - -
146A ASP* 3.3 12.1 + - - +
148A ILE* 1.3 75.5 - - - +
150A ASN* 1.3 58.5 + - - +
152A LYS* 3.4 11.2 + - - +
153A ARG* 2.9 48.9 + - - +
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Residues in contact with ASN 150 (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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146A ASP* 3.1 27.4 + - - +
147A TYR* 3.7 8.1 - - - +
149A THR* 1.3 76.6 - - - +
151A LEU* 1.3 60.0 + - - +
153A ARG* 3.0 33.3 + - - +
154A LEU* 3.0 36.4 + - + +
166A PHE* 4.3 16.4 - - + -
170A THR* 5.5 3.8 - - + +
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Residues in contact with LEU 151 (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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92A THR* 3.8 27.6 - - + -
93A LEU* 3.9 20.6 - - + -
96A MET* 3.8 21.5 - - + -
147A TYR 2.9 22.5 + - - +
148A ILE* 3.7 5.6 - - - +
150A ASN* 1.3 76.2 - - - +
152A LYS* 1.3 62.9 + - - +
154A LEU* 3.3 8.0 + - - +
155A GLY 3.3 0.2 + - - -
156A LEU* 3.2 54.4 + - + +
163A GLU* 5.1 1.1 - - - -
166A PHE* 3.7 37.2 - - + -
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Residues in contact with LYS 152 (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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93A LEU* 4.2 16.8 - - + -
97A GLN* 4.2 12.8 + - - -
148A ILE* 3.0 39.9 + - + +
149A THR* 3.7 7.4 - - - +
151A LEU* 1.3 76.2 - - - +
153A ARG* 1.3 61.0 + - - +
155A GLY* 3.1 14.7 + - - -
156A LEU 4.7 8.0 - - - +
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Residues in contact with ARG 153 (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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149A THR* 2.9 36.1 + - - +
150A ASN* 3.0 40.2 + - - +
151A LEU 3.4 0.2 - - - -
152A LYS* 1.3 76.9 - - - +
154A LEU* 1.3 63.3 + - + +
155A GLY* 3.3 1.6 + - - -
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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