Contacts of the helix formed by residues 146 - 163 (chain A) in PDB entry 2BTO
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.7 7.4 - - - -
103A GLY* 3.7 2.2 - - - -
104A ASN 3.5 29.3 - - - +
108A GLY* 3.5 10.0 - - - -
145A GLY* 1.3 74.1 - - - -
147A THR* 1.3 56.8 + - - -
149A SER* 3.6 3.4 - - - -
150A GLY* 3.0 24.9 + - - -
1433A GTP 2.5 19.3 + - - -
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Residues in contact with THR 147 (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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11A ILE* 3.7 18.2 - - + +
12A GLY* 4.1 2.7 - - - +
71A VAL* 5.3 1.1 - - + -
72A ASP* 4.0 18.1 + - - +
73A LEU* 3.8 31.3 - - + +
101A ALA* 3.4 9.7 - - - +
146A GLY* 1.3 74.5 - - - +
148A GLY* 1.3 66.1 + - - +
149A SER 3.1 1.6 - - - -
151A PHE* 2.9 32.6 + - + +
152A GLY 3.1 4.7 + - - -
1433A GTP 2.9 34.7 + - - -
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.8 13.9 - - - -
141A HIS* 2.8 36.5 + - - -
142A ALA 3.3 19.5 - - - -
147A THR* 1.3 79.6 - - - +
149A SER* 1.3 55.8 + - - +
152A GLY* 3.2 13.0 - - - -
1433A GTP 3.2 10.8 + - - -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.6 10.1 - - - -
142A ALA 3.5 2.6 + - - -
143A ILE* 3.6 23.6 - - - -
145A GLY 2.5 30.9 + - - -
146A GLY* 3.5 3.7 + - - -
148A GLY* 1.3 76.6 - - - +
150A GLY* 1.3 67.4 + - - +
153A ALA* 2.9 30.5 + - - +
188A ASN* 3.8 10.6 - - - +
192A ALA* 3.9 22.3 - - - +
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Residues in contact with GLY 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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105A PHE* 3.3 35.4 - - - -
108A GLY 3.4 7.2 - - - -
109A TYR* 3.5 12.8 - - - -
146A GLY 3.0 7.1 + - - -
149A SER* 1.3 80.6 + - - +
151A PHE* 1.3 61.1 + - - +
153A ALA 3.4 0.9 + - - -
154A LEU* 3.0 23.6 + - - +
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Residues in contact with PHE 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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11A ILE* 3.8 22.0 - - + -
71A VAL* 3.8 22.4 - - + -
73A LEU* 5.3 1.8 - - + -
108A GLY* 3.3 16.3 + - - +
113A GLY* 3.3 35.9 - - - -
116A VAL* 3.7 10.8 - - + -
117A LEU* 3.7 20.6 - - + -
120A VAL* 3.6 34.3 - - + -
147A THR* 2.9 22.4 + - + +
150A GLY* 1.3 72.2 - - - +
152A GLY* 1.3 59.9 + - - +
154A LEU* 3.1 5.4 + - + -
155A LEU* 2.8 46.5 + - + +
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Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 20.8 - - - +
139A VAL* 5.2 0.2 - - - -
141A HIS* 4.3 8.5 - - - -
147A THR 3.1 10.7 + - - -
148A GLY 3.2 17.4 + - - -
150A GLY 3.3 0.4 - - - -
151A PHE* 1.3 77.0 - - - +
153A ALA* 1.3 58.9 + - - +
155A LEU* 3.9 1.4 - - - +
156A ILE* 2.8 34.6 + - - +
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Residues in contact with ALA 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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105A PHE* 3.9 15.7 - - + -
109A TYR* 4.0 7.4 - - + -
141A HIS* 5.3 1.0 + - - -
149A SER 2.9 20.7 + - - +
150A GLY 3.8 3.6 - - - +
152A GLY* 1.3 75.0 - - - +
154A LEU* 1.3 63.2 + - - +
156A ILE* 4.4 1.1 - - - -
157A GLU* 3.1 28.6 + - - +
192A ALA* 4.6 5.4 - - + +
195A THR* 3.4 34.8 - - - +
196A LEU* 6.4 1.1 - - - -
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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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108A GLY 4.2 1.1 - - - +
109A TYR* 3.7 21.0 - - + +
113A GLY 3.8 24.5 - - - +
114A ARG* 3.4 54.3 - - - +
117A LEU* 3.9 25.6 - - + -
150A GLY 3.0 16.9 + - - +
151A PHE* 3.1 8.9 + - + +
153A ALA* 1.3 77.8 - - - +
155A LEU* 1.3 57.6 + - - +
157A GLU* 3.4 5.1 + - + +
158A SER* 3.0 33.7 + - - +
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Residues in contact with LEU 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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9A VAL* 3.6 34.3 - - + -
11A ILE* 4.0 12.6 - - + -
117A LEU* 4.1 11.4 - - + +
120A VAL* 3.7 18.8 - - + -
121A MET* 3.7 18.4 - - - -
124A LEU* 3.7 27.6 - - + -
139A VAL* 4.9 9.2 - - + -
151A PHE* 2.8 28.2 + - + +
152A GLY 3.9 3.1 - - - +
154A LEU* 1.3 72.0 - - - +
156A ILE* 1.3 60.5 + - + +
158A SER* 3.3 3.7 + - - -
159A LEU* 2.8 33.4 + - + +
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Residues in contact with ILE 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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139A VAL* 3.5 40.4 - - + -
141A HIS* 5.2 2.0 - - + +
152A GLY 2.8 27.2 + - - +
153A ALA* 3.8 5.4 - - - +
155A LEU* 1.3 76.8 - - + +
157A GLU* 1.3 63.1 + - - +
159A LEU* 3.2 6.8 + - + +
160A LYS* 3.0 25.0 + - + +
168A VAL* 3.8 15.9 - - + -
170A SER* 4.9 9.9 - - - -
195A THR* 3.9 9.2 - - + -
196A LEU* 5.1 7.0 - - + -
199A SER* 4.0 9.6 - - - +
200A ALA* 3.9 33.2 - - + +
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Residues in contact with GLU 157 (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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109A TYR* 2.5 32.4 + - - -
153A ALA 3.1 15.4 + - - +
154A LEU* 3.7 6.6 - - + +
156A ILE* 1.3 77.9 - - - +
158A SER* 1.3 61.6 + - - +
160A LYS* 3.3 2.0 + - - +
161A GLU* 3.0 37.1 + - + +
194A ASN* 5.1 4.7 + - - -
195A THR* 2.8 29.4 + - + -
199A SER* 3.7 24.0 + - - +
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Residues in contact with SER 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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117A LEU* 3.4 27.5 - - - +
121A MET* 4.0 22.1 - - - +
154A LEU* 3.0 21.2 + - - +
155A LEU 3.6 4.3 - - - -
157A GLU* 1.3 75.6 - - - +
159A LEU* 1.3 63.4 + - - +
161A GLU* 3.3 14.4 + - - +
162A LYS* 3.1 25.6 + - - +
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Residues in contact with LEU 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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121A MET* 3.8 21.8 - - + -
124A LEU* 3.9 29.4 - - + -
128A ILE* 4.5 4.5 - - + -
137A ILE* 3.9 39.5 - - + -
139A VAL* 5.2 2.9 - - + -
155A LEU* 2.8 25.0 + - + +
156A ILE* 3.5 5.6 - - - +
158A SER* 1.3 77.7 - - - +
160A LYS* 1.3 58.4 + - - +
163A TYR* 2.8 51.9 + - + +
164A GLY 3.5 0.3 + - - -
166A ILE* 6.3 0.9 - - + -
168A VAL* 4.2 16.8 - - + -
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Residues in contact with LYS 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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156A ILE* 3.0 20.7 + - + +
157A GLU 4.0 3.4 - - - +
159A LEU* 1.3 73.4 - - - +
161A GLU* 1.3 66.3 + - + +
164A GLY* 3.1 45.6 + - - +
166A ILE 2.6 25.5 + - - +
168A VAL* 3.7 23.6 - - + -
199A SER* 3.3 35.2 - - - +
201A ASP* 2.8 26.3 + - - +
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Residues in contact with GLU 161 (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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157A GLU* 3.0 25.3 + - + +
158A SER* 3.7 15.0 + - - +
159A LEU 3.3 0.2 - - - -
160A LYS* 1.3 81.7 - - + +
162A LYS* 1.3 60.1 + - - +
163A TYR 5.1 0.2 - - - -
164A GLY* 5.1 0.5 + - - -
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Residues in contact with LYS 162 (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 MET* 4.3 10.5 - - + +
125A ASP* 2.8 35.2 + - - +
158A SER 3.1 15.3 + - - +
161A GLU* 1.3 80.0 - - + +
163A TYR* 1.3 95.5 + - + +
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Residues in contact with TYR 163 (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 MET* 4.3 7.0 - - + -
125A ASP* 2.7 36.1 + - - +
128A ILE* 3.8 35.7 - - + +
159A LEU* 2.8 29.7 + - + +
162A LYS* 1.3 113.1 + - + +
164A GLY* 1.3 49.8 + - - +
165A GLU* 2.4 33.7 + - + +
166A ILE* 3.8 34.5 - - + -
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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