Contacts of the helix formed by residues 146 - 164 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ALA* 3.8 5.4 - - - -
103B GLY* 3.9 3.2 - - - -
104B ASN 3.6 28.7 - - - +
108B GLY* 3.5 17.3 - - - -
145B GLY* 1.3 73.2 - - - -
147B THR* 1.3 63.1 + - - +
149B SER* 3.4 5.8 - - - -
150B GLY* 3.2 15.8 + - - -
1433B GTP 2.8 15.0 + - - -
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Residues in contact with THR 147 (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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11B ILE* 3.7 17.5 - - + -
12B GLY* 4.2 5.8 - - - +
71B VAL* 5.6 1.1 - - + -
72B ASP* 4.0 18.6 + - - +
73B LEU* 3.4 43.2 - - + +
101B ALA* 3.6 2.6 - - - +
146B GLY* 1.3 70.2 - - - +
148B GLY* 1.3 67.6 + - - +
149B SER 3.1 1.1 - - - -
151B PHE* 2.8 34.2 + - + +
152B GLY 3.2 3.8 + - - -
1433B GTP 2.8 31.9 + - - -
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.8 28.2 + - - +
12B GLY* 4.8 0.2 - - - -
141B HIS* 3.0 14.1 + - - -
142B ALA 3.5 18.4 - - - -
147B THR* 1.3 73.1 - - - +
149B SER* 1.3 56.6 + - - +
152B GLY* 2.9 26.0 - - - -
1433B GTP 2.9 13.6 + - - -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.4 22.9 - - - +
141B HIS* 5.7 0.3 - - - -
142B ALA 3.6 3.6 + - - -
143B ILE* 3.5 23.6 - - - +
145B GLY 2.5 28.5 + - - -
146B GLY* 3.4 6.2 - - - -
147B THR 4.2 0.4 - - - +
148B GLY* 1.3 73.8 - - - +
150B GLY* 1.3 67.8 + - - +
153B ALA* 2.9 30.5 + - - +
188B ASN 3.9 6.7 - - - -
192B ALA* 3.9 13.4 - - - +
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Residues in contact with GLY 150 (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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105B PHE* 3.3 34.3 - - - -
108B GLY 3.5 6.5 - - - -
109B TYR* 3.4 14.4 - - - -
146B GLY 3.2 8.0 + - - -
149B SER* 1.3 80.8 + - - +
151B PHE* 1.3 60.8 + - - +
153B ALA 3.3 1.6 + - - -
154B LEU* 2.9 22.0 + - - +
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Residues in contact with PHE 151 (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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11B ILE* 3.5 24.5 - - + -
71B VAL* 3.7 27.4 - - + -
73B LEU* 5.9 2.0 - - + -
108B GLY* 3.5 15.3 + - - +
113B GLY* 3.5 24.5 - - - -
116B VAL* 3.3 27.8 - - + -
117B LEU* 3.7 24.9 - - + -
120B VAL* 3.7 23.8 - - + -
147B THR* 2.8 21.2 + - + +
150B GLY* 1.3 69.6 - - - -
152B GLY* 1.3 57.3 + - - +
153B ALA 3.2 0.2 - - - -
154B LEU* 3.9 6.3 - - + -
155B LEU* 2.7 46.5 + - + +
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.2 13.8 - - - +
139B VAL* 5.1 2.0 - - - +
141B HIS* 4.1 11.4 - - - -
147B THR 3.2 3.0 + - - -
148B GLY 2.9 24.1 + - - -
149B SER 3.9 0.2 - - - -
151B PHE* 1.3 77.3 - - - +
153B ALA* 1.3 61.1 + - - +
155B LEU* 4.2 2.1 - - - +
156B ILE* 3.1 35.5 + - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.9 10.8 - - + -
109B TYR* 3.8 13.9 - - + -
141B HIS* 5.3 0.4 - - - -
149B SER 2.9 22.0 + - - +
150B GLY 3.4 5.4 - - - +
152B GLY* 1.3 76.1 - - - +
154B LEU* 1.3 63.9 + - - +
156B ILE* 5.3 0.4 - - - -
157B GLU* 3.1 29.8 + - - +
192B ALA* 4.8 4.5 - - - -
195B THR* 3.4 30.9 - - - +
196B LEU* 6.5 0.7 - - - -
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Residues in contact with LEU 154 (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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108B GLY 3.9 10.5 - - - +
109B TYR* 3.4 30.9 - - + +
113B GLY 3.9 22.0 - - - +
114B ARG* 3.5 41.5 - - - +
117B LEU* 4.3 17.7 - - + -
150B GLY 2.9 17.0 + - - +
151B PHE* 3.1 11.2 + - + +
153B ALA* 1.3 78.9 - - - +
155B LEU* 1.3 53.2 + - - +
157B GLU* 3.6 7.6 + - + +
158B SER* 2.7 40.7 + - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.7 32.8 - - + -
11B ILE* 4.0 13.7 - - + -
117B LEU* 4.1 10.1 - - + -
120B VAL* 3.8 16.8 - - + -
121B MET* 3.9 13.0 - - - -
124B LEU* 3.7 28.7 - - + -
139B VAL* 4.9 11.9 - - + -
151B PHE* 2.7 30.8 + - + +
152B GLY* 4.2 2.2 - - - +
154B LEU* 1.3 72.6 - - - +
156B ILE* 1.3 56.1 - - + +
158B SER* 3.3 4.8 + - - -
159B LEU* 2.7 40.1 + - + +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 4.1 35.4 - - + -
141B HIS* 4.3 4.0 - - + -
152B GLY 3.1 20.2 + - - +
153B ALA* 4.2 2.2 - - - +
155B LEU* 1.3 72.3 - - + +
157B GLU* 1.3 67.2 + - - +
159B LEU* 3.1 8.4 + - - +
160B LYS* 3.0 24.2 + - + +
168B VAL* 4.3 14.1 - - + -
170B SER* 4.3 9.4 - - - -
195B THR* 4.3 6.7 - - + -
196B LEU* 3.8 27.8 - - + -
199B SER* 4.0 11.4 - - - +
200B ALA* 3.8 29.2 - - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 2.6 34.3 + - - -
153B ALA 3.1 18.5 + - - +
154B LEU* 3.6 7.5 - - + +
156B ILE* 1.3 77.4 - - - +
158B SER* 1.3 60.5 - - - +
160B LYS* 3.3 3.0 + - - +
161B GLU* 3.2 34.3 + - - +
194B ASN* 5.2 4.0 + - - -
195B THR* 2.7 32.1 + - + -
199B SER* 4.0 17.2 + - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.6 28.0 - - - +
121B MET* 3.7 18.7 - - - +
154B LEU* 2.7 26.4 + - - +
155B LEU* 3.5 8.5 - - - -
157B GLU* 1.3 72.3 - - - +
159B LEU* 1.3 67.3 + - - +
161B GLU* 3.4 11.3 + - - +
162B LYS* 3.1 25.8 + - - +
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Residues in contact with LEU 159 (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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121B MET* 4.3 6.7 - - - +
124B LEU* 3.7 31.0 - - + -
137B ILE* 3.7 39.5 - - + -
139B VAL* 4.9 7.0 - - + -
155B LEU* 2.7 26.0 + - + +
156B ILE* 3.1 8.0 + - - +
158B SER* 1.3 73.5 - - - +
160B LYS* 1.3 58.4 + - - +
163B TYR* 2.9 52.3 + - + +
164B GLY 3.8 0.2 + - - -
166B ILE* 6.4 0.2 - - + -
168B VAL* 3.7 32.8 - - + -
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Residues in contact with LYS 160 (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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156B ILE* 3.0 18.0 + - + +
157B GLU* 3.8 5.4 - - - +
158B SER 3.2 0.2 - - - -
159B LEU* 1.3 74.5 - - - +
161B GLU* 1.3 61.5 + - + +
164B GLY* 2.8 53.0 + - - +
165B GLU 4.5 1.4 + - - -
166B ILE 2.8 17.5 + - - -
168B VAL* 3.8 15.3 - - + -
199B SER* 3.4 28.7 - - - +
201B ASP* 2.7 41.2 + - - +
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Residues in contact with GLU 161 (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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157B GLU* 3.2 22.4 + - - +
158B SER* 3.4 10.4 + - - +
160B LYS* 1.3 79.8 - - + +
162B LYS* 1.3 61.6 + - + +
164B GLY* 4.6 1.2 + - - -
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Residues in contact with LYS 162 (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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121B MET* 4.1 21.5 - - + +
125B ASP* 3.5 32.6 + - - -
158B SER 3.1 16.8 + - - +
161B GLU* 1.3 79.6 - - - +
163B TYR* 1.3 84.9 + - + +
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Residues in contact with TYR 163 (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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121B MET* 4.8 4.7 - - + -
124B LEU* 5.1 4.9 - - + -
125B ASP* 2.4 42.2 + - - -
128B ILE* 4.2 30.7 - - + +
159B LEU* 2.9 38.5 + - + +
162B LYS* 1.3 103.2 - - + +
164B GLY* 1.3 52.9 + - - +
165B GLU* 2.6 21.5 + - - +
166B ILE* 3.8 35.6 + - + +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU 3.8 1.2 + - - -
160B LYS* 2.8 59.6 + - - +
161B GLU 5.2 0.4 - - - -
162B LYS 3.7 0.8 - - - -
163B TYR* 1.3 70.4 - - - +
165B GLU* 1.3 59.5 + - - -
166B ILE 3.3 1.7 + - - -
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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
------------------------------------------------------------
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