Contacts of the helix formed by residues 148 - 166 (chain B) in PDB entry 2BKU
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 PRO 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B GLU 3.7 2.9 - - - +
147B GLN* 1.3 99.7 - - + +
149B GLU* 1.3 68.0 + - - +
150B ASN* 3.2 11.0 - - - +
151B VAL* 3.1 32.9 + - + -
152B LYS* 3.2 10.3 + - - +
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Residues in contact with GLU 149 (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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147B GLN 3.8 0.6 + - - -
148B PRO* 1.3 73.1 - - - +
150B ASN* 1.3 60.4 + - - +
152B LYS* 3.4 8.2 + - - +
153B ARG* 3.0 27.0 + - + +
194B SER* 2.9 40.1 + - - +
196B ALA* 4.1 12.6 - - + +
197B VAL* 3.3 17.5 - - + +
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Residues in contact with ASN 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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104B LEU 4.8 1.6 - - - +
105B VAL 3.0 27.7 + - - -
106B SER 3.4 16.7 + - - +
107B ILE* 4.2 16.3 - - - +
148B PRO* 3.7 19.6 - - - +
149B GLU* 1.3 79.3 + - - +
151B VAL* 1.3 71.4 + - - +
153B ARG* 3.2 12.6 + - - +
154B ALA* 3.2 27.9 + - - +
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Residues in contact with VAL 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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104B LEU* 5.4 1.3 - - - +
105B VAL* 3.9 33.7 - - + +
142B ASN* 3.7 34.9 - - + +
147B GLN* 4.1 13.7 - - + +
148B PRO* 3.1 30.8 + - + +
150B ASN* 1.3 83.4 - - - +
152B LYS* 1.3 61.0 + - - +
154B ALA* 4.8 0.3 - - - +
155B SER* 2.7 31.5 + - - -
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Residues in contact with LYS 152 (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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142B ASN 3.3 21.1 - - - +
143B THR* 3.9 11.4 + - - +
144B GLY 3.1 22.2 - - - +
145B ALA* 3.2 23.1 + - - +
147B GLN* 3.4 19.6 + - + +
148B PRO 3.2 6.9 + - - +
149B GLU* 3.7 14.1 - - - +
151B VAL* 1.3 74.5 - - - +
153B ARG* 1.3 65.4 + - - +
155B SER* 3.5 1.4 + - - -
156B LEU* 3.0 32.1 + - + +
193B THR* 5.1 14.6 - - - +
194B SER* 5.8 1.0 - - - +
197B VAL* 4.1 22.4 - - + -
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Residues in contact with ARG 153 (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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109B PRO* 3.4 35.3 + - - +
112B ALA* 4.0 2.0 - - - +
113B ASN* 3.0 34.2 + - - +
149B GLU* 3.0 20.2 + - + +
150B ASN* 3.2 11.4 + - - +
152B LYS* 1.3 78.2 - - - +
154B ALA* 1.3 80.0 + - - +
156B LEU* 3.3 4.8 + - - +
157B LEU* 3.0 35.8 + - - +
196B ALA* 3.8 28.7 - - - +
197B VAL* 4.2 8.3 - - + +
200B ALA* 3.6 24.4 - - + +
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Residues in contact with ALA 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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104B LEU* 3.3 37.6 - - + +
112B ALA* 3.6 22.0 - - + +
116B ALA* 3.9 1.4 - - - +
150B ASN 3.2 10.0 + - - +
151B VAL 5.0 0.4 - - - +
153B ARG* 1.3 90.3 - - - +
155B SER* 1.3 56.9 + - - +
157B LEU* 3.4 10.0 - - - +
158B ALA* 2.8 28.6 + - - +
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Residues in contact with SER 155 (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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104B LEU* 3.9 10.6 - - - +
105B VAL* 5.5 0.5 - - - +
139B MET* 4.2 14.3 - - - +
142B ASN* 3.0 37.0 + - - -
143B THR* 4.6 2.9 - - - -
151B VAL* 2.7 22.9 + - - -
152B LYS 3.5 3.1 + - - -
153B ARG 3.1 0.6 - - - -
154B ALA* 1.3 77.4 - - - +
156B LEU* 1.3 60.7 + - - +
158B ALA* 3.2 7.5 + - - +
159B LEU* 2.8 35.3 + - - +
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Residues in contact with LEU 156 (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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143B THR* 3.8 19.7 + - + +
152B LYS* 3.0 23.5 + - + +
153B ARG 3.5 3.1 - - - +
155B SER* 1.3 71.2 - - - +
157B LEU* 1.3 61.7 + - - +
159B LEU* 3.3 11.0 + - + +
160B GLY 2.9 24.3 + - - -
183B ALA 3.4 26.2 - - - +
184B ILE* 3.9 17.0 - - + +
187B GLY* 4.5 4.5 - - - -
197B VAL* 3.7 38.8 - - + +
200B ALA* 4.3 13.0 - - + +
201B ALA* 3.9 13.0 - - + +
204B ALA* 3.3 12.3 - - + +
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Residues in contact with LEU 157 (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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113B ASN* 3.3 33.4 - - - +
116B ALA* 4.1 8.7 - - + -
153B ARG* 3.0 19.7 + - - +
154B ALA* 3.4 10.5 - - - +
156B LEU* 1.3 76.6 - - - +
158B ALA* 1.3 56.8 + - - +
160B GLY* 2.9 18.5 + - - -
161B TYR* 3.0 69.0 + - + +
200B ALA* 4.7 12.9 + - + +
203B ASN* 6.0 5.8 - - + -
204B ALA* 4.8 5.4 - - + +
207B ASP* 5.3 2.9 - - - +
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Residues in contact with ALA 158 (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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104B LEU* 4.2 6.7 - - + -
116B ALA* 3.9 29.3 - - + +
119B ILE* 5.0 2.9 - - + -
120B ALA* 4.6 0.9 - - - +
139B MET* 4.2 9.9 - - - -
154B ALA 2.8 20.4 + - - +
155B SER* 3.2 7.2 + - - +
157B LEU* 1.3 72.8 - - - +
159B LEU* 1.3 55.8 + - - +
161B TYR* 3.4 3.3 + - - +
162B MET* 2.8 48.6 + - + +
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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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136B MET* 4.8 2.0 - - - -
139B MET* 3.8 33.4 - - + +
140B VAL* 5.1 0.7 - - - +
143B THR* 4.2 18.2 - - - +
155B SER 2.8 19.1 + - - +
156B LEU* 3.4 11.9 - - + +
158B ALA* 1.3 68.2 - - - +
160B GLY* 1.3 69.3 + - - +
162B MET* 3.4 13.1 - - + +
163B CYS* 3.0 29.0 + - - -
180B ILE* 3.7 39.0 - - + -
183B ALA* 4.3 17.5 - - + -
184B ILE* 4.0 16.2 - - + -
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Residues in contact with GLY 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 LEU 2.9 14.4 + - - -
157B LEU* 2.9 5.6 + - - -
159B LEU* 1.3 78.1 - - - +
161B TYR* 1.3 63.0 + - - -
163B CYS* 3.1 2.1 + - - +
164B GLU* 3.0 22.3 + - - +
204B ALA* 3.9 19.9 - - - +
207B ASP* 4.0 10.2 - - - +
208B SER* 3.8 13.8 + - - -
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Residues in contact with TYR 161 (chain B).
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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110A ARG* 3.3 67.2 + - + +
113B ASN* 4.2 1.0 - - - +
116B ALA* 4.0 8.5 - - + -
117B GLN* 3.6 39.9 + - + -
120B ALA* 3.7 17.2 - - + +
157B LEU* 3.0 58.5 + - + +
158B ALA 3.8 3.1 - - - +
160B GLY* 1.3 73.5 - - - +
162B MET* 1.3 62.5 - - - +
164B GLU* 3.3 6.2 + - - +
165B SER* 3.1 26.2 + - - -
207B ASP* 4.0 11.0 - - - -
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Residues in contact with MET 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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119B ILE* 4.0 15.5 - - + -
120B ALA* 3.9 11.6 - - - +
123B ALA* 3.8 21.3 - - + -
124B ASP* 4.1 3.4 - - - +
127B LEU* 4.9 3.8 - - + -
135B LEU* 3.9 10.5 - - + -
136B MET* 3.7 29.2 - - - -
139B MET* 3.8 20.2 - - + -
158B ALA* 2.8 55.2 + - + +
159B LEU* 3.4 13.5 - - + +
161B TYR* 1.3 76.1 - - - +
163B CYS* 1.3 64.8 + - - +
165B SER* 3.5 4.4 + - - -
166B ALA* 3.2 21.5 + - - +
173B LEU* 4.7 8.1 - - + +
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Residues in contact with CYS 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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159B LEU* 3.0 17.1 + - - +
162B MET* 1.3 81.7 - - - +
164B GLU* 1.3 64.0 + - - +
166B ALA* 3.1 19.2 + - - +
173B LEU* 4.3 18.8 - - - -
180B ILE* 3.9 25.1 - - - -
208B SER* 3.4 32.3 - - - +
211B PHE* 3.1 28.7 - - + -
212B ILE* 5.7 3.4 - - - -
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Residues in contact with GLU 164 (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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106A ARG* 3.3 30.3 + - - -
110A ARG* 2.8 26.4 + - - -
160B GLY 3.0 15.1 + - - +
161B TYR* 3.3 6.7 + - - +
163B CYS* 1.3 77.8 - - - +
165B SER* 1.3 66.6 + - - +
207B ASP* 3.3 32.7 + - + +
211B PHE* 2.8 35.2 - - + -
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Residues in contact with SER 165 (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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70B VAL* 5.9 2.2 - - - -
120B ALA* 4.7 3.3 + - - +
124B ASP* 2.8 38.3 + - - +
161B TYR 3.1 14.6 + - - -
162B MET* 3.5 2.9 + - - -
163B CYS 3.2 0.2 - - - -
164B GLU* 1.3 85.2 - - - +
166B ALA* 1.3 66.0 + - - +
167B ASP* 3.6 9.7 - - - +
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Residues in contact with ALA 166 (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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124B ASP* 4.3 6.3 - - - +
162B MET 3.2 9.5 + - - +
163B CYS* 3.1 18.6 + - - +
164B GLU 3.4 0.2 - - - -
165B SER* 1.3 82.0 - - - +
167B ASP* 1.3 65.7 + - - +
173B LEU* 3.2 33.2 - - + -
211B PHE* 4.4 17.9 - - + -
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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