Contacts of the helix formed by residues 148 - 166 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D GLU 4.0 1.3 - - - +
147D GLN* 1.3 101.0 - - + +
149D GLU* 1.3 67.3 + - - +
150D ASN* 3.2 13.0 - - - +
151D VAL* 3.0 35.0 + - + -
152D LYS* 3.1 11.0 + - - +
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Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D GLN 3.8 0.8 + - - -
148D PRO* 1.3 72.8 - - - +
150D ASN* 1.3 58.6 + - - +
152D LYS* 3.6 6.7 + - - +
153D ARG* 3.1 27.1 + - + +
194D SER* 3.0 36.2 + - - +
196D ALA* 3.7 17.2 - - + +
197D VAL* 3.6 12.1 - - + +
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Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU 4.7 1.0 - - - +
105D VAL* 3.1 30.5 + - - +
106D SER 4.0 11.0 + - - +
107D ILE* 4.6 16.5 - - + +
148D PRO* 3.7 15.9 - - - +
149D GLU* 1.3 78.3 + - - +
151D VAL* 1.3 83.1 + - - +
153D ARG* 3.8 11.6 + - - +
154D ALA* 3.1 28.9 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU 5.4 0.2 - - - -
105D VAL* 3.7 28.9 - - + +
142D ASN* 3.5 37.4 - - + +
147D GLN* 3.8 14.6 - - - +
148D PRO* 3.0 32.0 + - + +
150D ASN* 1.3 89.4 - - - +
152D LYS* 1.3 61.0 + - - +
154D ALA* 4.8 1.2 - - - +
155D SER* 2.6 32.1 + - - -
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ASN 3.4 19.7 - - - +
143D THR* 3.8 12.3 + - + +
144D GLY 3.2 22.0 - - - +
145D ALA* 3.2 21.0 + - - +
147D GLN* 3.5 15.4 + - + +
148D PRO 3.1 10.4 + - - +
149D GLU* 3.8 10.1 - - - +
151D VAL* 1.3 75.8 - - - +
153D ARG* 1.3 65.1 + - - +
155D SER* 3.9 1.0 - - - -
156D LEU* 3.1 31.7 + - + +
192D GLU* 3.7 19.1 + - - +
193D THR* 5.8 3.0 + - - -
194D SER* 6.0 1.1 - - - -
197D VAL* 4.2 26.9 - - + -
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PRO* 3.6 32.6 + - - +
112D ALA* 4.1 10.7 - - - +
113D ASN* 3.2 31.8 - - - +
149D GLU* 3.1 19.1 + - - +
150D ASN* 3.3 11.4 + - - +
152D LYS* 1.3 76.7 - - - +
154D ALA* 1.3 66.8 + - - +
156D LEU* 3.2 5.0 + - - +
157D LEU* 2.9 43.7 + - - +
196D ALA* 3.6 30.5 - - + +
197D VAL* 4.6 7.9 - - + +
200D ALA* 3.6 25.5 - - + +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.3 40.9 - - + +
112D ALA* 3.9 16.6 - - + +
113D ASN* 5.5 0.4 - - - +
116D ALA* 4.4 0.9 - - - +
150D ASN 3.1 11.8 + - - +
151D VAL 4.8 0.9 - - - +
153D ARG* 1.3 89.5 - - - +
155D SER* 1.3 57.4 + - - +
157D LEU* 3.5 9.2 - - + +
158D ALA* 2.8 28.6 + - - +
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.0 9.6 - - - +
105D VAL* 5.6 0.2 - - - +
139D MET* 4.0 16.1 - - - +
142D ASN* 3.0 36.2 + - - +
143D THR* 4.4 3.4 - - - -
151D VAL* 2.6 24.2 + - - +
152D LYS 3.9 2.5 - - - -
153D ARG 3.2 0.6 - - - -
154D ALA* 1.3 76.8 - - - +
156D LEU* 1.3 54.2 + - - +
158D ALA* 3.3 7.7 + - - +
159D LEU* 2.8 38.5 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D THR* 3.9 23.1 - - + +
152D LYS* 3.1 24.8 + - + +
153D ARG 3.6 3.4 - - - +
155D SER* 1.3 71.6 - - - +
157D LEU* 1.3 66.2 + - - +
159D LEU* 3.2 8.7 + - + +
160D GLY 3.0 19.1 + - - -
183D ALA* 3.7 25.1 - - + +
184D ILE* 4.1 18.8 - - + +
187D GLY* 4.8 4.0 - - - -
197D VAL* 3.8 38.1 - - + +
200D ALA* 4.4 11.9 - - + +
201D ALA* 3.9 12.6 - - + -
204D ALA* 3.5 11.8 - - + +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASN* 3.3 31.2 - - - +
116D ALA* 3.9 12.1 - - + -
153D ARG* 2.9 21.7 + - - +
154D ALA* 3.5 10.3 - - - +
156D LEU* 1.3 76.0 - - - +
158D ALA* 1.3 63.2 + - - +
160D GLY* 3.1 3.6 + - - -
161D TYR* 3.0 69.8 + - + +
200D ALA* 4.7 12.2 - - + +
203D ASN* 5.9 6.3 - - + -
204D ALA* 5.1 3.1 - - - +
207D ASP* 5.1 4.5 - - - +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.3 7.4 - - + -
116D ALA* 4.2 23.7 - - + +
119D ILE* 5.2 3.4 - - + -
120D ALA* 4.8 1.0 - - - +
139D MET* 4.1 10.5 - - - -
154D ALA 2.8 21.9 + - - +
155D SER* 3.4 7.0 - - - +
157D LEU* 1.3 73.2 - - - +
159D LEU* 1.3 50.8 + - - +
161D TYR* 3.3 6.1 + - - +
162D MET* 2.8 53.6 + - + +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D MET* 4.9 4.9 - - - -
139D MET* 3.7 35.9 - - + +
140D VAL* 4.8 1.8 - - - +
143D THR* 4.4 16.4 - - - +
155D SER 2.8 21.2 + - - +
156D LEU* 3.2 13.0 + - + +
158D ALA* 1.3 72.5 - - - +
160D GLY* 1.3 57.0 + - - +
162D MET* 3.4 13.6 + - + +
163D CYS* 3.0 38.1 + - - -
173D LEU* 6.4 0.7 - - + -
180D ILE* 3.8 39.9 - - + -
183D ALA* 4.8 12.8 - - + -
184D ILE* 4.4 10.3 - - + -
208D SER* 4.9 0.2 - - - -
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Residues in contact with GLY 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU 3.0 12.9 + - - -
157D LEU 3.1 3.1 + - - -
159D LEU* 1.3 73.7 - - - +
161D TYR* 1.3 66.6 + - - +
162D MET 3.2 0.2 + - - -
163D CYS* 3.2 2.9 + - - +
164D GLU* 3.0 25.1 + - - +
204D ALA* 4.0 19.8 - - - +
207D ASP* 3.8 11.2 - - - +
208D SER* 3.9 14.4 - - - -
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Residues in contact with TYR 161 (chain D).
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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110C ARG* 3.3 65.4 + - + +
113D ASN* 4.4 3.1 - - + +
116D ALA* 3.9 22.9 - - + -
117D GLN* 3.9 20.8 - - + +
120D ALA* 3.9 15.7 - - + +
157D LEU* 3.0 54.3 + - + +
158D ALA 3.6 6.1 - - - +
160D GLY* 1.3 73.6 - - - +
162D MET* 1.3 63.5 + - - +
164D GLU* 3.4 5.9 + - - +
165D SER* 3.2 25.3 + - - -
207D ASP* 4.0 12.6 - - - -
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Residues in contact with MET 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 4.1 15.3 - - + -
120D ALA* 4.2 11.6 - - - +
123D ALA* 3.8 20.2 - - + -
124D ASP* 4.6 2.1 - - - +
127D LEU* 4.8 4.9 - - + -
135D LEU* 3.7 23.1 - - + -
136D MET* 3.8 17.3 - - - -
139D MET* 3.9 26.0 - - + -
158D ALA* 2.8 37.3 + - + +
159D LEU* 3.5 14.1 - - + +
160D GLY 3.1 0.2 - - - -
161D TYR* 1.3 74.8 - - - +
163D CYS* 1.3 63.3 + - - +
165D SER* 3.6 5.0 + - - -
166D ALA* 3.1 24.7 + - - +
173D LEU* 4.5 7.3 - - + +
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Residues in contact with CYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LEU* 3.0 21.2 + - - +
162D MET* 1.3 77.6 - - - +
164D GLU* 1.3 63.5 + - - +
166D ALA* 3.4 14.1 - - - +
173D LEU* 4.1 20.6 - - - -
180D ILE* 4.0 26.2 - - - -
208D SER* 3.5 27.8 - - - +
211D PHE* 3.1 33.9 - - + -
212D ILE* 6.3 2.2 - - + -
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Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ARG* 4.4 20.1 + - - -
110C ARG* 3.3 28.4 + - - -
160D GLY 3.0 15.7 + - - +
161D TYR* 3.7 5.2 - - - +
163D CYS* 1.3 77.7 - - - +
165D SER* 1.3 63.0 + - - +
207D ASP* 3.3 38.4 + - + +
211D PHE* 2.9 34.6 - - + -
250D LYS* 6.2 1.1 - - - +
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Residues in contact with SER 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 6.2 0.4 - - - -
120D ALA* 4.6 4.0 + - - +
124D ASP* 2.7 40.2 + - - +
161D TYR 3.2 15.4 + - - -
162D MET* 3.6 3.1 + - - -
164D GLU* 1.3 80.7 - - - +
166D ALA* 1.3 67.0 + - - +
167D ASP* 3.5 11.3 - - - +
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 4.7 5.4 - - - +
162D MET 3.1 14.6 + - - +
163D CYS* 3.4 13.5 - - - +
164D GLU 3.4 1.6 - - - +
165D SER* 1.3 82.8 - - - +
167D ASP* 1.3 65.7 + - - +
169D GLN* 5.6 4.9 - - + +
173D LEU* 3.2 33.7 - - + -
211D PHE* 4.4 15.7 - - + -
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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
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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