Contacts of the strand formed by residues 186 - 195 (chain E) in PDB entry 2BNQ
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 TYR 186 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLY 2.9 24.9 + - - -
148E PHE* 2.7 46.9 + - + -
149E TYR* 3.5 28.9 - + - -
151E ASP* 3.6 38.5 + - + +
174E PRO* 3.9 16.8 - - + -
175E LEU 3.3 19.5 - - - +
176E LYS* 3.9 30.0 - - + -
177E GLU* 3.9 2.7 - - - -
182E ASN 5.3 2.4 + - - -
184E SER 3.6 6.5 + - - -
185E ARG* 1.3 75.5 - - - +
187E ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D TRP* 3.7 28.9 - - + -
145E ALA 3.1 11.2 - - - +
146E THR* 4.1 2.0 - - + -
148E PHE* 3.8 2.2 - - - -
171E ASP* 5.4 0.2 - - - +
174E PRO* 3.4 2.6 - - - +
175E LEU* 2.9 47.5 + - + +
177E GLU* 3.6 16.6 - - + +
186E TYR* 1.3 75.3 - - - +
188E LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D TRP* 5.3 1.6 - - - -
143E CYS 3.9 0.2 - - - +
144E LEU* 3.6 5.0 - - - +
145E ALA* 2.7 37.1 + - + +
148E PHE* 4.0 14.4 - - + -
153E VAL* 4.1 23.6 - - + +
155E LEU* 4.2 21.6 - - + +
170E THR* 4.1 16.6 - - + -
171E ASP* 3.6 42.4 - - + +
173E GLN 4.1 0.4 - - - +
174E PRO* 4.1 21.8 - - + -
187E ALA* 1.3 75.8 - - - +
189E SER* 1.3 64.5 + - - +
210E VAL* 6.2 0.2 - - + -
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Residues in contact with SER 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D THR* 3.1 18.8 - - - +
177D VAL* 4.1 9.0 - - - +
179D TRP* 4.7 0.4 - - - -
142E VAL* 6.3 0.7 - - - -
143E CYS 3.3 5.8 - - - -
144E LEU* 3.5 22.2 - - - -
155E LEU* 4.9 0.7 - - - -
170E THR* 3.7 3.1 - - - +
171E ASP* 2.6 48.7 + - - -
188E LEU* 1.3 76.9 - - - +
190E SER* 1.3 62.3 + - - +
191E ARG* 2.9 17.1 + - - -
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Residues in contact with SER 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 3.3 5.5 - - - +
143E CYS* 2.8 33.2 + - - -
155E LEU* 3.6 23.8 - - - +
157E TRP* 2.8 26.1 + - - -
168E VAL* 3.9 1.9 - - - +
169E CYS 3.4 8.5 + - - -
170E THR* 2.8 26.4 + - - -
189E SER* 1.3 76.8 - - - +
191E ARG* 1.3 66.9 + - - +
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Residues in contact with ARG 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 4.7 1.1 - - + -
159D THR* 3.0 27.1 + - - -
160D ASP 3.6 4.8 + - - -
162D CYS* 3.6 10.8 - - - +
164D LEU* 4.4 9.4 - - + -
175D SER* 2.7 41.5 + - - +
176D ALA* 3.7 4.4 - - - +
177D VAL* 3.9 9.4 - - + +
140E THR* 3.9 15.0 - - + -
141E LEU 3.3 8.5 - - - +
142E VAL* 4.3 11.9 - - + -
157E TRP* 4.0 2.9 - - - -
167E GLY 3.6 0.8 - - - +
168E VAL* 3.2 9.2 - - - +
169E CYS* 2.9 56.4 + - - -
171E ASP* 2.9 24.9 + - - +
189E SER* 2.9 26.9 + - - -
190E SER* 1.3 77.9 + - - +
192E LEU* 1.3 61.4 + - - +
193E ARG 4.1 0.2 - - - -
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E THR* 3.5 1.5 - - - -
141E LEU* 2.7 42.7 + - + +
157E TRP* 3.7 44.1 - - + +
159E VAL* 3.9 15.5 - - + -
164E VAL* 4.2 7.0 - - + -
166E SER 3.8 14.1 - - - +
167E GLY 3.5 2.0 - - - +
168E VAL* 3.5 22.0 - - + -
191E ARG* 1.3 74.8 - - - +
193E ARG* 1.3 65.4 + - - +
194E VAL* 4.2 12.1 - - + -
206E PHE* 3.9 28.0 - - + -
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Residues in contact with ARG 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D THR* 4.1 8.3 + - - +
141D ASP* 2.7 43.4 + - - -
164D LEU* 3.8 25.4 - - + -
166D MET* 3.5 28.2 - - - +
171D PHE* 3.5 9.9 - - - -
173D SER* 3.0 25.4 + - - -
132E GLU* 3.0 26.8 + - - +
136E THR* 3.7 16.8 + - - +
138E LYS* 3.6 13.7 - - + +
139E ALA 3.3 7.2 - - - +
140E THR* 3.1 15.8 + - - +
166E SER 4.8 0.7 - - - +
167E GLY* 2.9 20.2 + - - -
191E ARG 4.1 0.2 - - - -
192E LEU* 1.3 75.2 - - - +
194E VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 3.8 9.4 - - - -
138E LYS* 3.4 5.5 - - - +
139E ALA* 2.7 42.2 + - + +
141E LEU* 4.4 8.7 - - + -
159E VAL* 5.8 1.8 - - + -
192E LEU* 4.2 21.8 - - + -
193E ARG* 1.3 81.0 - - - +
195E SER* 1.3 66.6 + - - +
198E PHE* 4.2 24.2 - - + -
199E TRP* 4.1 22.4 - - + +
206E PHE* 4.2 8.1 - - + -
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Residues in contact with SER 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 4.1 5.7 - - - +
169D MET* 5.2 14.8 - - - -
137E GLN 3.9 6.5 - - - -
138E LYS* 4.4 2.0 - - - +
139E ALA 4.3 0.2 - - - -
194E VAL* 1.3 82.1 - - - +
196E ALA* 1.3 65.4 + - - +
197E THR* 2.9 23.2 + - - -
198E PHE* 3.0 21.9 + - - +
199E TRP* 3.2 10.0 + - - +
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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