Contacts of the strand formed by residues 138 - 148 (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 LYS 138 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D MET* 3.8 18.6 - - + -
169D MET* 4.0 26.8 - - + +
171D PHE* 3.6 55.2 - - + +
132E GLU* 3.5 12.4 - - - +
133E ILE* 3.5 13.2 - - - -
136E THR* 3.0 29.2 + - - +
137E GLN* 1.3 84.8 - - - +
139E ALA* 1.3 62.6 + - - +
193E ARG* 3.6 19.1 - - + +
194E VAL 3.4 11.0 - - - +
195E SER* 5.0 2.0 - - - -
196E ALA* 3.8 3.1 - - - +
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Residues in contact with ALA 139 (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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128E PRO* 3.6 18.4 - - + -
132E GLU* 3.7 3.1 - - - -
133E ILE* 4.2 8.5 - - + -
138E LYS* 1.3 77.3 - - - +
140E THR* 1.3 62.5 + - - +
141E LEU* 4.0 0.7 + - - +
192E LEU 3.7 0.9 - - - +
193E ARG* 3.3 1.8 - - - -
194E VAL* 2.7 44.8 + - + +
195E SER 4.3 2.2 - - - +
196E ALA* 4.5 1.3 - - - -
199E TRP* 3.6 30.7 - - + -
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Residues in contact with THR 140 (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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126D LEU* 3.3 19.6 - - - +
138D LEU* 3.7 26.4 - - + +
140D THR* 5.3 0.9 + - - -
164D LEU* 5.1 3.3 - - + +
175D SER* 5.8 1.3 - - - +
128E PRO* 3.3 14.3 - - - +
132E GLU* 2.6 32.6 + - - +
139E ALA* 1.3 72.2 - - - +
141E LEU* 1.3 72.7 + - - +
142E VAL* 4.3 3.4 - - + -
191E ARG* 3.9 19.7 - - + -
192E LEU 3.5 7.0 - - - +
193E ARG* 3.1 22.5 + - + +
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Residues in contact with LEU 141 (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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125E VAL* 4.3 12.1 - - + -
126E PHE 3.5 8.1 - - - +
127E GLU* 5.6 0.2 - - - -
128E PRO* 3.8 19.1 - - + -
139E ALA 4.1 8.5 - - - +
140E THR* 1.3 77.6 - - - +
142E VAL* 1.3 61.5 + - - +
157E TRP* 3.9 20.6 - - + -
191E ARG* 3.3 5.2 - - - -
192E LEU* 2.7 46.1 + - + +
194E VAL* 4.4 10.8 - - + -
199E TRP* 4.0 21.1 - - + -
206E PHE* 3.6 42.2 - - + -
237E ALA* 4.7 1.8 - - + -
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Residues in contact with VAL 142 (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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126D LEU* 3.5 17.5 - - + -
136D VAL* 3.4 21.3 - - + -
138D LEU* 4.2 21.8 - - + -
177D VAL* 4.3 15.9 - - + -
125E VAL* 3.4 2.3 - - - +
126E PHE* 2.7 64.5 + - + -
140E THR* 4.3 2.5 - - + -
141E LEU* 1.3 79.9 - - - +
143E CYS* 1.3 61.6 + - - +
144E LEU* 5.8 1.8 - - + -
157E TRP* 4.2 2.7 - - - -
189E SER* 6.3 0.7 - - - -
190E SER 3.3 10.1 - - - +
191E ARG* 4.3 4.9 - - + -
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Residues in contact with CYS 143 (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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123E VAL* 3.6 18.6 - - - -
124E ALA 3.4 5.4 - - - -
125E VAL* 4.5 0.7 - - - +
142E VAL* 1.3 74.2 - - - +
144E LEU* 1.3 67.6 + - - +
145E ALA 4.8 0.4 - - - -
155E LEU* 4.2 8.4 - - - +
157E TRP* 3.5 18.1 - - + -
188E LEU 3.9 0.3 - - - +
189E SER* 3.3 6.6 - - - -
190E SER* 2.8 35.7 + - - +
208E CYS* 2.0 50.7 - - + -
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Residues in contact with LEU 144 (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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136D VAL* 3.4 27.6 - - + -
177D VAL* 4.5 6.5 - - + -
179D TRP* 3.7 50.3 - - + +
122E GLU 3.5 1.7 - - - +
123E VAL* 3.3 4.5 - - - +
124E ALA* 2.9 32.2 + - + +
126E PHE* 3.7 22.4 - - + -
142E VAL* 4.2 2.9 - - + -
143E CYS* 1.3 77.6 - - - +
145E ALA* 1.3 60.1 + - - +
146E THR* 3.9 13.2 + - + +
188E LEU 3.6 1.6 - - - +
189E SER* 3.5 28.9 - - - -
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Residues in contact with ALA 145 (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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121E PRO* 4.4 7.6 - - + -
122E GLU 3.4 6.5 - - - +
123E VAL* 4.5 1.3 - - - -
143E CYS* 4.2 0.8 - - - -
144E LEU* 1.3 72.5 - - - +
146E THR* 1.3 60.1 + - - +
148E PHE* 3.5 16.8 - - + -
153E VAL* 5.9 0.2 - - + -
155E LEU* 4.8 5.4 - - + +
187E ALA* 3.1 4.0 - - - -
188E LEU* 2.7 46.9 + - + +
210E VAL* 4.0 28.9 - - + -
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Residues in contact with THR 146 (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* 4.3 17.3 - - + +
120E PRO 4.3 0.5 - - - +
121E PRO* 3.5 0.9 - - - +
122E GLU* 2.9 55.9 + - - +
144E LEU* 4.2 21.5 + - + +
145E ALA* 1.3 80.2 - - - +
147E GLY* 1.3 64.2 - - - +
148E PHE* 3.4 5.2 + - - -
177E GLU* 3.5 10.3 - - - +
186E TYR 3.6 4.0 - - - -
187E ALA* 4.1 8.7 - - + +
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Residues in contact with GLY 147 (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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119E PHE* 3.3 9.7 - - - +
120E PRO 3.7 3.4 - - - +
146E THR* 1.3 72.2 - - - +
148E PHE* 1.3 55.2 + - - -
177E GLU* 2.9 26.3 + - - -
185E ARG* 2.8 43.4 + - - -
186E TYR 2.9 9.8 + - - -
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Residues in contact with PHE 148 (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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119E PHE 3.2 11.9 - - - +
120E PRO 4.1 0.7 - - - -
121E PRO* 3.7 34.8 - - + -
145E ALA* 3.5 30.7 - - + -
146E THR 4.1 0.9 - - - -
147E GLY* 1.3 78.9 - - - +
149E TYR* 1.3 63.8 + - - +
150E PRO 3.6 13.7 - - - -
151E ASP* 3.8 14.8 - - - -
153E VAL* 3.7 34.5 - - + -
174E PRO* 4.1 5.4 - - + -
185E ARG* 3.4 0.7 - - - -
186E TYR* 2.7 68.4 + - + -
187E ALA* 3.8 1.3 - - - -
188E LEU* 3.9 14.4 - - + -
212E PHE* 4.3 3.1 - - + -
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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