Contacts of the strand formed by residues 171 - 180 (chain D) 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 PHE 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ILE* 6.4 1.6 - - + -
118D ASN 6.0 2.0 - - - -
141D ASP* 4.6 6.3 - - - -
164D LEU* 5.2 0.4 - - + -
165D ASP* 3.4 6.6 + - - +
166D MET* 2.7 49.2 + - + +
169D MET* 3.1 19.9 - - + +
170D ASP* 1.3 78.0 - - - +
172D LYS* 1.3 73.0 + - - +
173D SER* 3.6 15.9 - - - -
138E LYS* 3.6 37.2 - - + +
193E ARG* 3.5 29.4 - - - -
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Residues in contact with LYS 172 (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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15D GLU* 2.8 35.5 + - - +
82D PRO* 4.0 13.0 - - + +
114D PRO* 3.8 24.5 - - + -
115D TYR 3.7 23.6 - - - +
116D ILE* 4.9 13.0 - - + +
163D VAL* 5.9 3.1 - - + -
164D LEU 3.3 12.1 - - - +
165D ASP* 3.7 21.3 + - - +
167D ARG* 5.9 4.5 - - - +
170D ASP 6.5 0.4 - - - -
171D PHE* 1.3 90.1 - - - +
173D SER* 1.3 64.7 + - - +
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Residues in contact with SER 173 (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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114D PRO* 6.2 1.3 - - - +
116D ILE* 5.3 5.8 - - - -
140D THR* 4.7 1.1 + - - -
141D ASP* 3.4 13.7 - - - +
162D CYS 3.6 0.7 - - - +
163D VAL* 3.4 3.0 - - - +
164D LEU* 2.9 53.8 + - - +
171D PHE* 3.6 6.2 - - - -
172D LYS* 1.3 78.8 - - - +
174D ASN* 1.3 65.6 + - - +
175D SER* 5.3 0.3 - - - -
193E ARG* 3.0 31.2 + - - -
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Residues in contact with ASN 174 (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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114D PRO* 3.9 8.2 - - - +
116D ILE* 3.4 23.4 - - - +
140D THR* 3.0 6.9 + - - -
141D ASP* 3.0 27.1 + - - +
142D PHE* 3.0 50.2 + - + +
143D ASP 4.2 5.9 - - - -
144D SER* 4.4 3.4 - - - +
161D LYS* 4.9 10.1 - - + +
162D CYS 3.3 5.3 - - - +
163D VAL* 2.9 34.0 - - - +
173D SER* 1.3 73.3 - - - +
175D SER* 1.3 62.6 + - - +
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Residues in contact with SER 175 (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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138D LEU* 3.9 13.2 - - - -
139D PHE 3.1 12.8 - - - -
140D THR* 3.7 9.9 - - - -
142D PHE* 3.9 4.7 - - - -
161D LYS* 3.3 1.2 - - - -
162D CYS 2.8 32.4 + - - +
164D LEU* 4.9 7.5 - - - +
173D SER 5.3 0.7 - - - -
174D ASN* 1.3 80.2 - - - +
176D ALA* 1.3 60.8 + - - +
140E THR* 6.0 1.3 - - - -
191E ARG* 2.7 43.9 + - - +
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Residues in contact with ALA 176 (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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138D LEU* 3.7 3.6 - - - +
139D PHE* 2.9 34.2 + - + +
142D PHE* 4.8 0.9 - - + -
148D VAL* 3.8 30.1 - - + -
159D THR* 3.6 24.2 - - - +
160D ASP 4.1 3.6 - - - +
161D LYS* 4.4 0.2 - - - -
175D SER* 1.3 74.9 - - - +
177D VAL* 1.3 64.5 + - - +
191D PHE* 3.9 10.1 - - + -
191E ARG* 3.7 0.9 - - - +
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Residues in contact with VAL 177 (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 VAL* 4.0 25.6 - - + -
137D CYS 3.5 8.5 - - - +
138D LEU* 4.0 17.0 - - + -
157D TYR 3.8 0.7 - - - +
158D ILE* 3.3 3.6 - - - +
159D THR* 2.8 44.0 + - + +
176D ALA* 1.3 78.5 - - - +
178D ALA* 1.3 63.5 + - - +
179D TRP* 4.1 14.9 - - + -
191D PHE* 4.3 2.2 - - - -
142E VAL* 4.3 14.1 - - + -
144E LEU* 4.5 7.2 - - + -
189E SER* 4.1 6.7 - - - +
190E SER 5.7 0.2 - - - +
191E ARG* 3.9 21.5 - - + +
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Residues in contact with ALA 178 (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 VAL* 3.6 1.0 - - - +
137D CYS* 2.8 39.0 + - + +
157D TYR 3.1 5.6 - - - -
158D ILE* 3.7 19.5 - - + -
177D VAL* 1.3 76.6 - - - +
179D TRP* 1.3 64.5 + - - +
185D PHE* 3.8 16.6 - - + -
190D ALA* 4.1 5.4 - - + -
191D PHE* 3.6 25.8 - - + -
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Residues in contact with TRP 179 (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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135D SER 4.1 7.6 - - - +
136D VAL* 3.9 16.6 - - + -
156D VAL* 3.8 1.2 - - - +
157D TYR* 3.0 79.4 + + + -
159D THR* 3.9 24.7 - - + -
177D VAL* 4.1 6.7 - - + -
178D ALA* 1.3 81.8 - - - +
180D SER* 1.3 67.9 + - - +
181D ASN* 5.1 3.8 + - - -
185D PHE* 3.8 11.1 - - - -
144E LEU* 3.7 43.1 - - + +
146E THR* 4.3 11.7 - - + +
175E LEU* 4.1 9.4 - - + -
177E GLU* 5.7 0.4 + - - -
187E ALA* 3.7 33.0 - - + -
188E LEU 5.2 0.4 - - - -
189E SER* 4.9 2.0 - - - -
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Residues in contact with SER 180 (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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135D SER 5.2 3.9 + - - +
155D ASP 3.0 20.9 + - - -
156D VAL* 3.9 6.4 - - - +
157D TYR* 4.6 1.6 - - - -
179D TRP* 1.3 87.1 - - - +
181D ASN* 1.3 74.5 + - - +
182D LYS* 2.9 25.8 + - - +
185D PHE* 3.7 34.7 - - - -
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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