Contacts of the strand formed by residues 166 - 172 (chain D) in PDB entry 2BP1
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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.8 18.2 - - + -
135D GLN* 4.4 4.6 - - - +
136D VAL* 3.2 28.0 - - + -
139D PHE* 3.6 21.3 - + + -
157D CYS* 3.3 39.3 - - + -
160D LEU* 3.9 7.8 + - + -
161D HIS* 3.1 54.2 + - + +
164D GLY* 3.3 3.1 - - - -
165D LYS* 1.3 79.8 + - - +
167D VAL* 1.3 60.5 + - - +
168D GLU 3.1 32.8 - - - +
169D LEU* 3.8 16.8 - - + -
192D ILE* 4.1 4.0 - - + -
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Residues in contact with VAL 167 (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 GLN* 3.7 28.5 - - + +
136D VAL 3.0 12.9 + - - +
137D ASP* 3.5 21.8 - - + +
161D HIS* 3.1 28.0 + - + -
166D PHE* 1.3 72.9 - - - +
168D GLU* 1.3 73.2 + - + +
192D ILE* 3.6 4.2 - - - +
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Residues in contact with GLU 168 (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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137D ASP 3.1 12.6 + - - +
138D LEU* 3.4 10.9 - - + +
139D PHE 2.9 25.6 + - - -
166D PHE* 3.1 10.8 - - - -
167D VAL* 1.3 91.4 - - + +
169D LEU* 1.3 60.1 + - - +
192D ILE* 4.5 2.5 - - + -
195D THR* 2.5 32.6 + - + +
196D VAL* 4.0 0.6 - - - +
222D ARG* 2.9 41.0 + - - -
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Residues in contact with LEU 169 (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 3.5 - - - +
139D PHE* 3.4 18.2 - - + +
141D LEU* 4.6 7.9 - - + -
154D LEU* 4.7 13.5 - - + -
157D CYS* 3.9 33.0 - - + -
166D PHE* 3.8 15.4 - - + -
168D GLU* 1.3 74.2 - - - +
170D GLY* 1.3 67.9 + - - +
171D LEU* 5.6 1.3 - - + -
192D ILE* 3.8 35.2 - - + +
193D LEU 4.2 4.2 + - - +
194D PRO* 3.2 26.1 - - + +
195D THR* 2.8 32.6 + - - -
196D VAL 3.6 1.7 + - - -
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Residues in contact with GLY 170 (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* 3.8 8.8 - - - +
139D PHE 2.8 10.6 + - - +
140D TYR* 3.4 18.1 - - - -
141D LEU 3.1 20.6 + - - -
169D LEU* 1.3 78.9 - - - +
171D LEU* 1.3 69.0 + - - +
194D PRO* 4.5 2.0 - - - -
196D VAL 3.1 12.6 - - - -
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Residues in contact with LEU 171 (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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140D TYR* 3.8 4.2 - - - -
141D LEU* 3.8 23.6 - - + -
154D LEU* 5.4 1.1 - - + -
169D LEU* 5.6 1.6 - - + -
170D GLY* 1.3 80.4 - - - +
172D SER* 1.3 60.8 + - - +
174D TYR* 4.0 16.6 - - + -
179D VAL* 4.0 31.9 - - + -
182D ILE* 3.8 34.5 - - + -
194D PRO* 3.9 29.2 - - + -
196D VAL 3.0 6.8 + - - +
197D TYR* 3.3 17.7 - - + -
198D GLN 2.9 25.1 + - - -
221D LEU* 4.8 2.0 - - + -
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Residues in contact with SER 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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106D LYS* 5.1 1.3 - - - -
140D TYR* 4.4 5.8 - - - -
141D LEU 3.0 10.1 + - - +
142D HIS* 3.1 23.1 - - - +
143D ALA* 3.4 1.6 - - - -
171D LEU* 1.3 76.2 - - - +
173D ASN* 1.3 73.1 + - - +
174D TYR* 3.0 21.0 - - - -
197D TYR* 4.2 1.3 - - - -
198D GLN* 2.7 28.2 + - - -
1361D NDP 2.9 27.0 + - - -
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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