Contacts of the strand formed by residues 166 - 172 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.8 18.8 - - + -
135A GLN* 4.0 6.2 - - - +
136A VAL* 3.1 27.1 - - + +
139A PHE* 3.5 22.4 - + + +
157A CYS* 3.3 40.2 - - + -
160A LEU* 3.7 10.7 + - + -
161A HIS* 2.9 50.0 + - + +
164A GLY* 3.4 1.1 - - - -
165A LYS* 1.3 79.7 + - - +
167A VAL* 1.3 60.3 + - - +
168A GLU 3.4 30.5 - - - -
169A LEU* 4.0 12.6 - - + -
192A ILE* 4.0 11.7 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLN* 3.4 32.3 - - + +
136A VAL 3.0 11.1 + - - +
137A ASP* 3.5 23.3 - - + +
161A HIS* 3.2 26.7 + - + -
166A PHE* 1.3 73.0 - - - +
168A GLU* 1.3 70.6 + - + +
192A ILE* 3.7 5.0 - - - +
155C HIS* 6.3 3.6 - - + +
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP 3.0 16.7 + - - +
138A LEU* 3.3 11.0 - - + +
139A PHE 2.8 31.2 + - - -
166A PHE* 3.4 8.4 - - - -
167A VAL* 1.3 86.6 - - + +
169A LEU* 1.3 55.1 + - - +
192A ILE* 4.6 1.6 - - - -
195A THR* 2.6 29.7 + - + +
196A VAL* 4.9 0.4 - - - -
222A ARG* 3.0 41.5 + - - -
155C HIS* 5.2 10.5 - - - -
159C ARG* 4.0 8.2 + - - -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.0 2.9 - - - +
139A PHE* 3.4 18.2 - - + +
141A LEU* 4.8 6.5 - - + -
154A LEU* 4.3 20.6 - - + -
157A CYS* 3.8 34.1 - - + -
166A PHE* 4.0 16.3 - - + -
168A GLU* 1.3 73.8 - - - +
170A GLY* 1.3 66.1 + - - +
171A LEU* 5.3 2.5 - - + -
192A ILE* 4.0 24.7 - - + +
193A LEU 4.1 4.7 + - - +
194A PRO* 3.9 31.9 - - + -
195A THR* 2.8 32.5 + - - -
196A VAL 3.6 1.6 + - - -
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Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.9 4.4 - - - +
139A PHE 2.8 13.0 + - - +
140A TYR* 3.3 19.5 - - - -
141A LEU 3.0 22.9 + - - -
169A LEU* 1.3 77.4 - - - +
171A LEU* 1.3 70.4 + - - +
194A PRO* 4.3 2.0 - - - -
196A VAL 3.2 13.0 - - - -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 3.7 4.1 - - - -
141A LEU* 3.7 28.9 - - + -
154A LEU* 5.2 2.0 - - + -
169A LEU* 5.3 2.2 - - + -
170A GLY* 1.3 82.4 - - - +
172A SER* 1.3 61.6 + - - +
174A TYR* 4.0 13.9 - - + -
179A VAL* 3.9 34.1 - - + -
182A ILE* 4.0 28.9 - - + -
194A PRO* 3.9 30.5 - - + -
196A VAL 3.0 6.9 + - - +
197A TYR* 3.3 16.6 - - + -
198A GLN 2.9 24.3 + - - -
221A LEU* 4.8 1.1 - - + -
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS* 5.1 1.1 - - - -
140A TYR* 4.5 6.3 - - - -
141A LEU 3.0 9.8 + - - -
142A HIS* 3.2 23.8 - - - +
143A ALA* 3.5 3.5 - - - -
171A LEU* 1.3 76.6 - - - +
173A ASN* 1.3 71.2 + - - +
174A TYR* 3.0 19.7 - - - -
197A TYR* 4.2 1.1 - - - -
198A GLN* 2.8 24.2 + - - -
1361A NDP 2.8 29.7 + - - -
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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