Contacts of the strand formed by residues 169 - 177 (chain A) in PDB entry 2QBW
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 ASP 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLU* 3.5 7.1 - - - +
141A THR* 3.0 36.7 + - + +
168A VAL* 1.3 77.1 - - - +
170A TYR* 1.3 59.2 + - - +
192A ASN* 6.1 2.2 - - + +
193A TYR 3.7 5.5 - - - +
194A ARG* 3.1 42.9 + - - +
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Residues in contact with TYR 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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120A LEU* 5.5 1.1 - - + -
138A TYR* 4.7 6.3 - + + -
139A GLY* 3.4 25.6 - - - -
140A GLU* 3.8 17.8 + - + +
141A THR* 3.2 6.5 + - - -
148A GLN* 6.0 1.3 - - - -
163A GLY 5.0 0.5 + - - -
164A LEU* 3.8 36.3 - - + +
165A LYS* 3.0 46.6 + - - +
168A VAL* 3.4 29.4 - - + -
169A ASP* 1.3 72.3 - - - +
171A THR* 1.3 59.4 + - - +
172A ILE* 4.1 16.4 + - + +
191A ILE 3.9 0.2 - - - +
192A ASN* 3.2 4.5 - - - -
193A TYR* 2.8 36.8 + - - +
195A THR* 4.2 11.0 - - + -
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Residues in contact with THR 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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137A THR* 3.8 0.9 + - - +
138A TYR* 3.4 5.4 - - - -
139A GLY 2.9 31.1 + - - -
141A THR* 2.8 26.5 + - - +
170A TYR* 1.3 71.8 - - - +
172A ILE* 1.3 63.1 + - - +
173A THR* 4.2 15.3 + - - +
190A SER* 4.4 9.2 - - - +
191A ILE 3.3 5.8 - - - +
192A ASN* 2.7 24.7 + - - +
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Residues in contact with ILE 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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110A LEU* 3.9 9.4 - - + +
120A LEU* 3.5 32.8 - - + -
122A ILE* 4.0 28.0 - - + -
136A ILE* 4.6 3.6 - - + -
137A THR 3.4 6.7 - - - +
138A TYR* 4.1 9.0 - - + -
161A ILE* 3.8 29.4 - - + -
164A LEU* 5.8 0.4 - - + -
170A TYR* 4.6 8.5 - - + +
171A THR* 1.3 76.8 - - - +
173A THR* 1.3 66.3 - - - +
190A SER* 3.0 4.2 - - - -
191A ILE* 2.8 48.5 + - + +
193A TYR* 4.8 7.2 - - + -
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Residues in contact with THR 173 (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 ARG 3.7 0.9 - - - +
136A ILE* 3.4 4.3 - - - +
137A THR* 2.9 48.2 + - - +
171A THR* 4.2 9.2 + - - +
172A ILE* 1.3 77.0 - - - +
174A VAL* 1.3 66.8 + - - +
175A TYR* 3.5 28.9 - - + +
188A PRO* 3.9 15.5 - - + -
189A ILE 3.3 13.2 - - - +
190A SER* 3.4 13.5 - - - -
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Residues in contact with VAL 174 (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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107A PRO* 3.6 27.6 - - + +
110A LEU* 3.9 31.2 - - + -
122A ILE* 4.2 14.6 - - + -
124A TRP* 4.2 11.0 - - + -
134A TYR* 3.9 19.7 - - + -
135A ARG 3.4 6.7 - - - +
136A ILE* 4.3 9.9 - - + -
172A ILE* 5.0 0.9 - - + -
173A THR* 1.3 77.0 - - - +
175A TYR* 1.3 64.1 + - - +
188A PRO* 3.4 5.0 - - - +
189A ILE* 2.9 39.2 + - + +
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Residues in contact with TYR 175 (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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134A TYR* 3.2 9.1 - - - +
135A ARG* 2.8 73.0 + - - +
137A THR* 3.8 19.0 + - + +
173A THR* 3.5 26.3 - - + +
174A VAL* 1.3 77.4 - - - +
176A ALA* 1.3 61.7 + - - +
177A TYR* 3.6 19.3 + - + -
185A HIS* 3.7 36.3 - + + -
186A TYR 5.6 0.2 - - - -
188A PRO* 3.8 22.1 - - + +
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Residues in contact with ALA 176 (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 VAL* 3.5 39.2 + - + +
131A VAL* 4.0 7.0 - - + -
133A TYR 3.9 4.9 - - - -
134A TYR* 3.7 24.0 - - + -
175A TYR* 1.3 72.9 - - - +
177A TYR* 1.3 60.8 + - - +
185A HIS* 3.2 4.9 - - - +
186A TYR* 3.1 33.9 + - + +
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Residues in contact with TYR 177 (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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131A VAL* 3.5 3.7 - - - -
132A SER* 2.6 32.2 + - - -
133A TYR* 3.0 53.5 + + + +
135A ARG* 3.0 45.4 + - + -
175A TYR* 3.6 22.3 - - + -
176A ALA* 1.3 74.9 - - - +
178A SER* 1.3 53.5 + - - +
179A ASP 3.8 4.0 - - - +
182A GLY* 3.3 36.1 - - - -
184A HIS 3.3 15.9 - - - +
185A HIS* 3.7 28.5 - + + -
186A TYR* 4.7 0.4 - - - -
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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