Contacts of the strand formed by residues 161 - 167 (chain A) in PDB entry 2QJ3
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 GLN 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL 4.2 1.8 - - - -
135A LEU* 5.3 13.7 - - + +
157A ASN* 3.1 44.4 + - + +
158A ALA* 3.4 30.4 + - + +
159A ALA 3.2 4.4 - - - +
160A GLY* 1.3 79.8 - - - +
162A ILE* 1.3 64.3 + - - +
273A THR* 6.2 1.6 - - - +
277A ILE* 4.4 12.7 - - - +
280A ARG* 3.1 34.5 + - - -
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Residues in contact with ILE 162 (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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133A ALA* 3.6 1.7 - - - +
134A VAL* 2.6 51.6 + - + +
136A GLY* 6.1 0.9 - - - -
139A GLU* 5.3 12.3 - - + +
142A VAL* 4.4 18.8 - - + -
143A LEU* 5.1 8.5 - - + -
146A LEU* 4.2 14.6 - - + -
153A PRO* 4.2 17.3 - - + -
155A ASN 3.5 6.1 - - - +
156A ARG* 3.9 26.2 - - + +
158A ALA 4.7 5.2 - - - +
160A GLY* 4.7 6.1 - - - +
161A GLN* 1.3 85.7 - - - +
163A VAL* 1.3 74.8 + - - +
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Residues in contact with VAL 163 (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 MET* 3.7 28.7 - - + -
132A SER 3.9 4.0 - - - +
133A ALA* 4.4 6.3 - - + -
153A PRO* 3.4 7.1 - - - +
154A ALA* 2.9 27.0 + - + -
155A ASN* 2.8 47.6 + - + +
157A ASN* 4.4 8.3 - - - +
162A ILE* 1.3 79.8 - - - +
164A ALA* 1.3 72.3 + - - +
187A LEU* 3.9 24.0 - - + -
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Residues in contact with ALA 164 (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 MET* 3.1 7.3 - - - +
132A SER 2.8 40.0 + - - +
134A VAL* 4.3 4.0 - - + +
146A LEU* 3.9 20.6 - - + -
151A LEU* 4.6 4.0 - - + -
152A VAL 3.4 4.5 - - - -
162A ILE 4.1 1.0 + - - -
163A VAL* 1.3 75.0 - - - +
165A ALA* 1.3 60.9 + - - +
171A LEU* 3.8 7.1 - - + +
174A LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 165 (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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130A GLY 3.4 5.6 - - - +
131A MET* 3.7 18.2 - - + -
151A LEU* 3.3 10.9 - - - -
152A VAL* 2.9 31.3 + - - +
154A ALA* 3.7 16.2 - - + -
164A ALA* 1.3 77.6 - - - +
166A GLY* 1.3 57.2 + - - +
171A LEU* 4.4 0.9 - - - -
192A ALA* 3.9 3.1 - - + -
193A PHE 4.1 1.1 - - - +
195A THR* 3.4 27.8 - - + +
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Residues in contact with GLY 166 (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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129A THR* 3.2 8.4 - - - -
130A GLY 2.9 31.1 + - - +
150A ASP 4.9 3.6 - - - -
151A LEU* 3.7 8.9 - - - +
165A ALA* 1.3 77.3 - - - +
167A ARG* 1.3 63.8 + - - -
171A LEU* 3.7 1.7 - - - +
192A ALA* 3.4 4.4 - - - +
197A PHE* 3.8 20.4 - - - -
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Residues in contact with ARG 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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127A GLU* 3.8 32.8 + - + +
128A PRO 3.7 8.5 - - - +
129A THR* 3.8 7.0 - - + -
150A ASP 5.4 1.4 + - - -
151A LEU* 4.2 3.4 - - - +
166A GLY* 1.3 72.4 - - - -
168A LEU* 1.3 66.2 + - - +
169A THR* 3.8 17.5 - - - +
170A ALA* 2.9 21.9 + - + +
171A LEU* 3.0 11.8 + - - +
197A PHE* 3.5 33.8 - - + -
185B ARG* 5.6 4.9 - - - +
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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