Contacts of the strand formed by residues 161 - 167 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL 3.6 2.9 - - - -
135B LEU* 4.8 16.5 - - + +
156B ARG* 4.2 0.2 - - - -
157B ASN* 3.3 32.7 + - + +
158B ALA* 2.9 38.4 + - - +
159B ALA 4.7 3.5 - - - +
160B GLY* 1.3 83.0 - - - +
162B ILE* 1.3 67.4 + - - +
277B ILE* 4.2 25.0 - - - +
280B ARG* 5.1 10.6 - - - -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA* 3.6 1.2 - - - -
134B VAL* 2.6 46.1 + - + +
136B GLY 6.1 0.4 - - - +
139B GLU* 4.9 15.0 - - + -
142B VAL* 3.9 35.9 - - + -
143B LEU* 4.6 9.4 - - + -
146B LEU* 4.4 7.6 - - + -
153B PRO* 4.2 15.7 - - + -
155B ASN 3.5 10.8 - - - +
156B ARG* 3.7 26.7 - - + +
157B ASN* 5.5 0.2 - - - +
158B ALA 5.5 1.3 - - - +
160B GLY 5.1 2.7 - - - +
161B GLN* 1.3 80.6 - - - +
163B VAL* 1.3 72.5 + - - +
164B ALA 4.6 0.4 - - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B MET* 3.8 31.2 - - + -
132B SER 3.4 9.4 - - - +
133B ALA* 4.4 4.7 - - + -
153B PRO* 3.3 4.2 - - - +
154B ALA* 2.8 33.2 + - + -
155B ASN* 2.9 43.1 + - + +
157B ASN* 4.1 10.1 - - - +
162B ILE* 1.3 77.5 - - - +
164B ALA* 1.3 64.3 + - - +
187B LEU* 3.9 23.8 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B MET* 3.2 7.1 - - - +
132B SER 2.7 35.5 + - - +
134B VAL* 4.3 9.6 - - + -
146B LEU* 3.6 34.5 - - + -
151B LEU* 4.1 11.9 - - + -
152B VAL 3.6 4.7 - - - -
162B ILE* 3.9 2.4 + - - +
163B VAL* 1.3 72.7 - - - +
165B ALA* 1.3 62.5 + - - +
171B LEU* 3.9 7.6 - - + +
174B LEU* 4.4 3.1 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 3.6 10.8 - - - +
131B MET* 4.0 6.5 - - + -
150B ASP 4.1 0.3 - - - +
151B LEU* 3.3 11.7 - - - +
152B VAL* 2.8 33.9 + - - +
154B ALA* 3.7 25.1 - - + -
164B ALA* 1.3 78.0 - - - +
166B GLY* 1.3 58.9 + - - +
171B LEU* 4.3 1.7 - - - +
192B ALA* 4.0 5.4 - - + -
193B PHE 4.1 0.9 - - - +
195B THR* 3.7 18.5 - - + +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR* 3.3 8.6 - - - -
130B GLY 3.1 31.0 + - - +
150B ASP 4.4 4.0 - - - -
151B LEU* 3.9 7.8 - - - +
165B ALA* 1.3 76.3 - - - +
167B ARG* 1.3 64.6 + - - -
171B LEU* 3.4 3.2 - - - +
192B ALA* 3.5 9.0 - - - +
195B THR* 5.4 0.4 - - - -
197B PHE* 3.9 13.7 - - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 3.2 36.8 + - - -
128B PRO* 3.7 11.9 - - - +
129B THR* 4.0 7.0 - - + -
150B ASP* 4.9 16.4 + - - +
151B LEU* 4.5 0.2 - - - +
166B GLY* 1.3 74.7 - - - -
168B LEU* 1.3 53.5 + - - +
169B THR* 3.3 9.0 - - - +
170B ALA* 3.1 21.6 + - + +
171B LEU* 2.8 32.3 + - - +
197B PHE* 3.6 29.8 - - + -
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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