Contacts of the strand formed by residues 181 - 188 (chain A) in PDB entry 2QBX
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 GLY 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.7 12.1 - - - -
86A ILE 3.1 14.1 - - - -
88A ARG 3.9 5.4 - - - -
125A GLU* 3.4 6.8 - - - +
126A ALA 3.0 24.0 + - - +
177A VAL* 5.7 0.4 - - - -
179A ARG* 2.9 6.6 + - - +
180A SER* 1.3 84.6 + - - +
182A PHE* 1.3 67.9 + - - +
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Residues in contact with PHE 182 (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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31A LEU* 4.4 2.0 - - + -
85A PHE* 3.7 4.8 - - - -
86A ILE* 2.7 78.1 + - + +
87A ARG 4.4 7.4 - - - -
88A ARG* 4.4 6.7 - - + -
94A ILE* 3.8 41.7 - - + -
123A TYR* 5.0 2.5 - - + -
124A TYR 3.3 16.2 - - - +
125A GLU* 3.9 12.1 - - + +
126A ALA 4.6 0.9 - - - +
174A PHE* 4.2 6.7 - + - -
177A VAL* 4.1 15.7 - - + -
181A GLY* 1.3 78.6 - - - +
183A TYR* 1.3 67.3 + - - +
184A LEU* 3.9 20.2 - - + -
200A VAL* 3.8 18.2 - - + -
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Residues in contact with TYR 183 (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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82A ARG* 4.2 8.1 - - + -
83A THR* 3.4 24.9 - - - +
84A LYS* 4.1 0.9 - - - -
85A PHE* 3.5 38.1 - + + -
86A ILE* 4.9 0.2 - - - -
123A TYR* 3.2 8.8 - - - +
124A TYR* 2.8 53.1 + + - +
126A ALA* 4.3 14.4 - - + -
129A ASP* 2.5 25.9 + - - -
130A SER* 3.1 6.0 + - - -
131A ALA* 2.8 41.4 + - + +
136A PRO* 5.4 1.3 - - + -
143A TRP* 3.5 21.3 - + + -
182A PHE* 1.3 74.7 - - - +
184A LEU* 1.4 64.1 + - - +
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Residues in contact with LEU 184 (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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82A ARG* 3.3 8.7 - - - +
83A THR* 3.1 45.5 + - + -
86A ILE* 4.3 6.5 - - + -
96A VAL* 3.6 33.0 - - + -
121A LEU* 4.4 4.9 - - + -
122A TYR 3.3 7.2 - - - +
123A TYR* 3.9 13.5 - - + -
143A TRP* 3.6 2.2 - - - -
174A PHE* 4.0 13.5 - - + -
182A PHE* 3.9 17.7 - - + -
183A TYR* 1.4 81.6 - - - +
185A ALA* 1.3 60.4 + - - +
186A PHE* 4.1 11.4 - - + -
198A VAL* 4.1 9.4 - - + -
200A VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 185 (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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80A TRP* 3.5 37.2 - - + -
81A LEU 3.1 9.9 - - - +
82A ARG* 4.9 0.4 - - + -
120A ASN 3.8 0.3 - - - +
121A LEU* 3.3 9.2 - - - +
122A TYR* 2.9 34.7 + - + -
143A TRP* 3.6 20.6 - - + -
184A LEU* 1.3 75.0 - - - +
186A PHE* 1.3 66.1 + - - +
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Residues in contact with PHE 186 (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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43A TRP* 4.2 5.4 - + - -
51A TRP* 3.4 23.4 + - + -
80A TRP* 3.5 1.7 - - - +
81A LEU* 2.8 50.6 + - + +
83A THR* 3.9 23.6 - - + -
98A MET* 4.3 17.3 - - + -
119A PHE* 4.1 17.5 - + + -
120A ASN 3.4 5.4 - - - +
121A LEU* 3.5 30.3 - - + -
184A LEU* 4.1 10.5 - - + -
185A ALA* 1.3 75.3 - - - +
187A GLN* 1.3 60.3 + - - +
195A LEU* 3.8 26.2 - - + -
198A VAL* 3.9 25.6 - - + -
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Residues in contact with GLN 187 (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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51A TRP* 4.6 1.3 - - - -
78A ASN* 3.0 30.3 + - - +
79A ASN 3.3 3.8 - - - -
80A TRP* 3.6 30.3 - - + +
119A PHE* 3.4 9.5 - - - +
120A ASN* 2.9 44.8 + - + +
122A TYR* 2.5 42.2 + - + -
185A ALA 4.2 0.4 - - - -
186A PHE* 1.3 73.5 - - - +
188A ASP* 1.3 63.6 + - - +
189A TYR* 3.7 14.1 - - + +
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Residues in contact with ASP 188 (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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51A TRP* 4.0 10.4 - - + +
69A VAL* 3.6 30.9 - - + +
71A ASN 5.3 1.4 + - - -
77A GLN* 4.4 0.3 - - - +
78A ASN* 3.5 2.9 - - - -
79A ASN* 2.8 62.5 + - + +
118A THR 4.9 1.5 - - - +
119A PHE* 4.8 2.9 - - - -
187A GLN* 1.3 76.0 - - - +
189A TYR* 1.3 66.8 + - - +
190A GLY* 3.2 9.6 + - - -
191A GLY* 2.7 34.9 + - - +
193A MET* 3.7 11.6 - - + +
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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