Contacts of the strand formed by residues 142 - 149 (chain B) in PDB entry 2XLR
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 THR 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE* 3.4 5.0 - - - -
137B ASN* 2.8 40.5 + - - -
140B SER* 2.5 37.2 + - - +
141B GLN* 1.3 77.8 - - - +
143B PHE* 1.3 69.0 + - - +
159B ALA* 4.9 10.5 - - + +
160B PHE 3.5 17.3 - - - +
161B ASP* 3.8 18.4 - - - +
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Residues in contact with PHE 143 (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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134B VAL* 4.1 20.4 - - + -
135B GLU 3.2 4.9 - - - +
136B PHE* 3.6 31.6 - + + -
137B ASN* 4.3 0.7 - - - -
142B THR* 1.3 77.5 - - - +
144B THR* 1.3 61.1 + - - +
145B VAL* 3.9 1.7 + - + -
158B ALA 3.7 0.5 - - - +
159B ALA* 3.3 5.4 - - - -
160B PHE* 2.7 50.2 + - + +
161B ASP 3.7 11.7 - - - -
162B TYR* 4.1 0.9 - - - -
163B VAL* 3.7 24.5 - - + -
290B LEU* 3.9 12.8 - - + -
312B ASN* 3.9 13.9 - - - -
314B LYS* 3.7 41.5 - - + -
315B PHE* 3.9 19.7 - + + -
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Residues in contact with THR 144 (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 HIS 3.6 1.7 - - - +
134B VAL* 3.4 3.5 - - - -
135B GLU* 2.7 47.0 + - - +
137B ASN* 3.1 22.4 + - - +
143B PHE* 1.3 73.8 - - - +
145B VAL* 1.3 61.4 + - - +
146B THR* 4.4 5.9 + - - +
157B SER* 3.9 26.7 - - - +
158B ALA 3.5 8.3 - - - +
159B ALA* 5.2 3.8 - - - +
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Residues in contact with VAL 145 (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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11B ALA* 4.4 4.0 - - + -
13B LEU* 4.6 4.0 - - + -
42B PHE* 4.0 15.9 - - + -
131B VAL* 4.4 7.4 - - + -
133B HIS 3.4 7.6 - - - +
134B VAL* 4.3 17.5 - - + -
143B PHE* 4.6 2.2 - - + +
144B THR* 1.3 76.0 - - - +
146B THR* 1.3 61.8 + - - +
147B VAL* 3.9 21.9 + - + +
156B TYR* 3.9 0.7 - - - +
157B SER* 3.2 3.8 - - - -
158B ALA* 2.9 32.7 + - - +
160B PHE* 3.5 27.4 - - + -
163B VAL* 4.3 20.6 - - + -
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Residues in contact with THR 146 (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 VAL* 3.9 0.9 - - - +
132B ARG* 2.7 39.0 + - + +
133B HIS* 2.8 31.4 + - + +
144B THR* 4.1 7.1 + - - +
145B VAL* 1.3 69.8 - - - +
147B VAL* 1.3 61.6 + - - +
155B ILE* 3.7 25.6 - - + -
156B TYR 3.4 9.9 - - - +
157B SER* 3.5 13.7 - - - -
133C HIS* 5.2 5.3 + - + +
287C ASN* 3.9 18.4 + - - +
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Residues in contact with VAL 147 (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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42B PHE* 4.0 22.9 - - + -
129B THR* 3.6 17.5 - - + -
130B ALA 3.2 13.2 - - - +
131B VAL* 4.1 7.6 - - + -
132B ARG* 4.2 5.6 - - - +
145B VAL* 3.9 22.7 - - + +
146B THR* 1.3 81.2 - - - +
148B GLN* 1.3 60.6 + - - +
154B THR 3.9 0.3 - - - +
155B ILE* 3.3 6.2 - - - +
156B TYR* 2.8 71.3 + - + +
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Residues in contact with GLN 148 (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* 4.1 2.5 - - - -
130B ALA 2.8 33.5 + - - +
132B ARG* 3.0 39.7 + - + +
147B VAL* 1.3 73.9 - - - +
149B ASP* 1.3 63.5 + - - +
150B HIS* 3.3 32.2 + - + +
153B ASP* 3.3 23.8 + - - -
154B THR 3.4 6.1 - - - +
155B ILE* 3.8 21.6 - - + +
282C HIS* 4.7 9.4 + - - -
284C PRO* 5.1 2.6 - - - +
291C ARG* 3.5 16.1 - - - +
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Residues in contact with ASP 149 (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 PHE 4.6 2.4 - - - +
128B ASN 3.8 7.0 - - - +
129B THR* 4.1 13.4 + - - +
147B VAL 4.0 1.4 - - - -
148B GLN* 1.3 71.0 - - - +
150B HIS* 1.3 50.7 + - - +
151B THR* 2.9 24.2 + - - -
152B THR* 3.0 29.0 + - - +
153B ASP* 2.7 31.1 + - - -
154B THR* 2.8 18.5 + - - +
156B TYR* 4.0 22.0 - - + -
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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