Contacts of the strand formed by residues 142 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.5 5.0 - - - -
137A ASN* 2.9 36.1 + - - -
140A SER* 2.3 41.7 + - - +
141A GLN* 1.3 80.2 - - - +
143A PHE* 1.3 68.2 + - - +
159A ALA* 4.9 10.2 - - + +
160A PHE 3.5 13.9 - - - +
161A ASP* 3.7 23.1 - - - +
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Residues in contact with PHE 143 (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 VAL* 4.1 14.4 - - + -
135A GLU 3.2 11.7 - - - +
136A PHE* 3.6 28.9 - + + -
137A ASN* 4.2 0.4 - - - -
142A THR* 1.3 76.4 - - - +
144A THR* 1.3 61.5 + - - +
145A VAL* 3.8 1.2 + - + -
158A ALA 3.6 0.5 - - - +
159A ALA* 3.3 5.5 - - - -
160A PHE* 2.6 45.4 + - + +
161A ASP 3.7 17.3 - - - -
162A TYR* 4.1 1.1 - - - -
163A VAL* 3.6 28.5 - - + -
290A LEU* 4.0 12.8 - - + -
312A ASN* 3.9 12.1 - - - -
314A LYS* 3.7 38.1 - - + -
315A PHE* 3.9 22.0 - + + -
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Residues in contact with THR 144 (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 HIS 3.8 1.2 - - - +
134A VAL* 3.5 2.9 - - - -
135A GLU* 2.8 41.7 + - + +
137A ASN* 3.1 25.6 + - - +
143A PHE* 1.3 73.3 - - - +
145A VAL* 1.3 60.3 + - - +
146A THR* 4.2 6.9 + - - +
157A SER* 3.9 26.7 - - - +
158A ALA 3.5 7.4 - - - +
159A ALA* 5.2 4.0 - - - +
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Residues in contact with VAL 145 (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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11A ALA* 4.4 4.5 - - + -
13A LEU* 4.7 4.3 - - + -
42A PHE* 4.1 15.6 - - + -
131A VAL* 4.3 12.6 - - + -
133A HIS 3.5 6.7 - - - +
134A VAL* 4.1 15.9 - - + -
143A PHE* 4.7 1.8 - - + -
144A THR* 1.3 75.4 - - - +
146A THR* 1.3 62.5 + - - +
147A VAL* 3.8 22.5 + - + +
156A TYR* 3.9 0.5 - - - +
157A SER* 3.1 3.2 - - - -
158A ALA* 3.0 31.2 + - - +
160A PHE* 3.7 29.6 - - + -
163A VAL* 4.3 18.2 - - + -
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Residues in contact with THR 146 (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* 3.9 0.9 - - - +
132A ARG* 2.8 38.6 + - + +
133A HIS* 2.9 29.3 + - + +
144A THR* 4.4 7.4 + - - +
145A VAL* 1.3 70.0 - - - +
147A VAL* 1.3 59.4 + - - +
155A ILE* 3.7 27.1 - - + -
156A TYR 3.4 9.9 - - - +
157A SER* 3.5 13.6 - - - -
133D HIS* 5.4 3.8 + - + +
287D ASN* 3.7 17.9 + - - +
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Residues in contact with VAL 147 (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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42A PHE* 3.8 24.5 - - + -
129A THR* 3.6 15.9 - - + -
130A ALA 3.2 8.7 - - - +
131A VAL* 4.0 11.7 - - + -
132A ARG* 4.2 5.2 - - - +
145A VAL* 3.8 22.2 - - + +
146A THR* 1.3 79.9 - - - +
148A GLN* 1.3 60.1 + - - +
154A THR 3.9 0.3 - - - +
155A ILE* 3.3 6.0 - - - +
156A TYR* 2.9 72.4 + - + +
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Residues in contact with GLN 148 (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 5.6 - - - -
130A ALA 2.7 36.8 + - - +
132A ARG* 3.1 40.0 + - - +
147A VAL* 1.3 73.3 - - - +
149A ASP* 1.3 64.6 + - - +
150A HIS* 3.3 31.0 + - + +
153A ASP* 3.3 24.0 + - - +
154A THR 3.5 5.6 - - - +
155A ILE* 3.8 21.0 - - + +
282D HIS* 4.8 8.8 + - - -
284D PRO* 5.2 2.4 - - - +
291D ARG* 3.5 18.4 - - - +
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Residues in contact with ASP 149 (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 PHE 4.5 1.7 - - - +
128A ASN 3.8 7.4 - - - +
129A THR* 4.0 13.6 + - - +
147A VAL 4.1 1.0 - - - -
148A GLN* 1.3 71.2 - - - +
150A HIS* 1.3 50.9 + - - +
151A THR* 3.1 23.2 + - - -
152A THR* 3.0 32.1 + - - +
153A ASP* 2.7 31.2 + - - -
154A THR 2.8 18.5 + - - +
156A TYR* 4.1 21.3 - - + +
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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