Contacts of the strand formed by residues 142 - 149 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D PHE* 3.4 8.1 - - - -
137D ASN* 2.9 36.1 + - - -
140D SER* 2.5 37.3 + - - +
141D GLN* 1.3 81.9 - - - +
143D PHE* 1.3 66.3 + - - +
159D ALA* 4.9 10.7 - - + +
160D PHE 3.5 13.2 - - - +
161D ASP* 3.7 22.0 - - - +
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Residues in contact with PHE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 4.0 18.2 - - + -
135D GLU 3.2 4.9 - - - +
136D PHE* 3.6 31.4 - + + -
137D ASN* 4.3 0.4 - - - -
142D THR* 1.3 77.7 - - - +
144D THR* 1.3 61.4 + - - +
145D VAL* 4.0 2.4 + - + -
158D ALA 3.7 0.9 - - - +
159D ALA* 3.3 6.1 - - - +
160D PHE* 2.7 50.6 + - + +
161D ASP 3.7 19.7 - - - -
162D TYR* 4.1 1.1 - - - -
163D VAL* 3.6 26.9 - - + -
290D LEU* 4.0 11.4 - - + -
312D ASN* 4.0 9.6 - - - -
314D LYS* 3.7 37.9 - - + -
315D PHE* 3.8 21.5 - + + -
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D HIS 3.7 1.7 - - - +
134D VAL* 3.4 3.8 - - - -
135D GLU* 2.8 42.4 + - - +
137D ASN* 3.1 23.7 + - - +
143D PHE* 1.3 72.6 + - - +
145D VAL* 1.3 62.7 + - - +
146D THR* 4.1 6.1 + - - +
157D SER* 3.9 26.7 - - - +
158D ALA 3.6 7.0 - - - +
159D ALA* 5.2 4.2 - - - +
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA* 4.4 9.0 - - + -
13D LEU* 4.7 4.7 - - + -
42D PHE* 4.1 14.3 - - + -
131D VAL* 4.3 7.6 - - + -
133D HIS 3.4 8.1 - - - +
134D VAL* 4.2 24.5 - - + -
143D PHE* 4.7 1.8 - - + -
144D THR* 1.3 77.2 - - - +
146D THR* 1.3 63.6 + - - +
147D VAL* 3.8 22.7 + - + +
156D TYR 3.8 0.2 - - - +
157D SER* 3.0 22.6 - - - -
158D ALA* 2.9 12.1 + - - +
160D PHE* 3.6 31.0 - - + -
163D VAL* 4.5 8.3 - - + -
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Residues in contact with THR 146 (chain D).
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* 5.3 4.9 + - + +
287A ASN* 3.8 17.2 + - - +
131D VAL* 3.8 1.0 - - - +
132D ARG* 2.8 32.2 + - + -
133D HIS* 2.9 29.0 + - + +
144D THR* 4.5 6.9 + - - +
145D VAL* 1.3 74.2 - - - +
147D VAL* 1.3 67.1 + - - +
155D ILE* 3.7 26.2 - - + -
156D TYR 3.3 8.7 - - - +
157D SER* 3.6 11.7 - - - -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.9 25.1 - - + -
129D THR* 3.6 16.8 - - + -
130D ALA 3.2 13.2 - - - +
131D VAL* 4.2 5.6 - - - -
132D ARG* 4.2 4.7 - - - +
145D VAL* 3.8 23.1 - - + +
146D THR* 1.3 82.4 - - - +
148D GLN* 1.3 58.8 + - - +
154D THR 3.9 0.7 - - - +
155D ILE* 3.3 4.7 - - - +
156D TYR* 2.8 73.0 + - + +
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A HIS* 4.8 8.3 + - - -
284A PRO* 5.4 2.3 - - - +
291A ARG* 3.3 19.6 - - - +
128D ASN 3.9 0.2 - - - +
129D THR* 3.4 4.5 - - - -
130D ALA 2.8 37.1 + - - +
132D ARG* 3.2 38.7 + - + +
147D VAL* 1.3 72.8 - - - +
149D ASP* 1.3 63.2 + - - +
150D HIS* 3.2 30.4 + - + +
153D ASP* 3.2 24.5 + - - +
154D THR 3.4 5.6 - - - +
155D ILE* 3.8 21.9 - - + +
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PHE 4.5 2.1 - - - +
128D ASN 3.8 7.5 - - - +
129D THR* 3.9 13.6 + - - +
147D VAL 4.0 1.2 + - - -
148D GLN* 1.3 70.3 - - - +
150D HIS* 1.3 51.9 + - - +
151D THR* 3.0 22.6 + - - -
152D THR* 3.0 31.9 + - - +
153D ASP* 2.7 30.7 + - - -
154D THR* 2.7 19.7 + - - +
156D TYR* 4.0 21.9 - - + -
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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