Contacts of the strand formed by residues 142 - 149 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C PHE* 3.4 8.4 - - - -
137C ASN* 2.8 36.5 + - - -
140C SER* 2.4 37.4 + - - +
141C GLN* 1.3 80.5 - - - +
143C PHE* 1.3 65.7 + - - +
159C ALA* 4.9 10.9 - - + +
160C PHE 3.6 13.2 - - - +
161C ASP* 3.8 21.5 - - - +
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 4.1 14.1 - - + -
135C GLU 3.2 11.2 - - - +
136C PHE* 3.5 28.5 - + + -
137C ASN* 4.3 0.2 - - - -
142C THR* 1.3 76.6 - - - +
144C THR* 1.3 61.6 + - - +
145C VAL* 4.0 2.0 + - + -
158C ALA 3.6 0.9 - - - +
159C ALA* 3.2 5.5 - - - +
160C PHE* 2.7 51.4 + - + +
161C ASP 3.6 18.8 - - - -
162C TYR* 4.1 1.1 - - - -
163C VAL* 3.6 29.2 - - + -
290C LEU* 3.9 16.2 - - + -
312C ASN* 4.0 7.2 - - - -
314C LYS* 3.7 37.9 - - + -
315C PHE* 3.9 20.2 - + + -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C HIS 3.7 1.7 - - - +
134C VAL* 3.4 3.1 - - - -
135C GLU* 2.7 44.3 + - + +
137C ASN* 3.1 22.0 + - - +
143C PHE* 1.3 73.6 + - - +
145C VAL* 1.3 62.8 + - - +
146C THR* 4.1 6.7 + - - +
157C SER* 4.0 24.5 - - - +
158C ALA 3.5 7.1 + - - +
159C ALA* 5.1 4.3 - - - +
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 4.4 4.3 - - + -
13C LEU* 4.6 4.5 - - + -
42C PHE* 4.1 15.2 - - + -
131C VAL* 4.3 7.4 - - + -
133C HIS 3.5 7.4 - - - +
134C VAL* 4.2 20.4 - - + -
143C PHE* 4.7 2.0 - - + -
144C THR* 1.3 76.8 - - - +
146C THR* 1.3 63.0 + - - +
147C VAL* 3.9 22.4 + - + +
156C TYR* 3.9 0.5 - - - +
157C SER* 3.1 3.8 - - - -
158C ALA* 2.9 30.7 + - - +
160C PHE* 3.6 31.2 - - + -
163C VAL* 4.3 17.7 - - + -
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Residues in contact with THR 146 (chain C).
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* 5.2 5.4 + - + +
287B ASN* 3.9 16.4 + - - +
131C VAL* 3.8 1.2 - - - +
132C ARG* 2.8 32.2 + - + -
133C HIS* 2.9 30.1 + - + +
144C THR* 4.5 6.9 + - - +
145C VAL* 1.3 73.7 - - - +
147C VAL* 1.3 66.6 + - - +
155C ILE* 3.7 23.3 - - + -
156C TYR 3.4 13.0 - - - +
157C SER* 3.6 11.5 - - - -
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.8 28.0 - - + -
129C THR* 3.6 16.2 - - + -
130C ALA 3.1 12.8 - - - +
131C VAL* 4.1 7.2 - - + -
132C ARG* 4.2 5.4 - - - +
145C VAL* 3.9 19.1 - - + +
146C THR* 1.3 80.4 - - - +
148C GLN* 1.3 59.2 + - - +
154C THR 3.9 0.3 - - - +
155C ILE* 3.4 5.4 - - - +
156C TYR* 2.9 65.4 + - + +
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B HIS* 4.7 8.9 + - - -
283B PHE 5.7 0.5 - - - +
284B PRO* 5.2 2.9 - - - +
291B ARG* 3.2 19.8 + - - +
129C THR* 3.3 4.8 - - - -
130C ALA 2.8 32.7 + - - +
132C ARG* 3.1 38.0 + - - +
147C VAL* 1.3 74.1 - - - +
149C ASP* 1.3 65.2 + - - +
150C HIS* 3.3 30.1 + - + +
153C ASP* 3.2 24.5 + - - +
154C THR 3.5 5.6 - - - +
155C ILE* 3.9 20.4 - - + +
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Residues in contact with ASP 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE 4.6 1.9 - - - +
128C ASN 3.8 6.9 - - - +
129C THR* 4.1 13.0 + - - +
147C VAL 4.1 1.2 + - - -
148C GLN* 1.3 70.8 - - - +
150C HIS* 1.3 58.8 + - - +
151C THR* 2.9 28.8 + - - -
152C THR* 3.1 30.9 + - - +
153C ASP* 2.7 24.8 + - - -
154C THR* 2.8 19.2 + - - +
156C TYR* 4.1 20.8 - - + -
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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