Contacts of the strand formed by residues 129 - 137 (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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.7 16.6 - - + +
43C GLU 2.9 26.1 + - - +
44C LYS* 3.3 3.0 + - - -
126C ARG* 3.7 21.7 + - + +
127C PHE 2.8 13.7 + - - -
128C ASN* 1.3 78.3 + - - +
130C ALA* 1.3 61.7 + - - +
147C VAL* 3.6 34.1 - - + -
148C GLN 3.3 9.9 - - - +
149C ASP* 4.1 12.9 + - - +
156C TYR* 4.5 5.2 + - - +
500C FAD 3.6 4.5 - - - -
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Residues in contact with ALA 130 (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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44C LYS* 4.0 11.7 - - + -
65C GLU* 3.5 36.6 - - - +
128C ASN 4.2 0.6 - - - -
129C THR* 1.3 73.0 - - - +
131C VAL* 1.3 63.1 + - - +
132C ARG* 3.5 10.4 + - - +
147C VAL* 3.1 5.2 - - - -
148C GLN* 2.8 37.2 + - - +
150C HIS* 4.0 7.1 - - - +
500C FAD 3.7 7.9 - - - +
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Residues in contact with VAL 131 (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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13C LEU* 4.0 21.3 - - + -
42C PHE* 3.7 27.4 - - + -
130C ALA* 1.3 73.1 - - - +
132C ARG* 1.3 69.2 + - - +
133C HIS 4.2 0.7 - - - +
134C VAL* 4.0 16.8 - - + -
145C VAL* 4.3 5.4 - - + -
146C THR 3.9 8.3 - - - +
147C VAL* 4.1 7.9 - - + -
285C PHE* 3.8 34.2 - - + +
500C FAD 2.9 40.7 + - + +
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Residues in contact with ARG 132 (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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132B ARG 5.6 2.6 - - - +
133B HIS* 6.5 0.4 - - + -
282B HIS* 4.5 7.1 - - - -
284B PRO* 3.3 39.5 + - - +
287B ASN* 6.1 0.2 - - - +
65C GLU* 2.3 45.4 + - - -
130C ALA* 4.0 12.4 - - - +
131C VAL* 1.3 80.8 + - - +
133C HIS* 1.3 65.0 + - + +
146C THR* 2.8 26.2 + - + +
147C VAL 4.4 2.7 - - - -
148C GLN* 3.1 37.0 + - + +
150C HIS* 4.0 1.6 + - - -
155C ILE* 5.2 9.1 - - + +
284C PRO 4.4 2.8 - - - +
285C PHE* 3.3 18.7 - - - +
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Residues in contact with HIS 133 (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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132B ARG* 6.5 1.3 - - + -
133B HIS* 2.9 44.8 - + + +
135B GLU* 5.0 0.4 - - - -
146B THR* 5.2 5.5 + - + -
131C VAL 3.8 0.6 - - - -
132C ARG* 1.3 84.1 + - + +
134C VAL* 1.3 78.4 + - - +
135C GLU* 3.4 35.0 + - + +
144C THR 3.7 1.2 - - - +
145C VAL* 3.5 0.9 - - - +
146C THR* 2.9 42.1 + - - +
285C PHE* 3.3 14.2 + - - +
287C ASN* 3.3 34.2 + - - -
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Residues in contact with VAL 134 (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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13C LEU* 4.5 9.6 - - + -
131C VAL* 4.0 18.8 - - + -
133C HIS* 1.3 89.1 + - - +
135C GLU* 1.3 68.7 + - - +
143C PHE* 4.1 23.1 - - + -
144C THR 3.4 6.3 - - - +
145C VAL* 4.2 20.0 - - + -
163C VAL* 4.6 2.9 - - + -
285C PHE* 2.8 11.7 + - + +
286C LEU* 3.6 31.4 - - + -
287C ASN* 4.6 4.0 + - - +
290C LEU* 4.3 12.6 - - + +
315C PHE* 4.4 7.2 - - + -
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Residues in contact with GLU 135 (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* 5.1 0.2 - - - -
135B GLU* 4.0 13.9 - - - +
133C HIS* 3.4 34.2 + - + +
134C VAL* 1.3 79.1 - - - +
136C PHE* 1.3 67.4 + - - +
137C ASN* 3.8 7.1 + - - +
142C THR 3.8 0.2 - - - +
143C PHE* 3.2 7.8 - - - -
144C THR* 2.7 49.1 + - - +
287C ASN* 4.4 12.6 + - - +
290C LEU* 5.0 1.8 - - - -
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Residues in contact with PHE 136 (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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135C GLU* 1.3 80.2 + - - +
137C ASN* 1.3 68.6 + - - +
138C GLU* 3.9 25.0 + - - +
141C GLN* 3.6 61.0 - - - -
142C THR 3.4 10.5 - - - -
143C PHE* 3.5 35.0 - + + -
289C ASP* 4.4 16.5 + - - +
290C LEU* 4.7 4.8 - - + +
312C ASN* 3.4 29.6 - - - +
314C LYS* 4.3 7.6 - - + -
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Residues in contact with ASN 137 (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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135C GLU* 4.5 10.0 - - - +
136C PHE* 1.3 78.3 - - - +
138C GLU* 1.3 60.6 + - - +
139C ASP* 3.2 5.6 - - + +
140C SER* 3.5 13.8 + - - +
141C GLN* 2.8 31.2 + - - -
142C THR* 2.8 34.0 + - - -
143C PHE 4.3 0.2 - - - -
144C THR* 3.1 29.4 + - - +
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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