Contacts of the strand formed by residues 127 - 136 (chain C) in PDB entry 1L9X
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 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C LEU 4.4 0.3 + - - -
126C LEU* 1.3 76.4 + - - +
128C ALA* 1.3 78.2 + - + +
129C THR* 3.7 1.7 - - - +
173C TRP* 3.3 8.1 - - - -
174C SER 2.8 33.3 + - - -
176C SER* 4.3 6.2 - - - -
179C ASN* 3.7 18.2 + - - -
201C ILE* 3.9 28.3 - - + -
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Residues in contact with ALA 128 (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 THR* 1.3 84.4 - - + +
129C THR* 1.3 64.7 + - - +
172C LYS 3.4 10.3 - - - +
173C TRP* 3.4 24.5 - - + -
198C ASP* 4.5 1.4 - - - +
200C LYS* 6.1 0.7 - - - +
201C ILE* 5.1 0.5 - - - +
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Residues in contact with THR 129 (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 THR 3.4 2.9 + - - +
128C ALA* 1.3 79.9 - - - +
130C ASP* 1.3 58.4 + - - +
131C THR* 2.7 29.9 + - - -
132C VAL* 4.9 1.4 + - - +
171C HIS 4.0 1.2 - - - +
172C LYS* 2.9 22.1 + - - +
173C TRP 3.8 1.6 - - - -
174C SER* 2.7 40.1 + - - +
198C ASP* 3.3 18.6 - - - +
201C ILE* 3.7 24.5 - - + -
203C PHE* 4.5 3.4 - - + -
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Residues in contact with ASP 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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129C THR* 1.3 68.1 - - - +
131C THR* 1.3 63.6 + - - +
132C VAL* 3.7 4.0 + - - +
134C VAL* 4.8 4.5 - - - +
136C MET* 5.1 0.9 - - - +
198C ASP* 3.1 29.6 + - - +
200C LYS* 5.2 11.6 - - - +
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Residues in contact with THR 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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129C THR* 2.7 21.8 + - - +
130C ASP* 1.3 80.9 - - - +
132C VAL* 1.3 59.8 + - - +
133C ASP 4.0 0.2 - - - -
134C VAL* 4.0 9.9 - - - -
136C MET* 3.6 24.9 - - + -
169C ASN* 3.2 14.1 - - - +
171C HIS* 2.6 52.0 + - - -
198C ASP* 3.7 17.9 - - + -
203C PHE* 3.7 16.2 - - + -
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Residues in contact with VAL 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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129C THR 5.2 0.9 - - - +
130C ASP* 3.7 3.7 + - - +
131C THR* 1.3 78.4 - - - +
133C ASP* 1.3 76.9 + - + +
134C VAL* 4.7 1.6 - - - +
169C ASN 4.0 0.7 - - - -
170C PHE* 4.1 13.2 - - + +
171C HIS* 3.4 27.1 - - - +
172C LYS* 3.6 26.0 - - + -
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Residues in contact with ASP 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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132C VAL* 1.3 85.1 - - + +
134C VAL* 1.3 56.8 + - - +
169C ASN 2.8 10.9 + - - -
170C PHE* 3.4 30.7 - - + -
231C LEU* 3.5 21.3 - - + +
232C ASP* 4.2 13.2 + - - +
233C GLY* 2.7 33.7 + - - -
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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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130C ASP 4.8 2.5 - - - +
131C THR* 4.0 16.8 - - - -
132C VAL 4.5 1.8 - - - +
133C ASP* 1.3 76.4 - - - +
135C ALA* 1.3 71.0 + - - +
136C MET* 3.5 34.8 - - + -
167C THR 3.6 0.5 - - - +
169C ASN* 2.9 37.9 + - + +
232C ASP 5.2 0.4 - - - -
233C GLY* 3.5 7.2 - - - -
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Residues in contact with ALA 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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134C VAL* 1.3 79.6 - - - +
136C MET* 1.3 62.0 + - - +
137C PRO* 4.7 0.5 - - - +
165C PRO* 3.5 35.1 - - + +
167C THR 3.3 7.6 - - - +
232C ASP 4.0 13.1 + - - +
233C GLY* 3.7 17.6 - - - +
234C ILE 5.0 0.2 - - - -
235C SER* 4.6 9.2 - - - +
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Residues in contact with MET 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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130C ASP 5.1 0.9 - - - +
131C THR* 3.6 26.0 - - + -
134C VAL* 3.5 33.7 - - + -
135C ALA* 1.3 79.3 - - - +
137C PRO* 1.3 78.0 - - + +
165C PRO* 3.7 5.8 - - - -
166C LEU 3.3 1.0 + - - -
167C THR* 2.6 41.3 + - - +
169C ASN* 3.7 23.6 - - - +
196C ASN* 3.7 27.6 - - - +
197C THR 3.7 17.9 - - - +
198C ASP* 5.0 1.3 - - - -
203C PHE* 4.3 0.7 - - + -
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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