Contacts of the strand formed by residues 127 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LEU* 1.3 76.4 + - - +
128A ALA* 1.3 67.3 + - - +
129A THR* 3.3 5.9 + - + +
173A TRP* 3.3 4.9 - - - -
174A SER 2.8 37.6 + - - -
176A SER* 3.7 22.7 + - - -
179A ASN* 3.8 11.4 + - - -
201A ILE* 3.3 39.0 - - + -
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Residues in contact with ALA 128 (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 THR* 1.3 81.1 - - - +
129A THR* 1.3 62.7 + - - +
172A LYS 3.4 10.1 - - - +
173A TRP* 3.5 27.2 - - + -
198A ASP* 4.5 0.3 - - - +
201A ILE* 3.6 8.1 - - - +
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Residues in contact with THR 129 (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 THR* 3.6 9.6 - - + +
128A ALA* 1.3 78.5 - - - +
130A ASP* 1.3 59.2 + - - +
131A THR* 2.8 32.5 + - - -
132A VAL* 5.0 1.4 - - - +
171A HIS 3.9 0.7 - - - +
172A LYS* 2.9 17.9 + - - +
173A TRP 3.8 5.9 - - - -
174A SER* 2.7 35.4 + - - +
198A ASP* 3.4 16.8 - - - +
201A ILE* 4.2 18.8 - - + -
203A PHE* 4.5 5.4 - - + -
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Residues in contact with ASP 130 (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* 1.3 67.2 - - - +
131A THR* 1.3 64.0 + - - +
132A VAL* 3.7 5.1 + - - +
134A VAL* 4.7 5.2 - - - +
198A ASP* 2.9 31.8 + - + +
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Residues in contact with THR 131 (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* 2.8 21.6 + - - +
130A ASP* 1.3 78.1 - - - +
132A VAL* 1.3 58.5 + - - +
134A VAL* 3.9 11.0 - - + -
136A MET* 4.6 9.9 - - + -
169A ASN* 3.3 17.2 - - - +
171A HIS* 2.6 51.2 + - - -
198A ASP* 3.7 12.8 - - + -
203A PHE* 3.7 34.3 - - + -
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Residues in contact with VAL 132 (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 5.0 1.1 - - - +
130A ASP* 3.7 5.0 + - - +
131A THR* 1.3 78.5 - - - +
133A ASP* 1.3 78.7 + - + +
134A VAL* 4.5 2.2 - - - +
169A ASN 4.1 0.4 - - - -
170A PHE* 4.7 10.5 - - + -
171A HIS* 3.5 17.5 - - - +
172A LYS* 3.4 40.6 - - + -
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Residues in contact with ASP 133 (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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132A VAL* 1.3 85.4 - - + +
134A VAL* 1.3 57.8 + - - +
169A ASN 2.9 10.9 + - - -
170A PHE* 3.4 30.1 - - + -
231A LEU* 3.5 13.5 - - - +
232A ASP* 3.4 20.4 + - - +
233A GLY* 2.7 34.5 + - - -
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Residues in contact with VAL 134 (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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130A ASP 4.7 3.4 - - - +
131A THR* 3.9 22.7 - - + -
132A VAL 4.5 1.6 - - - +
133A ASP* 1.3 78.0 - - - +
135A ALA* 1.3 71.6 + - - +
136A MET* 4.0 19.5 - - + -
169A ASN* 2.9 44.8 + - + +
232A ASP 5.1 0.4 - - - -
233A GLY* 3.4 7.5 - - - -
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Residues in contact with ALA 135 (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* 1.3 78.4 - - - +
136A MET* 1.3 61.7 + - - +
137A PRO* 4.7 0.5 - - - +
165A PRO* 3.4 37.7 - - + +
167A THR 3.3 7.4 - - - +
232A ASP 4.1 12.0 + - - +
233A GLY* 3.6 17.6 - - - +
235A SER* 4.5 9.6 - - - +
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Residues in contact with MET 136 (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 THR* 4.6 3.4 - - + -
134A VAL* 4.0 24.2 - - + +
135A ALA* 1.3 79.9 - - - +
137A PRO* 1.3 80.6 - - + +
165A PRO* 3.7 5.6 - - - -
166A LEU 3.3 1.2 + - - -
167A THR* 2.6 43.2 + - - +
169A ASN* 3.5 35.4 - - - +
196A ASN* 4.0 19.5 - - + +
197A THR 3.1 31.0 - - - +
198A ASP* 4.9 2.9 - - - -
203A PHE* 4.3 7.0 - - + -
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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