Contacts of the strand formed by residues 127 - 136 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B LEU 4.0 0.2 + - - -
126B LEU* 1.3 74.1 + - - +
128B ALA* 1.3 76.6 + - + +
129B THR* 3.5 5.4 + - - +
173B TRP* 3.3 6.4 - - - -
174B SER* 2.7 37.6 + - - -
176B SER* 4.1 12.4 + - - -
179B ASN* 3.4 24.3 + - - -
201B ILE* 4.7 17.5 - - + -
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 1.3 82.1 - - - +
129B THR* 1.3 64.8 + - - +
172B LYS 3.4 10.1 - - - +
173B TRP* 3.3 27.4 - - + -
201B ILE* 4.6 8.0 - - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 3.8 4.7 - - + +
128B ALA* 1.3 79.8 - - - +
130B ASP* 1.3 58.8 - - - +
131B THR* 2.7 32.2 + - - -
132B VAL* 4.9 1.6 + - - +
171B HIS 3.9 1.0 - - - +
172B LYS* 2.9 20.6 + - - +
173B TRP 3.9 0.3 - - - -
174B SER* 2.6 39.6 + - - +
198B ASP* 3.6 12.8 - - - +
201B ILE* 4.2 23.6 - - + -
203B PHE* 4.4 6.3 - - + -
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR* 1.3 67.8 - - - +
131B THR* 1.3 63.4 + - - +
132B VAL* 3.7 4.3 + - - +
134B VAL* 4.7 5.0 - - - +
198B ASP* 3.0 31.7 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR* 2.7 20.8 + - - +
130B ASP* 1.3 78.9 - - - +
132B VAL* 1.3 58.3 + - - +
134B VAL* 4.0 10.3 - - + -
136B MET* 4.8 7.2 - - - -
169B ASN* 3.3 19.8 - - - +
171B HIS* 2.6 53.1 + - - -
198B ASP* 3.8 13.0 - - + -
203B PHE* 3.6 34.3 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B THR 5.1 1.3 - - - +
130B ASP* 3.7 4.8 + - - +
131B THR* 1.3 77.0 - - - +
133B ASP* 1.3 78.3 + - + +
134B VAL* 4.7 1.7 - - - +
169B ASN 4.0 0.2 - - - -
170B PHE* 4.1 13.5 - - + +
171B HIS* 3.5 26.7 - - - +
172B LYS* 3.7 26.5 - - + -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 1.3 84.7 - - + +
134B VAL* 1.3 57.9 + - - +
169B ASN 2.9 11.5 + - - -
170B PHE* 3.4 29.8 - - + -
231B LEU* 3.4 20.7 - - + +
232B ASP* 4.1 15.5 + - - +
233B GLY* 2.8 33.3 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP 4.7 4.3 - - - +
131B THR* 4.0 21.8 - - + -
132B VAL 4.5 1.8 - - - +
133B ASP* 1.3 76.6 - - - +
135B ALA* 1.3 72.9 + - - +
136B MET* 4.1 16.8 - - + -
169B ASN* 2.9 43.8 + - + +
232B ASP 5.0 0.4 - - - -
233B GLY* 3.4 7.4 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 1.3 78.2 - - - +
136B MET* 1.3 63.7 + - - +
137B PRO* 4.7 0.2 - - - +
165B PRO* 3.5 36.8 - - + +
167B THR 3.3 7.2 - - - +
232B ASP 4.0 11.5 + - - +
233B GLY* 3.5 17.6 - - - +
234B ILE 5.0 0.2 - - - -
235B SER* 4.6 9.0 - - - -
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B THR* 4.8 3.4 - - - -
134B VAL* 4.1 21.5 - - + +
135B ALA* 1.3 80.6 - - - +
137B PRO* 1.3 75.8 - - + +
165B PRO* 3.7 5.6 - - - -
166B LEU 3.3 1.0 + - - -
167B THR* 2.7 41.1 + - - +
169B ASN* 3.6 34.8 - - - +
196B ASN* 3.6 27.8 - - + +
197B THR 3.0 30.5 - - - +
198B ASP* 5.1 1.1 - - - -
203B PHE* 4.4 4.9 - - - -
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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