Contacts of the strand formed by residues 167 - 174 (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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ALA* 3.3 5.7 - - - -
136C MET* 2.6 54.8 + - - +
137C PRO 3.8 5.0 + - - -
138C LEU* 3.7 30.2 - - + +
161C LEU* 4.1 10.8 - - + -
165C PRO 3.6 0.8 - - - -
166C LEU* 1.3 76.8 - - - +
168C ALA* 1.3 59.0 + - - +
169C ASN* 3.2 15.8 + - - -
196C ASN* 5.0 0.7 + - - -
219C TRP* 3.4 43.1 - - + -
235C SER* 5.7 0.2 - - - -
243C THR* 5.5 0.2 - - + -
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Residues in contact with ALA 168 (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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166C LEU 4.0 2.2 + - - -
167C THR* 1.3 69.5 - - - +
169C ASN* 1.3 60.7 + - - +
170C PHE* 3.9 15.3 - - + -
219C TRP* 3.2 5.9 - - - +
220C HIS* 2.9 55.7 + - + +
223C LYS* 4.3 8.3 - - + -
224C ALA 5.8 0.4 - - - +
233C GLY 3.2 21.1 - - - +
234C ILE* 4.3 9.0 - - + -
235C SER 4.9 3.0 - - - +
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Residues in contact with ASN 169 (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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131C THR 3.2 14.4 - - - +
133C ASP 2.8 21.8 + - - -
134C VAL* 2.9 28.6 + - + +
136C MET* 3.7 25.0 - - + +
167C THR* 3.2 24.4 + - - -
168C ALA* 1.3 73.5 + - - +
170C PHE* 1.3 65.2 - - - +
171C HIS* 2.7 26.6 + - - +
196C ASN* 5.3 3.0 + - - +
203C PHE* 3.9 14.6 - - - -
205C SER* 5.8 1.2 - - - -
218C GLN* 4.9 1.6 - - - +
219C TRP* 4.0 11.0 - - - +
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Residues in contact with PHE 170 (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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110C CYS* 3.8 2.7 - - - -
131C THR 3.7 1.6 - - - -
132C VAL* 4.1 12.6 - - + +
133C ASP* 3.4 46.9 - - + +
168C ALA* 3.9 8.5 + - + -
169C ASN* 1.3 78.2 - - - +
171C HIS* 1.3 62.0 + - - +
220C HIS* 4.1 14.4 - + - +
223C LYS* 3.9 22.9 - - + -
231C LEU* 3.8 21.5 - - + -
233C GLY* 3.8 15.3 - - - -
234C ILE* 3.7 32.8 - - + -
1004C BME 2.9 31.5 - - - +
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Residues in contact with HIS 171 (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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110C CYS* 3.7 9.6 - - - -
114C GLU* 4.1 3.6 - - - +
131C THR* 2.6 62.4 + - - +
132C VAL* 3.4 6.0 - - - +
169C ASN* 2.7 28.8 + - + -
170C PHE* 1.3 85.9 - - - +
172C LYS* 1.3 58.7 - - - +
173C TRP 2.7 21.2 + - - +
174C SER* 2.8 21.0 + - - -
203C PHE* 3.7 9.0 - + - -
218C GLN* 3.3 45.9 - - + +
1004C BME 4.8 2.5 - - - -
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Residues in contact with LYS 172 (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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128C ALA* 3.4 8.3 - - - +
129C THR* 2.9 29.3 + - - +
132C VAL* 3.6 23.6 - - + -
171C HIS* 1.3 74.3 - - - +
173C TRP* 1.3 78.8 + - + +
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Residues in contact with TRP 173 (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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114C GLU* 3.5 23.2 + - - +
126C LEU* 4.0 34.3 - - + -
127C THR* 3.3 13.2 - - - -
128C ALA* 3.4 38.4 - - + -
129C THR* 3.8 0.2 - - - -
171C HIS* 2.7 25.0 + - - +
172C LYS* 1.3 99.8 - - + +
174C SER* 1.3 59.4 + - - +
218C GLN* 3.8 1.0 - - - +
1005C BME 5.6 4.3 - - - -
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Residues in contact with SER 174 (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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126C LEU* 3.3 9.7 - - - -
127C THR* 2.8 32.6 + - - +
129C THR* 2.7 38.0 + - - +
171C HIS* 2.8 23.1 - - - -
173C TRP* 1.3 71.0 - - - +
175C LEU* 1.3 61.9 + - - +
176C SER 3.7 1.3 + - - -
203C PHE* 3.6 25.2 - - - -
218C GLN* 3.9 7.6 - - - -
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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