Contacts of the strand formed by residues 179 - 189 (chain C) in PDB entry 4IJ3
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 LEU 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C ALA* 4.6 5.8 - - + -
122C THR* 4.1 18.2 - - + +
149C GLY* 3.2 35.7 - - - +
150C TYR 3.8 3.8 - - - +
151C PHE* 3.6 27.6 - - + -
175C LEU* 3.6 3.1 - - - -
176C GLU* 2.7 38.7 + - - +
177C SER* 2.8 11.3 + - - +
178C ASP* 1.3 83.3 - - + +
180C TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 180 (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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115C THR* 3.4 27.8 - - + +
117C SER* 5.8 0.5 - - - -
149C GLY 3.0 16.8 + - - -
150C TYR* 2.8 50.4 + - + +
151C PHE* 3.8 26.6 - + - -
152C PRO* 4.2 1.6 - - + -
153C GLU* 3.8 51.3 + - + -
173C ALA* 4.3 5.2 - - + -
174C VAL* 3.5 10.8 - - - -
175C LEU* 3.5 37.3 - - + +
179C LEU* 1.3 71.3 - - - +
181C THR* 1.3 67.9 + - - +
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Residues in contact with THR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 5.7 0.7 - - + -
178B THR* 6.1 3.4 - - + -
146C LEU* 4.1 16.2 - - + -
147C VAL 3.3 16.8 - - - +
148C LYS* 3.5 17.4 - - + +
149C GLY* 3.3 11.8 + - - -
150C TYR* 4.3 0.2 - - - -
172C PRO 4.6 0.3 - - - +
173C ALA* 3.6 1.3 - - - -
174C VAL* 3.0 42.4 + - + +
176C GLU* 3.1 29.4 + - - +
179C LEU 4.4 0.5 + - - -
180C TYR* 1.3 81.2 + - - +
182C LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 3.5 6.3 - - - +
147C VAL* 2.9 47.9 + - + +
150C TYR* 3.4 21.5 - - - +
153C GLU* 5.5 0.9 - - - +
155C VAL* 3.5 18.8 - - + +
157C VAL* 4.3 6.7 - - + -
170C THR* 4.0 20.0 - - + -
171C PHE 3.5 21.3 - - - +
172C PRO 4.2 2.5 - - - +
173C ALA* 3.7 13.9 - - + +
181C THR* 1.3 76.5 - - - +
183C SER* 1.3 92.2 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.9 5.2 - - - -
135B PHE* 4.0 14.4 - - - -
162B SER* 6.0 0.2 - - - -
176B SER* 3.0 27.5 + - - -
178B THR* 4.7 3.2 + - - -
129C LEU* 5.0 0.2 - - - -
145C CYS 3.2 13.5 - - - -
146C LEU* 4.0 13.5 - - - -
170C THR* 3.7 0.2 - - - -
171C PHE* 2.9 34.5 + - - +
182C LEU* 1.3 84.5 - - - +
184C SER* 1.3 61.2 + - - +
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Residues in contact with SER 184 (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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135B PHE* 3.6 5.5 - - - -
144C GLY* 3.1 3.3 - - - -
145C CYS* 2.9 34.6 + - - +
157C VAL* 3.9 22.5 - - - +
159C TRP* 3.0 25.6 + - - -
168C VAL* 3.6 4.5 - - - +
169C HIS 3.2 5.3 + - - -
170C THR* 3.0 27.4 + - - -
182C LEU* 4.3 0.4 - - - +
183C SER* 1.3 75.4 - - - +
185C SER* 1.3 61.7 + - - +
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Residues in contact with SER 185 (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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135B PHE* 3.3 39.5 - - - -
137B ASN* 3.2 22.7 + - - -
142C THR* 4.3 3.5 - - - +
143C LEU 3.4 5.8 - - - -
159C TRP* 4.4 0.2 - - - -
167C GLY 5.1 0.3 + - - -
168C VAL* 3.2 5.2 - - - +
169C HIS* 2.7 50.1 + - - +
171C PHE* 4.2 0.2 - - - -
184C SER* 1.3 75.6 + - - +
186C VAL* 1.3 60.8 + - - +
187C THR* 5.4 0.2 + - - -
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Residues in contact with VAL 186 (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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141C VAL 4.1 0.2 - - - +
142C THR* 3.5 1.4 - - - +
143C LEU* 3.0 47.1 + - + +
159C TRP* 3.7 39.9 - - + +
164C LEU* 4.0 25.8 - - + -
166C SER 4.6 1.8 - - - +
167C GLY 3.3 6.1 - - - +
168C VAL* 3.7 21.3 - - + -
185C SER* 1.3 76.1 - - - +
187C THR* 1.3 69.4 + - - +
188C VAL* 4.3 8.2 - - + +
198C VAL* 4.3 8.1 - - + -
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Residues in contact with THR 187 (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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137B ASN* 4.9 6.2 + - - -
140C MET* 3.5 34.7 - - + +
141C VAL 3.4 10.3 - - - +
142C THR* 3.0 24.6 + - - +
166C SER 4.5 9.0 - - - +
167C GLY* 3.0 21.0 + - - +
185C SER* 5.4 0.3 + - - -
186C VAL* 1.3 77.4 - - - +
188C VAL* 1.3 69.8 + - - +
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Residues in contact with VAL 188 (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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140C MET* 3.4 8.5 - - - +
141C VAL* 2.7 54.6 + - + +
143C LEU* 4.9 5.6 - - + -
164C LEU* 4.0 36.8 - - + -
186C VAL* 4.5 6.7 - - + +
187C THR* 1.3 80.6 - - - +
189C PRO* 1.3 71.0 - - + +
192C THR* 3.5 14.1 - - - +
193C TRP* 4.1 13.5 - - + -
198C VAL* 4.8 10.3 - - + -
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Residues in contact with PRO 189 (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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139C SER 3.5 9.6 - - - +
140C MET* 3.6 15.0 - - + -
141C VAL* 4.2 0.2 - - - -
188C VAL* 1.3 92.8 - - + +
190C SER* 1.3 53.9 + - - +
191C SER* 3.0 19.5 - - - +
192C THR* 2.5 50.5 + - + +
193C TRP 3.6 2.8 + - - -
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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