Contacts of the strand formed by residues 153 - 164 (chain D) in PDB entry 3STJ
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 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D ALA 3.6 1.2 - - - +
144D VAL* 3.4 6.2 - - - +
145D GLY 2.8 31.6 + - - -
147D PRO* 3.7 30.0 - - + +
150D LEU* 4.7 1.4 - - - +
151D GLY 3.0 4.7 + - - -
152D GLN* 1.3 71.3 - - - +
154D ALA* 1.3 60.8 - - - +
155D THR* 4.1 17.0 - - + +
186D ASN* 4.8 2.4 - - - +
160E SER* 3.7 13.2 - - - -
164E ARG* 2.8 24.8 + - - -
177E GLN* 3.3 25.5 + - - +
215E ILE* 4.5 2.9 - - + -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.6 4.5 - - + -
23D LEU* 4.6 7.2 - - + -
142D VAL* 4.3 11.2 - - + -
143D ALA 3.2 7.0 - - - +
144D VAL* 4.4 9.0 - - + +
153D THR* 1.3 73.1 - - - +
155D THR* 1.3 58.3 + - - +
137E VAL* 3.9 24.9 - - + -
158E ILE* 3.3 13.8 - - + +
160E SER* 2.8 39.0 + - - -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL* 3.3 5.4 - - - +
143D ALA* 2.7 45.8 + - - +
153D THR* 4.1 14.6 - - + -
154D ALA* 1.3 78.7 - - - +
156D SER* 1.3 59.9 + - - +
180D ALA* 4.1 1.5 - - - +
181D SER* 2.6 43.9 + - - +
186D ASN* 5.2 1.4 + - - -
158E ILE* 4.0 4.0 - - - -
160E SER* 4.0 3.8 - - - +
179E ASP* 3.5 27.4 - - + -
214E GLY 4.4 4.5 - - - +
215E ILE* 5.4 2.5 - - + -
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.9 16.3 - - - +
140D PHE* 5.6 5.0 - - - +
141D ALA 3.6 7.5 + - - -
142D VAL* 4.4 2.3 - - - +
155D THR* 1.3 74.8 - - - +
157D GLY* 1.3 62.3 + - - +
179D ASP 4.6 1.4 - - - +
180D ALA* 3.7 12.5 - - - -
181D SER 4.7 0.5 + - - -
194D LEU* 6.1 0.3 - - - +
140E PHE* 5.2 3.7 - - - -
157E GLY* 6.0 0.9 - - - -
158E ILE* 4.0 29.0 - - - +
179E ASP* 3.0 15.5 + - - +
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 3.6 11.1 - - - +
141D ALA* 2.9 30.0 + - - +
156D SER* 1.3 78.1 + - - +
158D ILE* 1.3 65.3 + - - +
178D THR* 4.6 0.7 - - - -
179D ASP* 3.3 13.5 - - - -
180D ALA* 3.8 8.9 - - - +
156F SER* 6.1 1.3 - - - -
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY* 3.9 14.4 - - - +
139D ASP 3.3 6.5 - - - +
140D PHE* 3.7 29.2 - - + -
141D ALA* 4.6 2.2 - - - -
157D GLY* 1.3 76.3 - - - -
159D VAL* 1.3 72.3 + - - +
160D SER 3.4 0.7 + - - -
178D THR* 2.8 27.2 + - - -
179D ASP* 2.7 23.8 + - - +
15F LEU* 3.9 18.4 - - + -
19F LEU* 5.0 0.4 - - + -
142F VAL* 4.7 2.5 - - + -
154F ALA* 3.3 40.8 - - + +
155F THR* 3.9 10.1 - - - -
156F SER* 3.9 11.9 - - - +
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 4.5 7.2 - - + -
136D ARG 3.7 20.4 - - - +
137D VAL* 3.4 7.3 - - - +
138D GLY* 2.9 24.8 + - - -
139D ASP* 2.8 28.8 + - + +
140D PHE 5.1 0.2 - - - +
141D ALA* 4.5 5.4 - - + -
158D ILE* 1.3 73.6 - - - +
160D SER* 1.3 58.0 + - - +
161D ALA 3.7 20.0 - - - +
162D LEU* 3.8 24.2 - - + -
176D ILE* 4.0 11.0 - - + -
177D GLN 3.7 3.1 - - - -
178D THR* 4.8 0.7 - - - +
191D LEU* 5.6 0.4 - - + -
199D ILE* 4.3 24.2 - - + -
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.5 12.3 - - - +
158D ILE 3.4 2.0 + - - -
159D VAL* 1.3 73.0 - - - +
161D ALA* 1.4 59.9 + - - +
177D GLN* 2.7 28.3 + - - -
178D THR* 3.8 1.2 - - - -
179D ASP* 3.5 20.4 + - - +
214D GLY 4.9 0.2 + - - -
152F GLN 4.2 1.4 - - - +
153F THR* 3.7 18.3 - - - -
154F ALA 2.6 43.4 + - - -
155F THR* 3.9 7.1 - - - +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.8 10.0 - - - +
159D VAL* 3.6 4.6 - - - +
160D SER* 1.4 79.2 - - - +
162D LEU* 1.3 66.5 + - - +
164D ARG* 3.4 42.8 - - + +
175D PHE 4.8 0.4 - - - -
176D ILE* 3.7 0.9 - - - -
177D GLN* 2.9 38.8 + - + +
152F GLN 3.9 3.6 - - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER 4.9 3.6 - - - +
135D LEU* 3.4 43.1 - - + +
136D ARG* 3.8 11.9 - - - -
137D VAL* 4.0 14.4 - - + +
159D VAL* 3.8 18.4 - - + -
161D ALA* 1.3 78.8 - - - +
163D GLY* 1.3 66.9 + - - +
164D ARG* 3.3 10.2 + - - +
175D PHE 3.9 3.6 - - - -
176D ILE* 3.9 22.9 - - + -
293D LYS* 6.4 0.2 - - - +
296D ASN* 3.5 12.8 + - - +
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Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU* 1.3 75.4 - - - +
164D ARG* 1.4 60.7 + - - +
165D SER* 3.6 7.8 + - - -
174D ASN* 3.1 32.1 + - - +
175D PHE 3.2 6.9 + - - -
176D ILE* 5.9 0.2 - - - +
296D ASN* 3.1 29.4 - - - +
297D SER* 4.8 0.5 + - - -
300D GLU* 4.8 1.9 - - - +
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Residues in contact with ARG 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ALA* 3.4 25.0 - - + +
162D LEU 4.5 6.1 + - - +
163D GLY* 1.4 73.6 - - - +
165D SER* 1.3 63.4 + - - +
167D LEU* 4.4 11.4 - - + -
173D GLU* 3.8 0.2 - - - +
174D ASN 3.7 1.7 + - - -
175D PHE* 2.9 53.1 + - + +
177D GLN* 2.8 27.0 + - + +
217D PHE* 4.4 10.3 - - + -
150F LEU* 3.4 32.3 + - - +
151F GLY* 3.5 14.3 + - - -
152F GLN 2.8 18.4 + - - +
153F THR* 2.8 28.3 + - - -
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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