Contacts of the strand formed by residues 153 - 163 (chain N) in PDB entry 4R2G
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N SER 3.6 15.2 - - - +
151N GLY* 3.1 18.7 + - - +
152N GLY* 1.3 83.4 - - - +
154N ALA* 1.3 62.6 + - - +
201N THR* 4.6 11.5 - - - +
202N VAL 3.2 23.6 - - - +
203N PRO* 4.4 6.3 - - + -
204N SER* 4.3 2.8 - - - -
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Residues in contact with ALA 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N PRO* 4.1 10.1 - - + -
146N SER 3.9 21.5 - - - -
153N THR* 1.3 76.0 - - - +
155N ALA* 1.3 62.1 + - - +
156N LEU* 4.2 0.4 - - - -
200N VAL 3.6 0.3 - - - +
201N THR* 3.0 28.7 - - - -
202N VAL* 2.8 16.3 + - + +
204N SER* 4.6 3.4 - - - -
207N LEU* 4.0 28.9 - - + -
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Residues in contact with ALA 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M THR* 4.5 13.7 - - + +
119M PHE* 3.2 35.4 - - + -
144N PRO* 3.5 14.9 - - - +
145N SER 5.7 0.2 - - - +
146N SER 5.0 1.6 + - - -
154N ALA* 1.3 79.6 - - - +
156N LEU* 1.3 63.5 + - - +
199N VAL* 5.0 6.1 - - + -
200N VAL 3.4 8.5 - - - +
201N THR* 4.8 9.2 - - + -
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Residues in contact with LEU 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M PHE* 4.5 1.3 - - - -
142N LEU 3.4 7.4 - - - -
144N PRO* 3.6 21.5 - - + -
154N ALA 5.1 0.4 - - - -
155N ALA* 1.3 75.7 - - - +
157N GLY* 1.3 60.5 + - - +
172N TRP* 4.4 6.5 - - + -
199N VAL* 3.1 26.9 - - - +
200N VAL* 3.2 15.2 + - + +
202N VAL* 3.7 38.1 - - + -
207N LEU* 4.4 6.1 - - + -
212N TYR* 3.6 34.5 - - + -
229N VAL* 3.5 37.5 - - + +
231N PRO* 5.8 0.7 - - + -
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Residues in contact with GLY 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141N PRO* 3.7 4.0 - - - +
142N LEU* 2.7 43.7 + - - +
156N LEU* 1.3 80.0 - - - +
158N CYS* 1.3 59.3 + - - -
172N TRP* 3.4 15.4 - - - -
198N SER 2.9 13.7 - - - -
199N VAL* 4.1 2.2 - - - -
229N VAL* 3.9 5.7 - - - +
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Residues in contact with CYS 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N VAL* 3.7 13.5 - - + -
140N PHE 3.8 4.0 - - - -
141N PRO* 5.0 0.9 - - - -
142N LEU* 3.8 3.4 - - - +
157N GLY* 1.3 74.7 - - - -
159N LEU* 1.3 58.3 + - - +
160N VAL* 3.9 11.6 + - + -
170N VAL* 4.8 1.1 - - + -
172N TRP* 3.6 6.6 - - + -
197N SER* 3.1 7.6 - - - -
198N SER* 2.8 37.2 + - - +
214N CYS* 2.0 61.2 - - - -
216N VAL* 4.1 4.5 - - + -
229N VAL* 5.5 0.9 - - - -
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Residues in contact with LEU 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M GLU* 4.0 12.6 - - - +
132M THR* 3.8 16.6 - - - +
134M VAL* 4.1 9.0 - - + -
178M TYR* 3.8 31.6 - - + -
138N SER 3.7 0.7 - - - +
139N VAL* 3.3 5.6 - - - -
140N PHE* 3.0 40.4 + - + +
142N LEU* 3.7 26.3 - - + +
158N CYS* 1.3 72.4 - - - +
160N VAL* 1.3 63.0 + - - +
161N LYS* 3.5 39.2 + - + -
195N SER* 4.9 2.2 - - - -
196N LEU 3.6 5.2 - - - +
197N SER* 4.2 0.9 - - - +
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Residues in contact with VAL 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137N PRO* 3.4 28.5 - - + -
138N SER 4.2 2.0 - - - -
139N VAL* 4.5 4.7 - - + +
158N CYS* 4.2 9.0 - - + +
159N LEU* 1.3 72.9 - - - +
161N LYS* 1.3 58.1 + - - +
163N TYR* 4.1 11.8 - - + -
168N VAL* 4.3 4.0 - - + -
170N VAL* 4.1 7.9 - - + -
195N SER* 3.2 5.6 - - - -
196N LEU* 2.7 61.0 + - + +
216N VAL* 3.5 38.4 - - + -
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Residues in contact with LYS 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M GLU* 2.7 25.1 + - - +
130M LYS* 4.0 20.2 - - - +
132M THR* 3.6 15.4 - - - +
137N PRO* 3.3 3.4 - - - +
138N SER* 3.1 39.3 + - - +
140N PHE* 3.5 24.3 - - + -
159N LEU* 3.5 37.9 - - + -
160N VAL* 1.3 72.8 - - - +
162N ASP* 1.3 88.8 + - - +
163N TYR* 3.8 1.8 - - - -
194N TYR 4.0 0.2 - - - -
195N SER* 3.7 7.2 - - - +
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Residues in contact with ASP 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LYS* 3.8 15.4 - - - +
136N GLY 3.2 14.0 - - - +
138N SER* 4.5 5.2 + - - +
161N LYS* 1.3 100.4 - - - +
163N TYR* 1.3 58.8 + - - +
189N GLN* 3.0 25.9 + - - +
191N SER* 5.5 0.3 + - - -
193N LEU* 3.5 22.2 - - + -
194N TYR 3.2 6.6 + - - -
195N SER* 3.1 11.2 + - - -
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Residues in contact with TYR 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LYS* 3.4 15.5 - - - +
137N PRO* 3.7 30.5 - - + -
160N VAL* 4.1 18.4 - - + -
162N ASP* 1.3 74.5 - - - +
164N PHE* 1.3 67.6 + - - +
165N PRO 4.0 2.0 - - - -
166N GLU* 3.7 26.6 - - + +
168N VAL* 3.9 21.2 - - + +
186N ALA* 3.5 14.4 - - - +
193N LEU* 3.5 3.3 - - - -
194N TYR* 2.8 66.0 + + + -
195N SER* 4.1 2.9 - - - -
196N LEU* 3.0 30.5 - - + +
218N HIS* 3.8 15.0 - + - +
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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