Contacts of the strand formed by residues 153 - 163 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D GLY* 1.3 80.9 + - - +
154D ALA* 1.3 63.5 + - - +
201D THR* 5.0 15.0 - - - +
202D VAL 4.2 9.9 - - - +
203D PRO* 4.5 11.0 - - + -
204D SER* 3.9 7.1 + - - +
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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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144D PRO* 5.7 0.2 - - + -
145D SER 4.3 16.2 - - - +
153D THR* 1.3 75.6 - - - +
155D ALA* 1.3 62.8 + - - +
156D LEU* 4.1 1.3 + - + -
200D VAL 3.9 0.2 - - - +
201D THR* 3.5 13.0 - - - +
202D VAL* 3.1 38.9 + - + +
204D SER* 4.6 12.1 - - - -
207D LEU* 4.6 20.0 - - + -
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Residues in contact with ALA 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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117C THR* 3.9 31.0 - - + +
119C PHE* 3.6 12.2 - - + -
144D PRO* 3.2 25.1 - - - +
145D SER 4.1 8.2 + - - +
154D ALA* 1.3 74.9 - - - +
156D LEU* 1.3 59.9 + - - +
199D VAL* 5.8 2.7 - - + -
200D VAL 4.2 2.2 - - - -
201D THR* 5.3 4.7 - - + +
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Residues in contact with LEU 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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119C PHE* 3.9 3.1 - - - -
144D PRO* 4.0 10.5 - - + -
154D ALA* 4.1 0.9 + - + +
155D ALA* 1.3 74.5 - - - +
157D GLY* 1.3 60.5 + - - +
172D TRP* 3.4 32.5 - - + -
199D VAL* 3.5 2.4 - - - +
200D VAL* 3.2 47.5 + - + +
202D VAL* 4.9 8.5 - - + -
207D LEU* 4.1 21.8 - - + -
212D TYR* 3.5 35.9 - - + -
229D VAL* 3.7 33.4 - - + +
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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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119C PHE* 3.7 8.7 - - - -
142D LEU* 3.0 41.7 + - - -
156D LEU* 1.3 76.2 - - - +
158D CYS* 1.3 62.6 + - - +
172D TRP* 3.6 5.9 - - - -
198D SER 3.3 10.3 - - - -
199D VAL* 4.4 0.7 - - - -
229D VAL* 3.4 14.9 - - - +
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Residues in contact with CYS 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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139D VAL* 4.6 14.1 - - - -
140D PHE 3.9 8.7 - - - -
141D PRO* 4.6 1.1 - - - -
142D LEU* 3.4 6.3 - - - +
157D GLY* 1.3 75.3 - - - +
159D LEU* 1.3 67.1 + - - +
160D VAL* 3.9 4.6 + - - +
170D VAL* 5.1 1.6 - - - -
172D TRP* 3.4 13.2 - - + -
197D SER* 3.9 0.2 - - - -
198D SER* 2.9 33.1 + - - +
214D CYS* 2.0 44.4 - - + -
216D VAL* 4.7 9.9 - - - -
227D LYS* 5.1 2.2 - - - -
229D VAL* 4.9 0.9 - - + -
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Residues in contact with LEU 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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125C GLU* 4.6 7.2 - - - +
132C THR* 3.5 23.6 - - - +
134C VAL* 3.5 25.1 - - + -
178C TYR* 4.8 7.4 - - + -
139D VAL* 3.2 6.6 - - - +
140D PHE* 2.9 50.1 + - + +
142D LEU* 3.3 23.7 - - + +
158D CYS* 1.3 73.1 - - - +
160D VAL* 1.3 63.7 + - - +
161D LYS* 3.4 39.5 - - + +
195D SER* 5.6 0.2 - - - -
196D LEU 4.0 4.7 - - - +
197D SER* 4.1 9.9 - - - +
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Residues in contact with VAL 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 PRO* 3.4 31.0 - - + -
139D VAL* 3.6 13.7 - - + +
158D CYS* 3.9 9.4 - - - +
159D LEU* 1.3 78.7 - - - +
161D LYS* 1.3 61.7 + - - +
163D TYR* 4.1 6.3 - - + -
168D VAL* 4.9 1.3 - - + -
170D VAL* 4.5 5.8 - - + -
195D SER* 3.3 21.3 - - - -
196D LEU* 3.0 39.9 + - + +
197D SER* 5.2 0.4 - - - -
198D SER 5.4 0.2 - - - +
216D VAL* 3.5 29.6 - - + -
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Residues in contact with LYS 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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125C GLU* 6.1 0.9 - - - +
132C THR* 4.4 25.6 - - + +
178C TYR* 4.1 24.8 - - + +
180C SER* 4.8 6.0 + - - -
137D PRO* 3.6 0.7 - - - +
138D SER* 3.0 43.9 + - - +
140D PHE* 4.9 10.3 - - + -
159D LEU* 3.4 21.9 - - + +
160D VAL* 1.3 73.1 - - - +
162D ASP* 1.3 87.2 + - - +
189D GLN* 3.6 22.4 + - - +
195D SER* 3.2 25.9 + - - +
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Residues in contact with ASP 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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135D LYS* 3.3 25.8 + - - +
136D GLY 3.2 14.7 - - - +
138D SER* 5.4 2.7 - - - -
161D LYS* 1.3 100.3 - - + +
163D TYR* 1.3 57.8 + - - +
189D GLN* 2.8 30.7 + - - +
191D SER* 4.2 2.8 + - - -
193D LEU* 3.9 17.1 - - + +
194D TYR 3.3 5.1 + - - -
195D SER* 2.9 13.9 + - - -
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Residues in contact with TYR 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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135D LYS* 3.7 9.9 - - - +
137D PRO* 3.7 23.3 - - + -
160D VAL* 4.1 8.7 - - + -
162D ASP* 1.3 74.8 - - - +
164D PHE* 1.3 66.0 + - - +
165D PRO 4.5 0.2 - - - -
166D GLU* 3.7 20.3 + - + +
167D PRO 4.1 7.2 - - - -
168D VAL* 3.4 33.6 + - + +
186D ALA* 3.4 21.3 - - - +
193D LEU* 3.5 3.6 - - - -
194D TYR* 2.7 83.3 + - + +
195D SER* 3.4 8.1 - - - -
196D LEU* 3.4 30.8 - - + +
218D HIS* 3.6 14.4 - + - +
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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