Contacts of the strand formed by residues 127 - 139 (chain E) in PDB entry 3ZXR
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 127 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E LEU* 3.6 5.5 - - - +
125E ALA* 3.7 0.8 - - - +
126E ASP* 1.3 95.3 + - - +
128E ALA* 1.3 61.3 + - - +
129E TYR* 3.6 39.2 + - + +
234E SER* 3.9 17.3 - - - -
280E SER 3.9 0.2 - - - +
281E LEU* 3.5 5.7 - - - +
282E TRP* 2.9 40.2 + - - +
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Residues in contact with ALA 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLU* 6.3 1.9 - - + +
119E LEU* 3.5 13.5 - - + +
127E THR* 1.3 73.5 - - - +
129E TYR* 1.3 63.4 + - - +
130E PHE* 3.6 20.7 - - + -
234E SER* 3.3 3.6 - - - -
235E LEU* 3.0 29.6 + - + -
280E SER 3.5 5.4 - - - +
281E LEU* 3.7 18.2 - - + -
305E TYR* 5.7 0.2 - - - +
384E LEU* 3.8 14.6 - - + -
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Residues in contact with TYR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E THR* 3.6 26.4 + - + +
128E ALA* 1.3 71.0 - - - +
130E PHE* 1.3 62.2 + - - +
232E PHE* 3.6 35.4 - + + -
233E ASN* 3.5 21.8 - - - -
234E SER* 3.6 11.9 - - - -
278E HIS 3.4 0.7 - - - +
279E GLN* 3.3 8.0 - - - +
280E SER* 2.9 40.9 + - - +
282E TRP* 3.4 52.1 - + + -
501E IQ1 3.6 4.3 - - - +
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Residues in contact with PHE 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ALA* 3.6 25.4 - - + -
129E TYR* 1.3 78.3 - - - +
131E GLY* 1.3 59.2 + - - +
132E ALA 4.1 1.3 + - - -
232E PHE* 3.4 4.7 - - - -
233E ASN 2.8 29.2 + - - +
235E LEU* 3.6 32.8 - - + -
238E ALA* 3.8 22.5 - - + +
277E CYS* 4.6 6.3 - - + -
278E HIS 3.4 2.9 - - - -
279E GLN* 3.7 35.0 - - + -
305E TYR* 4.4 2.7 - - - -
380E PHE* 3.5 60.1 - + + -
383E MET* 4.2 4.3 - - - -
384E LEU* 4.4 8.1 - - + -
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Residues in contact with GLY 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE* 1.3 72.6 - - - +
132E ALA* 1.3 59.6 + - - -
230E TYR 5.6 0.2 - - - -
232E PHE* 3.7 17.9 - - - -
276E HIS 3.5 0.7 - - - +
277E CYS* 3.4 3.4 - - - -
278E HIS* 2.7 40.2 + - - +
501E IQ1 3.6 26.2 - - - +
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Residues in contact with ALA 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE 4.1 1.8 + - - -
131E GLY* 1.3 74.4 - - - +
133E GLU* 1.3 66.1 + - - +
134E ALA 3.9 1.4 + - - -
228E ILE 5.0 0.9 - - - +
229E ASN* 4.3 8.8 + - - -
230E TYR* 4.7 21.8 + - + +
242E MET* 3.4 30.5 - - + -
275E MET* 4.4 4.7 - - + -
276E HIS 3.3 6.7 - - - +
277E CYS* 4.7 3.6 - - - +
380E PHE* 4.3 17.0 - - + -
501E IQ1 4.0 9.4 - - - +
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Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ALA* 1.3 78.0 - - - +
134E ALA* 1.3 60.7 + - - +
135E GLU* 3.4 4.3 + - + +
227E GLU* 2.9 19.4 - - - +
228E ILE 5.1 0.2 - - - -
229E ASN* 3.9 12.6 - - - +
274E GLY 3.0 16.1 - - - +
275E MET* 3.1 11.3 - - - -
276E HIS* 3.0 24.5 + - + +
278E HIS* 2.9 13.2 + - - -
366E GLU* 3.0 2.4 - - - +
501E IQ1 4.0 11.2 - - + -
503E MG 2.1 27.4 - - - -
504E MG 2.0 33.4 - - - -
505E P3S 2.9 3.6 + - - -
506E PO4 2.8 11.5 + - - -
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ALA 3.9 1.8 - - - -
133E GLU* 1.3 69.7 - - - +
135E GLU* 1.3 65.5 + - - +
136E PHE* 3.5 5.4 - - - -
227E GLU* 5.3 1.3 - - - -
228E ILE 4.7 5.0 + - - -
230E TYR* 6.3 0.8 - - - -
242E MET* 3.6 26.4 - - + +
245E TYR* 2.8 49.9 + - + -
262E PHE* 3.8 6.5 - - + -
274E GLY 3.8 4.0 - - - -
275E MET* 4.5 1.3 - - + -
372E SER* 3.6 15.9 - - - +
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 4.3 4.3 - - + +
134E ALA* 1.3 76.6 - - - +
136E PHE* 1.3 60.8 + - - +
219E GLU* 3.0 15.4 - - + +
225E GLN* 4.4 4.9 - - - +
226E ALA 3.4 11.9 - - - +
227E GLU* 3.4 18.6 - - - +
262E PHE* 3.3 16.1 - - - +
273E SER* 3.6 20.9 - - - +
274E GLY* 2.8 32.9 + - - +
276E HIS* 4.8 4.3 - - - -
372E SER* 4.5 1.7 + - - -
502E MG 2.2 29.2 - - - -
505E P3S 2.6 36.7 + - - -
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Residues in contact with PHE 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ALA 3.5 13.2 - - - -
135E GLU* 1.3 75.4 - - - +
137E TYR* 1.3 63.5 + - - +
138E ILE* 3.6 29.6 - - + -
202E MET* 3.8 14.4 - - - -
225E GLN* 3.3 3.7 - - - +
226E ALA* 2.7 61.8 + - + +
228E ILE* 4.4 11.0 - - + -
245E TYR* 3.4 19.1 - + - -
249E ILE* 3.5 31.6 - - + -
260E VAL* 3.8 10.5 - - + -
261E THR 3.5 14.6 - - - +
262E PHE* 3.6 23.3 - + + -
273E SER* 4.0 5.1 + - - -
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Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E PHE* 1.3 74.2 - - - +
138E ILE* 1.3 61.6 + - - +
139E PHE* 3.5 39.0 + + + -
221E GLY* 3.3 16.3 - - - -
222E SER 3.2 22.4 - - - -
223E GLY 3.8 1.6 - - - -
224E GLY 3.7 0.7 - - - -
225E GLN* 3.4 43.5 - - + -
260E VAL* 3.3 8.3 - - - +
261E THR* 3.1 32.1 + - + +
263E MET 5.3 0.2 - - - -
266E PRO* 3.5 26.7 - - + -
267E LEU* 3.7 16.2 - - + +
270E ASP* 4.4 0.3 - - - +
271E ASN 2.6 27.2 + - - -
273E SER* 3.5 17.5 - - - -
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Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E PHE* 3.6 30.3 - - + -
137E TYR* 1.3 71.6 - - - +
139E PHE* 1.3 60.5 + - - +
157E ALA* 4.3 0.7 - - - +
195E TYR* 3.9 36.5 + - + -
198E LEU* 3.7 27.6 - - + -
199E ARG* 4.3 13.7 - - + -
202E MET* 3.9 12.8 - - + -
223E GLY 3.4 12.3 - - - +
224E GLY* 2.9 20.7 + - - +
226E ALA* 4.2 9.4 - - + -
258E LYS* 3.8 19.7 - - + -
259E THR 4.1 1.8 - - - -
260E VAL* 4.1 10.5 - - + -
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Residues in contact with PHE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E TYR* 3.5 26.9 + + + -
138E ILE* 1.3 76.2 - - - +
140E ASP* 1.3 62.2 + - - +
141E SER 4.1 4.9 - - - +
142E VAL* 5.7 2.0 - - + -
155E VAL* 3.7 44.4 - - + -
156E ASP 3.4 7.9 - - - +
157E ALA* 3.9 11.4 - - + -
162E TRP* 4.9 2.0 - + - -
223E GLY 3.5 23.6 - - - -
258E LYS* 3.6 7.4 - - - +
259E THR* 2.8 44.2 + - + +
260E VAL 5.9 0.2 - - - -
261E THR* 3.6 30.7 - - + -
266E PRO* 3.8 14.8 - - + -
267E LEU* 4.1 12.1 - - + -
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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