Contacts of the strand formed by residues 179 - 192 (chain E) in PDB entry 5J0Z
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 ARG 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D VAL* 5.4 4.9 - - - +
91D ASP* 3.0 15.4 + - - +
93D SER* 3.3 19.0 + - - -
101D GLN* 6.1 0.4 - - - +
133E ARG* 3.7 27.4 - - - +
134E SER* 3.8 22.9 + - - +
135E VAL* 4.5 6.9 - - - +
136E ASP* 3.0 41.0 + - - +
175E ALA* 3.4 4.1 - - - -
176E LEU 2.9 29.0 + - - +
177E GLU 2.9 9.4 + - - +
178E ASP* 1.3 79.9 - - + +
180E LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 180 (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 ARG* 4.0 4.5 - - - +
134E SER* 2.9 54.6 + - - +
139E ASN* 3.9 28.7 + - - +
140E ILE 3.6 14.8 - - - +
141E VAL* 5.0 4.0 - - + -
173E ASN* 4.2 21.8 - - + +
174E PHE* 3.4 15.5 - - - +
175E ALA* 4.4 1.6 - - + +
179E ARG* 1.3 77.1 - - - +
181E GLU* 1.3 74.2 + - - +
182E SER* 4.1 0.7 - - - +
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Residues in contact with GLU 181 (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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42D PHE* 3.6 2.8 - - - -
77E ARG* 3.6 2.9 + - - -
131E ILE* 3.5 20.2 - - + +
132E VAL 3.5 18.8 - - - +
133E ARG* 2.8 43.4 + - - +
173E ASN* 3.4 3.5 - - - +
174E PHE* 2.9 42.7 + - + +
176E LEU* 3.6 23.2 - - + +
180E LEU* 1.3 74.6 - - - +
182E SER* 1.3 58.9 + - - +
183E LYS 4.2 0.2 - - - -
403E ACT 2.4 39.5 - - - +
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Residues in contact with SER 182 (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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131E ILE* 4.1 1.3 - - - -
132E VAL* 3.1 35.5 + - - -
140E ILE 3.6 21.1 - - - -
141E VAL* 3.7 6.0 - - - -
142E LEU* 3.1 30.0 + - - +
171E PRO* 3.7 6.8 - - - +
173E ASN* 2.9 26.5 + - - -
180E LEU* 4.1 1.2 - - - +
181E GLU* 1.3 72.4 - - - +
183E LYS* 1.3 59.5 + - - +
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Residues in contact with LYS 183 (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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152D ASN* 4.8 5.0 - - - +
154D ASP* 3.3 28.6 + - - -
79E VAL* 4.5 9.4 - - - -
129E TYR* 3.6 35.2 - - + -
130E LEU 3.3 8.1 - - - +
131E ILE* 3.8 16.2 - - + -
171E PRO* 3.4 21.3 - - - +
172E ALA* 3.4 21.9 + - + +
173E ASN* 3.6 0.4 + - - -
174E PHE* 4.0 27.8 - - + -
182E SER* 1.3 73.9 + - - +
184E LEU* 1.3 69.6 + - - +
185E ASP* 6.3 0.2 - - + -
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Residues in contact with LEU 184 (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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20E THR* 3.0 31.4 - - + +
129E TYR* 3.6 6.8 - - - +
130E LEU* 2.7 39.8 + - + +
142E LEU* 3.7 28.5 - - + +
143E ALA* 4.0 9.2 - - - -
144E VAL* 3.7 15.7 - - + -
168E VAL 3.2 26.9 - - - +
169E VAL 3.9 8.5 - - - +
171E PRO* 4.1 13.5 - - + -
183E LYS* 1.3 82.3 - - - +
185E ASP* 1.3 61.2 + - - +
186E TYR* 4.1 13.7 - - + -
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Residues in contact with ASP 185 (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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127E HIS* 3.2 17.0 + - - -
128E ILE 4.3 0.2 - - - -
129E TYR* 3.4 22.9 + - + -
167E ALA* 3.6 1.4 - - - +
168E VAL* 3.0 40.6 + - + +
184E LEU* 1.3 79.9 - - - +
186E TYR* 1.3 65.8 + - - +
187E GLN* 3.1 36.3 + - - +
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Residues in contact with TYR 186 (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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20E THR* 2.8 40.5 + - - -
21E GLY 3.5 0.2 + - - -
22E ILE* 3.7 34.8 - - + -
127E HIS* 3.4 3.6 - - - -
128E ILE* 2.9 47.1 + - + +
130E LEU* 3.6 20.2 - - + -
144E VAL* 4.5 3.2 - - + +
149E VAL* 3.9 13.2 - - + +
165E PHE* 3.7 33.8 - + + -
166E THR 3.7 3.4 - - - -
167E ALA* 3.8 23.6 - - + +
184E LEU* 4.1 18.0 - - + +
185E ASP* 1.3 83.2 + - - +
187E GLN* 1.3 59.6 + - - +
188E LEU 4.2 0.3 + - - -
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Residues in contact with GLN 187 (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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125E THR* 4.2 4.4 - - + +
126E LEU 3.4 5.4 - - - +
127E HIS* 3.7 17.7 - - + +
164E SER 3.5 2.6 - - - +
165E PHE* 3.5 7.1 - - - -
166E THR* 2.9 39.1 + - - +
168E VAL* 3.3 24.4 - - + +
185E ASP* 3.1 38.4 + - - +
186E TYR* 1.3 70.5 - - - +
188E LEU* 1.3 60.3 + - - +
189E ARG* 3.1 39.7 + - - +
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Residues in contact with LEU 188 (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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24E LEU* 4.2 19.5 - - + -
27E CYS* 3.8 27.6 - - + -
37E PHE* 4.4 12.3 - - + -
124E GLN 4.1 0.2 - - - +
125E THR* 3.6 0.4 - - - -
126E LEU* 2.6 69.9 + - + +
128E ILE* 5.8 3.8 - - + +
151E LYS* 5.1 0.2 - - + -
157E LEU* 5.6 1.6 - - + -
162E ILE* 3.5 31.9 - - + -
164E SER 3.5 11.9 - - - +
165E PHE* 3.8 16.2 - - + -
186E TYR 4.2 0.4 + - - -
187E GLN* 1.3 70.6 - - - +
189E ARG* 1.3 56.7 + - - +
190E ILE* 4.5 6.7 - - + -
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Residues in contact with ARG 189 (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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123E SER* 6.5 0.2 - - - -
124E GLN 3.2 7.0 - - - +
125E THR* 3.4 35.4 + - - +
162E ILE* 3.8 2.1 - - - +
163E GLU* 2.9 36.6 + - + +
164E SER* 3.1 29.6 + - - +
166E THR* 3.0 27.3 + - - +
187E GLN* 3.1 38.1 + - - +
188E LEU* 1.3 73.2 - - - +
190E ILE* 1.3 65.2 + - - +
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Residues in contact with ILE 190 (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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30E LEU* 3.3 35.0 - - + -
123E SER* 3.2 5.3 - - - -
124E GLN* 2.7 50.2 + - + +
126E LEU* 3.8 18.4 - - + -
157E LEU* 3.9 12.3 - - + -
160E TRP* 3.6 22.7 - - + -
161E ASP 3.2 15.9 - - - +
162E ILE* 3.9 20.9 - - + -
163E GLU* 3.8 4.0 - - - -
188E LEU* 4.5 9.2 - - + -
189E ARG* 1.3 80.5 - - - +
191E SER* 1.3 59.4 - - - +
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Residues in contact with SER 191 (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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122E ASP 3.8 0.7 - - - -
123E SER* 3.0 20.9 - - - -
160E TRP* 3.4 4.7 - - - -
161E ASP* 2.8 51.0 + - - +
163E GLU* 3.4 15.9 + - - -
190E ILE* 1.3 72.9 - - - +
192E ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 192 (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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32E ASP* 2.1 43.6 + - - -
116E PHE* 4.1 2.0 - - - -
119E TYR* 3.2 23.3 - - - -
120E PRO* 3.7 21.4 - - - +
121E PHE* 5.5 1.2 - - - -
122E ASP* 2.4 73.4 + - - +
159E GLY 3.6 9.8 + - - +
160E TRP* 3.1 35.7 - - + +
161E ASP* 4.8 2.1 - - - +
191E SER* 1.3 74.1 + - - +
193E GLN* 1.3 67.2 + - - +
194E TYR* 3.1 18.5 + - - +
197E TYR* 3.9 23.2 + - + -
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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