Contacts of the strand formed by residues 160 - 176 (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 TRP 160 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E LEU* 3.7 35.5 + - + +
32E ASP* 4.0 2.9 + - - -
114E LEU* 5.4 0.9 - - + -
116E PHE* 5.9 0.2 - + - -
122E ASP* 3.7 9.6 - - - -
124E GLN* 3.8 26.7 - - + -
157E LEU* 2.8 48.2 + - + +
158E THR 3.5 12.9 + - - -
159E GLY* 1.3 86.0 + - - +
161E ASP* 1.3 65.6 + - - +
162E ILE* 4.1 2.9 + - - +
190E ILE* 3.6 17.5 - - + -
191E SER 3.4 10.3 - - - -
192E ARG* 3.1 73.4 - - + +
193E GLN* 3.4 15.2 + - - -
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Residues in contact with ASP 161 (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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160E TRP* 1.3 75.7 - - - +
162E ILE* 1.3 61.4 + - - +
163E GLU* 3.8 7.1 - - - +
190E ILE* 3.2 7.4 - - - +
191E SER* 2.8 49.9 + - - +
192E ARG 4.8 1.0 - - - +
193E GLN* 3.5 29.7 + - - +
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Residues in contact with ILE 162 (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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27E CYS* 5.2 1.6 - - - -
151E LYS* 4.1 23.6 - - + -
155E VAL* 3.5 43.3 - - + +
156E PHE* 4.3 0.7 - - - -
157E LEU* 3.9 26.7 - - + +
160E TRP 4.5 1.3 - - - +
161E ASP* 1.3 77.8 - - - +
163E GLU* 1.3 68.7 + - - +
188E LEU* 3.5 32.8 - - + -
189E ARG 3.8 3.8 - - - +
190E ILE* 4.0 9.9 - - + -
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Residues in contact with GLU 163 (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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151E LYS* 3.6 12.1 + - - -
161E ASP* 3.8 6.5 - - - +
162E ILE* 1.3 78.0 - - - +
164E SER* 1.3 62.7 + - - +
189E ARG* 2.9 27.5 + - + +
190E ILE 3.8 3.3 - - - -
191E SER* 3.4 37.6 + - - -
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Residues in contact with SER 164 (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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151E LYS* 4.0 7.6 - - - +
163E GLU* 1.3 82.4 - - - +
165E PHE* 1.3 60.8 + - - +
166E THR* 4.1 15.4 + - - -
188E LEU* 3.5 8.7 - - - +
189E ARG* 3.1 57.0 + - - +
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Residues in contact with PHE 165 (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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22E ILE* 3.3 31.2 - - + -
24E LEU* 3.6 31.6 - - + -
128E ILE* 4.4 10.3 - - + -
149E VAL* 4.2 13.8 - - + +
150E GLY* 3.3 23.5 - - - +
151E LYS* 3.7 26.9 + - + +
164E SER* 1.3 72.7 - - - +
166E THR* 1.3 63.7 + - - +
186E TYR* 3.7 40.8 - + + -
187E GLN 3.5 21.1 - - - -
188E LEU* 3.8 15.9 - - + -
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Residues in contact with THR 166 (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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149E VAL* 4.8 6.3 - - - -
164E SER* 4.1 14.3 + - - -
165E PHE* 1.3 82.1 - - - +
167E ALA* 1.3 65.4 + - - +
186E TYR* 3.7 4.5 - - - +
187E GLN* 2.9 26.5 + - - +
189E ARG* 3.0 28.9 + - - -
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Residues in contact with ALA 167 (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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144E VAL* 4.0 24.9 - - + -
146E LEU* 5.1 5.8 - - + +
149E VAL* 4.9 3.9 - - + +
166E THR* 1.3 79.5 - - - +
168E VAL* 1.3 59.4 + - - +
169E VAL* 2.9 19.4 + - - +
184E LEU* 5.6 0.2 - - + -
185E ASP 3.6 8.7 - - - +
186E TYR* 3.8 30.1 - - + -
187E GLN* 4.6 0.4 - - - +
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Residues in contact with VAL 168 (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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167E ALA* 1.3 66.3 - - - +
169E VAL* 1.3 65.7 - - + +
170E LYS* 3.2 23.8 + - + +
184E LEU* 3.2 20.7 - - - +
185E ASP* 3.0 27.4 + - + +
187E GLN* 3.3 33.8 - - - +
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Residues in contact with VAL 169 (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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143E ALA* 4.7 3.3 - - - +
144E VAL* 3.8 23.3 + - + +
146E LEU* 4.0 32.3 - - + -
167E ALA 2.9 15.6 + - - +
168E VAL* 1.3 72.9 - - + +
170E LYS* 1.3 64.1 + - + +
171E PRO* 3.3 12.3 - - - +
184E LEU* 3.9 5.9 - - - +
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Residues in contact with LYS 170 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E VAL* 3.2 21.0 + - + +
169E VAL* 1.3 83.7 - - + +
171E PRO* 1.3 79.8 - - + +
172E ALA* 3.3 5.0 + - - +
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Residues in contact with PRO 171 (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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141E VAL* 4.4 7.0 - - + -
142E LEU 3.1 25.8 - - - +
143E ALA* 5.2 2.0 - - + -
169E VAL 3.3 10.5 - - - +
170E LYS* 1.3 94.3 - - + +
172E ALA* 1.3 59.2 + - - +
173E ASN* 3.0 25.7 + - - +
182E SER* 3.7 9.6 - - - +
183E LYS 3.4 21.8 - - - +
184E LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 172 (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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170E LYS* 3.3 9.1 + - + +
171E PRO* 1.3 69.3 - - - +
173E ASN* 1.3 63.8 + - - +
174E PHE* 4.1 6.4 - - + -
183E LYS* 3.4 28.3 + - + +
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Residues in contact with ASN 173 (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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141E VAL* 3.3 30.3 - - - +
171E PRO* 3.0 19.9 + - - +
172E ALA* 1.3 76.0 - - - +
174E PHE* 1.3 67.6 + - - +
180E LEU* 4.2 17.1 - - + +
181E GLU 3.4 11.9 - - - +
182E SER* 2.9 30.0 + - - -
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Residues in contact with PHE 174 (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* 5.7 7.0 - - - -
131E ILE* 4.9 6.7 - - + -
172E ALA 4.1 3.8 - - - -
173E ASN* 1.3 83.7 - - - +
175E ALA* 1.3 68.8 + - - +
176E LEU* 3.7 7.8 + - + -
180E LEU* 3.4 10.8 - - - +
181E GLU* 2.9 48.4 + - + +
183E LYS* 4.0 43.5 - - + -
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Residues in contact with ALA 175 (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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174E PHE* 1.3 79.5 - - - +
176E LEU* 1.3 60.7 + - - +
177E GLU 4.2 0.4 + - - -
178E ASP* 5.3 8.1 - - - +
179E ARG 3.4 11.7 - - - +
180E LEU* 4.4 1.8 - - + +
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Residues in contact with LEU 176 (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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23D TYR* 3.3 49.8 - - + +
42D PHE* 3.5 29.2 - - + -
152D ASN* 5.2 1.8 - - - +
131E ILE* 5.6 1.1 - - + -
133E ARG* 3.1 12.9 + - - +
174E PHE* 3.7 10.2 + - + +
175E ALA* 1.3 73.4 - - - +
177E GLU* 1.3 82.5 + - + +
179E ARG 2.9 16.9 + - - +
181E GLU* 3.6 29.4 - - + +
403E ACT 4.1 9.4 - - + -
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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