Contacts of the helix formed by residues 178 - 191 (chain E) in PDB entry 1W88
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 GLN 178 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E ILE* 4.0 34.2 - - + +
145E GLY* 4.9 2.9 - - - -
174E GLY 4.0 8.4 + - - +
175E GLY* 3.1 16.8 + - - +
177E SER* 1.3 83.1 - - - +
179E GLY* 1.3 62.4 + - - +
180E ASN* 3.4 6.7 - - + +
181E PHE* 3.3 12.7 - - - +
182E TYR* 3.1 22.4 - - - -
1370E TPP 4.6 10.3 + - - +
183G GLN* 4.6 2.1 + - - +
57H LEU* 2.8 30.1 + - - +
58H ALA* 4.6 3.5 - - - -
59H GLU* 3.6 24.3 + - - +
88H GLU* 4.2 13.0 - - - +
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Residues in contact with GLY 179 (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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177E SER 4.2 0.4 + - - -
178E GLN* 1.3 72.8 + - - +
180E ASN* 1.3 60.4 + - - +
182E TYR* 3.2 8.6 + - - +
183E GLN* 2.8 38.0 + - - +
179G GLY* 4.2 23.6 - - - -
183G GLN* 4.4 9.0 - - - +
88H GLU* 4.7 11.4 + - - -
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Residues in contact with ASN 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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143E ILE* 5.9 0.4 - - - +
144E ILE 5.2 2.2 + - - +
145E GLY* 3.2 24.0 - - - +
146E ALA* 3.8 16.2 - - - +
148E TYR* 3.6 4.9 - - - +
149E ILE* 3.4 26.4 + - + +
178E GLN* 3.4 3.5 - - + +
179E GLY* 1.3 77.2 - - - +
181E PHE* 1.3 52.9 + - - +
183E GLN* 4.0 15.5 - - - +
184E GLY* 2.7 31.2 + - - -
60F SER* 4.7 9.4 - - - +
91F ASP* 3.7 22.0 + - - +
88H GLU* 5.1 8.7 + - - -
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Residues in contact with PHE 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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145E GLY* 4.5 2.5 + - - -
148E TYR* 3.3 44.7 - + + +
171E THR* 4.6 1.8 - - + -
175E GLY 3.3 21.3 - - - +
176E THR* 3.7 46.0 - - + -
178E GLN* 3.3 10.5 + - - +
179E GLY 3.2 0.6 - - - -
180E ASN* 1.3 78.2 - - - +
182E TYR* 1.3 76.8 + + - +
184E GLY* 3.8 0.3 - - - -
185E ILE* 3.1 40.6 + - + +
199E VAL* 3.7 9.9 - - + -
219E LEU 5.1 0.4 - - - -
222E LYS* 4.0 22.9 - - + -
260E LEU* 4.1 24.5 - - + -
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Residues in contact with TYR 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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176E THR 3.2 20.6 + - - -
177E SER* 4.5 6.4 - - - -
178E GLN 3.1 24.7 - - - -
179E GLY* 3.2 7.2 + - - +
181E PHE* 1.3 92.3 - + - +
183E GLN* 1.3 57.6 + - + +
185E ILE* 3.3 10.0 - - + +
186E ASN* 2.9 32.3 + - - +
222E LYS* 3.0 31.0 + - + -
225E ALA* 4.5 8.1 - - + -
179G GLY* 6.1 0.2 - - - -
182G TYR* 3.6 71.0 + + + -
183G GLN* 6.4 0.4 - - + -
186G ASN* 3.4 14.6 + - - -
225G ALA* 3.8 17.1 + - + -
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Residues in contact with GLN 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ILE* 4.3 3.8 - - + -
179E GLY* 2.8 19.3 + - - +
180E ASN* 4.0 12.5 - - - +
182E TYR* 1.3 77.9 - - + +
184E GLY* 1.3 57.9 + - - +
186E ASN* 4.4 4.5 - - + -
187E PHE* 2.8 44.2 + - + +
58F ALA* 3.8 17.6 - - + +
60F SER* 2.7 31.3 + - - -
61F GLY* 3.3 14.1 + - - -
88F GLU* 4.3 5.1 + - - -
177G SER 3.5 24.9 + - - +
178G GLN* 4.3 2.6 + - - +
179G GLY* 3.8 18.4 - - - +
182G TYR* 6.4 0.7 - - + -
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Residues in contact with GLY 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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148E TYR* 3.7 20.4 - - - -
149E ILE* 3.9 12.1 - - - +
152E ALA* 3.7 3.5 - - - +
180E ASN 2.7 22.3 + - - -
181E PHE 3.8 0.9 - - - -
182E TYR 3.3 0.2 - - - -
183E GLN* 1.3 73.6 - - - +
185E ILE* 1.3 61.3 + - - +
188E ALA* 3.1 26.7 + - - +
197E PHE* 3.6 8.1 - - - -
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Residues in contact with ILE 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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148E TYR* 4.1 10.1 - - + -
181E PHE* 3.1 33.0 + - + +
182E TYR* 3.3 20.6 - - + +
184E GLY* 1.3 74.9 - - - +
186E ASN* 1.3 56.0 + - + +
188E ALA* 4.0 0.9 - - - +
189E GLY* 2.9 25.3 + - - -
197E PHE* 3.8 36.8 - - + -
222E LYS 3.7 25.4 - - - +
223E ALA* 4.4 5.2 - - - -
225E ALA* 5.0 0.4 - - + -
226E ALA* 3.6 22.9 - - + +
228E ILE* 3.9 17.3 - - + +
260E LEU* 4.6 8.3 - - + -
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Residues in contact with ASN 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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182E TYR 2.9 20.3 + - - +
183E GLN* 3.9 4.9 - - - +
185E ILE* 1.3 76.0 - - - +
187E PHE* 1.3 61.9 + - + +
189E GLY* 3.3 0.9 + - - -
190E ALA* 2.9 30.7 + - - +
225E ALA 3.7 0.7 - - - +
226E ALA* 3.3 19.6 - - + +
56F PRO* 5.3 3.6 - - - +
177G SER* 4.5 12.9 + - - +
182G TYR* 4.6 5.9 + - - +
213G GLN 2.7 29.9 + - - -
214G THR* 3.1 25.6 + - - -
215G VAL 5.6 0.2 + - - -
222G LYS* 3.6 11.5 + - - +
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Residues in contact with PHE 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ILE* 3.8 20.4 - - + -
152E ALA* 4.0 5.8 - - + -
183E GLN* 2.8 33.6 + - + +
184E GLY 4.0 1.1 - - - +
186E ASN* 1.3 74.2 - - + +
188E ALA* 1.3 65.0 + - - +
190E ALA* 3.3 4.0 + - - -
191E PHE* 3.1 49.5 + + + -
55F THR* 4.4 7.2 - - - -
56F PRO* 3.9 40.2 - - + -
58F ALA* 3.7 24.2 - - + -
61F GLY* 3.6 37.0 - - - -
62F ILE* 3.9 6.7 - - + -
65F LEU* 4.2 11.0 - - + -
177G SER* 6.2 0.2 - - - -
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Residues in contact with ALA 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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152E ALA* 3.9 12.0 - - + +
184E GLY 3.1 18.4 + - - +
185E ILE 4.0 0.4 - - - +
187E PHE* 1.3 76.5 - - - +
189E GLY* 1.3 62.6 + - - +
191E PHE* 5.4 0.2 - - - -
192E LYS* 3.1 3.8 + - - -
193E ALA* 2.9 43.2 + - + -
195E ALA* 4.5 2.2 - - + -
197E PHE* 3.6 28.0 - - + -
258E PRO* 3.7 12.0 - - + +
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Residues in contact with GLY 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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185E ILE 2.9 20.2 + - - -
186E ASN* 3.6 2.0 - - - -
188E ALA* 1.3 76.1 - - - +
190E ALA* 1.3 59.2 + - - +
192E LYS* 3.2 15.8 + - - +
226E ALA 5.0 1.1 - - - -
228E ILE* 3.9 13.9 - - - -
258E PRO* 3.6 13.5 - - - +
215G VAL* 3.5 24.6 - - - +
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Residues in contact with ALA 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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186E ASN 2.9 19.6 + - - +
187E PHE 3.3 3.1 + - - +
189E GLY* 1.3 74.6 - - - +
191E PHE* 1.3 62.1 + - + +
192E LYS* 3.4 2.0 - - - +
56F PRO* 4.2 23.3 - - + -
213G GLN 4.3 17.9 - - - +
214G THR* 4.5 4.5 - - - +
215G VAL* 4.3 12.9 - - - +
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Residues in contact with PHE 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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152E ALA 6.1 0.2 - - - -
156E LEU* 3.9 32.8 - - + -
159E LYS* 2.7 33.5 + - - +
187E PHE* 3.1 43.9 + + - +
188E ALA 4.3 1.6 - - - +
190E ALA* 1.3 78.9 - - - +
192E LYS* 1.3 58.8 + - - +
193E ALA* 3.2 7.6 + - + +
53F PHE* 4.3 13.0 - + - -
54F ASP 3.8 23.6 - - - -
55F THR* 4.2 4.0 - - + -
56F PRO* 4.0 25.6 - - + -
65F LEU* 4.1 23.1 - - + -
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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