Contacts of the helix formed by residues 179 - 190 (chain F) in PDB entry 1GUL
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 PRO 179 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137F GLU* 3.2 11.9 - - - +
176F SER 4.2 2.9 - - - +
177F ALA* 3.0 13.0 - - - +
178F PHE* 1.3 91.3 - - - +
180F PHE* 1.3 71.1 + - + +
182F GLN* 3.2 16.0 + - - +
183F GLU* 3.0 22.7 + - - +
42H TYR* 3.5 47.8 - - + -
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Residues in contact with PHE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F GLU* 3.0 28.7 + - + +
140F LEU* 4.2 23.4 - - + +
141F ARG* 3.5 58.6 - - + -
144F GLY* 5.6 4.5 - - - -
179F PRO* 1.3 85.7 - - + +
181F LEU* 1.3 58.0 + - - +
183F GLU* 3.1 11.6 + - - +
184F TYR* 2.8 31.6 + - - +
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Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE* 3.5 54.7 - - + +
136F PHE* 3.9 17.0 - - + -
137F GLU* 2.7 19.8 + - - +
140F LEU* 3.8 18.6 - - + -
160F LEU* 4.6 3.6 - - + -
164F ILE* 4.4 11.0 - - + -
175F LEU* 3.7 13.5 - - + -
178F PHE* 3.4 19.7 - - + +
180F PHE* 1.3 73.7 - - - +
182F GLN* 1.3 62.4 + - - +
184F TYR* 3.5 15.2 - - + +
185F THR* 2.7 30.5 + - - -
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Residues in contact with GLN 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 2.9 44.8 + - + +
176F SER* 3.2 19.6 + - - +
178F PHE 2.6 18.4 + - - +
179F PRO* 3.6 11.2 - - - +
180F PHE 3.1 0.6 - - - -
181F LEU* 1.3 75.6 - - - +
183F GLU* 1.3 63.5 + - - +
185F THR* 3.3 2.5 + - - -
186F VAL* 3.1 28.1 + - + +
38H LYS* 6.2 0.2 - - - -
42H TYR* 3.8 16.9 + - - -
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F PRO 3.0 10.7 + - - +
180F PHE* 3.7 13.3 - - - +
182F GLN* 1.3 78.8 - - - +
184F TYR* 1.3 65.2 + - - +
186F VAL* 3.0 10.8 + - + +
187F LYS* 2.9 52.1 + - + +
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Residues in contact with TYR 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 3.7 32.1 - - + -
146F SER* 3.3 30.0 - - - +
148F LEU* 3.5 15.8 - - + +
157F ASP* 2.6 45.0 + - - -
160F LEU* 4.0 21.6 - - + +
161F LEU* 5.2 1.3 - - - -
164F ILE* 4.9 3.1 - - + -
180F PHE 2.8 17.2 + - - +
181F LEU* 3.5 17.9 - - + +
183F GLU* 1.3 76.9 - - - +
185F THR* 1.3 62.1 + - - +
187F LYS* 3.3 14.5 + - - +
188F LEU* 2.8 55.4 + - + +
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Residues in contact with THR 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F LEU* 4.0 22.7 - - + +
164F ILE* 3.9 20.5 - - + +
165F LEU* 4.1 17.5 - - + -
168F GLU* 5.2 2.9 - - - +
175F LEU* 3.8 12.2 - - + +
181F LEU 2.7 22.0 + - - -
182F GLN* 3.4 7.4 - - - -
184F TYR* 1.3 81.6 - - - +
186F VAL* 1.3 62.2 + - + +
188F LEU* 3.8 1.1 - - - +
189F SER* 2.4 38.6 + - - +
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Residues in contact with VAL 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F GLN* 3.1 17.2 + - + +
183F GLU* 3.0 12.7 + - + +
185F THR* 1.3 85.6 - - + +
187F LYS* 1.3 69.2 + - + +
189F SER* 3.1 11.2 + - - -
190F ASN* 2.8 32.2 + - - +
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Residues in contact with LYS 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN 4.6 3.2 + - - -
146F SER* 3.3 42.9 + - - +
183F GLU* 2.9 41.7 + - + +
184F TYR* 3.6 17.4 - - - +
186F VAL* 1.3 83.3 - - + +
188F LEU* 1.3 65.7 + - + +
190F ASN* 2.8 19.9 + - - +
191F ILE* 3.4 8.0 + - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F SER* 4.2 10.5 - - - +
147F PHE* 4.1 14.1 - - + -
153F LEU* 4.0 17.5 - - + -
157F ASP* 3.9 18.2 - - + +
161F LEU* 4.0 23.1 - - + -
184F TYR* 2.8 60.5 + - + +
185F THR 3.8 4.0 - - - +
187F LYS* 1.3 74.5 - - + +
189F SER* 1.3 64.4 + - - +
190F ASN 2.9 1.4 + - - -
191F ILE* 3.0 38.8 + - + +
194F ILE* 3.5 11.7 - - + +
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Residues in contact with SER 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F LEU* 4.0 12.2 - - - +
165F LEU* 5.1 3.5 - - - +
185F THR* 2.4 31.7 + - - +
186F VAL* 3.7 6.4 - - - -
187F LYS 3.0 0.4 - - - -
188F LEU* 1.3 80.5 - - - +
190F ASN* 1.3 62.4 + - - +
191F ILE 3.3 0.4 - - - -
194F ILE* 3.9 9.9 - - - -
195F LYS* 3.5 23.7 + - - +
198F LEU* 3.6 21.4 - - - +
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Residues in contact with ASN 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F VAL* 2.8 37.4 + - - +
187F LYS* 2.8 12.0 + - - +
189F SER* 1.3 83.0 - - - +
191F ILE* 1.3 65.1 + - - +
192F PRO* 3.2 9.5 - - - +
195F LYS* 4.1 27.8 - - + +
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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