Contacts of the helix formed by residues 189 - 204 (chain C) in PDB entry 5UWS
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 GLU 189 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C TRP* 3.8 25.9 + - + -
131C PRO* 4.4 8.3 - - - +
135C PRO 4.3 8.9 - - - +
138C ILE* 3.3 30.5 - - + +
139C PRO* 3.6 10.9 - - - +
185C SER 3.5 10.1 + - - +
186C MET* 3.3 6.4 + - - +
188C LYS* 1.3 80.8 - - + +
190C PHE* 1.3 62.2 + - - +
191C GLU 3.4 2.5 - - - -
192C GLN* 3.3 33.6 + - - +
193C ILE* 3.4 20.0 - - + +
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C MET 3.0 15.7 + - - +
187C SER* 3.5 8.3 + - - +
188C LYS 3.3 2.8 - - - -
189C GLU* 1.3 75.2 - - - +
191C GLU* 1.3 66.8 + - - +
192C GLN 3.2 2.2 - - - -
193C ILE* 3.0 26.5 + - + -
194C PHE* 2.8 46.6 + + + +
217C LEU* 6.1 0.2 - - + -
220C TYR* 3.8 32.3 - + - -
223C TRP* 4.0 21.8 - + + -
224C ILE* 3.5 30.3 - - + -
225C PRO* 5.1 1.6 - - + -
228C TYR* 3.6 43.5 - + - +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C SER 4.8 0.8 + - - +
188C LYS 4.4 8.1 + - - +
189C GLU 3.4 0.6 - - - -
190C PHE* 1.3 78.6 - - - +
192C GLN* 1.3 65.8 + - - +
194C PHE* 3.5 4.0 + - - +
195C LYS* 3.3 32.6 + - - +
227C ARG* 4.5 8.6 + - - +
228C TYR* 2.7 42.8 + - - +
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Residues in contact with GLN 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ILE* 3.8 8.4 - - + +
139C PRO* 4.4 12.1 - - - +
142C ILE* 3.4 31.5 - - + +
188C LYS 4.9 0.9 - - - +
189C GLU* 3.3 47.4 + - - +
191C GLU* 1.3 82.4 - - - +
193C ILE* 1.3 68.7 + - - +
194C PHE 3.2 0.2 - - - -
195C LYS* 3.4 12.5 + - + +
196C LEU* 3.3 17.7 + - - +
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C TRP* 6.4 0.4 - - + -
138C ILE* 3.9 34.3 - - + -
141C LEU* 6.3 0.7 - - + -
142C ILE* 4.5 5.2 - - + -
159C LEU* 4.1 21.5 - - + -
186C MET* 4.4 22.7 - - + +
189C GLU* 3.4 18.8 - - + +
190C PHE* 3.0 24.3 + - + +
192C GLN* 1.3 80.3 - - - +
194C PHE* 1.3 61.9 + - - +
196C LEU* 3.4 7.3 + - - +
197C CYS* 3.1 21.9 + - - -
220C TYR* 3.6 33.4 - - + +
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Residues in contact with PHE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PHE* 2.8 44.4 + + + +
191C GLU* 3.8 5.4 - - - +
193C ILE* 1.3 76.0 - - - +
195C LYS* 1.3 60.6 + - + +
197C CYS* 3.1 10.2 + - + +
198C PHE* 2.7 50.3 + + + +
217C LEU* 5.0 7.2 - - + -
220C TYR* 5.9 0.9 - + - -
224C ILE* 5.2 0.7 - - + -
228C TYR* 3.1 51.6 - + + -
229C ILE* 4.8 4.5 - - + -
232C THR* 3.9 22.0 - - + -
234C ILE* 3.9 28.3 - - + -
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLU* 3.3 23.6 + - - +
192C GLN* 3.7 13.0 - - + +
193C ILE 3.3 0.4 - - - -
194C PHE* 1.3 82.9 - - + +
196C LEU* 1.3 57.3 + - - +
198C PHE* 3.9 3.3 - - - +
199C GLN* 2.8 53.5 + - - +
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Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 4.0 19.7 - - + -
142C ILE* 4.1 24.7 - - + +
145C SER* 3.8 35.7 - - - +
152C CYS* 4.4 3.4 - - - -
155C ASN* 5.5 1.3 - - + -
156C MET* 3.9 16.2 - - + -
159C LEU* 4.7 10.1 - - + -
192C GLN 3.3 10.1 + - - +
193C ILE* 3.6 8.3 - - - +
195C LYS* 1.3 77.3 - - - +
197C CYS* 1.3 63.0 + - - +
199C GLN* 3.5 12.2 + - + +
200C VAL* 3.1 40.9 + - + +
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Residues in contact with CYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C MET* 4.0 24.0 - - - -
159C LEU* 5.3 1.1 - - - -
193C ILE* 3.1 20.9 + - - +
194C PHE* 3.1 14.8 + - + +
196C LEU* 1.3 78.2 - - - +
198C PHE* 1.3 62.2 + - - +
200C VAL 3.4 0.2 + - - -
201C LEU* 3.1 31.6 + - + +
213C THR* 3.7 15.8 - - + +
216C SER* 4.1 4.7 - - - -
217C LEU* 6.1 5.6 - - + -
220C TYR* 3.6 33.9 - - + -
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C PHE* 2.7 42.9 + + + +
195C LYS* 3.9 3.8 - - - +
197C CYS* 1.3 70.6 - - - +
199C GLN* 1.3 70.2 + - + +
201C LEU* 3.4 7.0 + - + +
202C GLU* 3.1 56.4 + - - +
232C THR* 4.3 4.5 - - + -
233C ASN* 4.0 20.4 - - + -
234C ILE* 3.6 45.3 - - + +
237C LEU* 4.2 10.0 - - + +
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LYS* 2.8 41.2 + - - +
196C LEU* 3.8 12.2 - - + +
198C PHE* 1.3 75.1 - - + +
200C VAL* 1.3 67.7 + - + +
202C GLU* 3.2 2.3 + - - -
203C GLN* 2.9 54.2 + - - +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C CYS* 4.0 17.7 - - - -
156C MET* 3.8 15.9 - - + -
196C LEU* 3.1 22.8 + - + +
197C CYS 3.7 4.5 - - - +
199C GLN* 1.3 76.1 - - + +
201C LEU* 1.3 59.9 + - - +
203C GLN* 5.3 0.4 - - - -
204C GLY* 2.7 32.6 + - - +
209C LEU* 3.7 25.4 - - + +
210C ILE* 3.5 12.4 - - + +
213C THR* 3.3 26.5 - - - +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C CYS* 3.1 22.1 + - + +
198C PHE* 3.9 6.1 - - - +
199C GLN 3.3 0.2 - - - -
200C VAL* 1.3 77.0 - - - +
202C GLU* 1.3 58.1 + - - +
204C GLY 4.7 0.2 + - - -
210C ILE* 4.2 12.8 - - + +
213C THR* 3.9 23.3 - - + -
214C LEU* 3.6 39.7 - - + -
217C LEU* 4.5 6.7 - - + -
234C ILE* 4.2 28.9 - - + -
237C LEU* 4.3 8.4 - - + +
238C LEU* 5.2 0.2 - - + -
241C LYS* 3.0 19.9 + - - +
242C PHE* 3.2 33.5 - - + -
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Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.1 48.8 + - + +
199C GLN* 4.0 3.4 - - - +
201C LEU* 1.3 79.0 - - - +
203C GLN* 1.3 65.0 + - + +
233C ASN* 4.4 12.0 + - - +
237C LEU* 4.3 19.0 - - + +
241C LYS* 3.2 16.1 + - - +
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Residues in contact with GLN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLN* 2.9 44.9 + - - +
200C VAL* 5.3 0.4 - - - -
202C GLU* 1.3 87.4 + - + +
204C GLY* 1.3 67.5 + - - +
205C SER* 3.7 2.9 + - - -
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Residues in contact with GLY 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C VAL* 2.7 29.7 + - - +
202C GLU 3.8 0.2 - - - -
203C GLN* 1.3 77.9 - - - +
205C SER* 1.3 59.9 + - - -
209C LEU* 5.4 7.2 - - - -
210C ILE* 3.8 18.4 - - - +
241C LYS* 4.7 10.4 + - - -
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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