Contacts of the helix formed by residues 194 - 204 (chain C) in PDB entry 3P3W
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 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ARG* 4.9 12.3 + - - -
138C ASP* 3.1 13.6 + - - +
140C GLU* 5.1 13.6 - - + +
141C ARG* 5.9 2.8 - - - +
193C CYS* 1.3 77.3 - - - +
195C VAL* 1.3 69.1 + - + +
196C GLU* 3.3 10.8 - - + +
197C ARG* 2.8 11.9 + - + +
198C ILE* 2.7 31.4 + - - -
221C ASN* 4.1 17.6 + - - +
277C TYR* 4.3 9.4 + - - -
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Residues in contact with VAL 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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193C CYS 4.1 0.4 + - - -
194C GLU* 1.3 83.0 + - + +
196C GLU* 1.3 76.9 + - - +
198C ILE* 4.0 5.8 - - - -
199C ASN* 3.0 43.3 + - - +
221C ASN* 3.4 20.9 + - - +
223C GLY* 3.9 10.3 - - - +
226C ASP* 4.6 15.9 - - + +
227C ILE* 3.8 23.1 - - + +
277C TYR* 6.3 0.9 - - + -
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Residues in contact with GLU 196 (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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15C ASN* 3.6 26.3 + - - +
194C GLU* 3.2 9.9 + - + +
195C VAL* 1.3 91.7 + - - +
197C ARG* 1.3 64.7 + - + +
199C ASN* 4.7 5.6 - - - +
200C THR* 3.6 19.7 - - - +
276C LYS* 6.0 0.3 + - - -
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Residues in contact with ARG 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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138C ASP* 4.5 16.6 - - - -
165C VAL 4.7 7.5 + - - -
166C GLY* 4.2 16.7 + - - -
167C ASN 5.5 0.2 - - - -
168C ILE 3.7 24.4 + - - -
169C LYS* 4.3 13.1 - - - +
174C PHE* 4.8 9.9 - - + -
193C CYS* 4.5 11.7 - - + -
194C GLU* 2.8 11.5 + - + +
196C GLU* 1.3 84.9 - - + +
198C ILE* 1.3 61.6 + - - +
199C ASN 3.4 0.4 - - - -
200C THR* 2.7 23.0 + - + +
201C ILE* 3.4 17.7 - - - +
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Residues in contact with ILE 198 (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 ILE* 3.7 22.0 - - + +
193C CYS* 3.1 33.9 - - + +
194C GLU 2.7 16.1 + - - +
195C VAL* 3.2 7.2 + - - +
197C ARG* 1.3 72.9 - - - +
199C ASN* 1.3 64.3 + - - +
201C ILE* 3.1 20.6 + - + +
202C LEU* 3.3 14.4 - - + +
219C LEU* 3.6 29.4 - - + -
221C ASN* 3.9 23.8 - - + +
227C ILE* 3.8 28.7 - - + -
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Residues in contact with ASN 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 VAL* 3.0 22.3 + - - +
196C GLU* 5.2 4.5 - - - +
198C ILE* 1.3 75.0 - - - +
200C THR* 1.3 51.6 + - + +
202C LEU* 3.2 10.2 + - - +
203C GLU* 2.8 32.9 + - - +
226C ASP 3.5 10.1 + - - -
227C ILE* 3.3 26.9 - - - +
228C LEU* 3.3 43.1 + - + +
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Residues in contact with THR 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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171C VAL* 5.1 9.6 - - + -
174C PHE* 4.4 14.4 - - - -
196C GLU 3.6 16.8 + - - +
197C ARG* 2.7 31.3 + - + +
199C ASN* 1.3 74.6 - - + +
201C ILE* 1.3 58.3 + - - +
203C GLU* 3.8 8.3 - - + -
204C GLN* 2.7 43.3 + - - +
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Residues in contact with ILE 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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136C LEU* 4.5 15.7 - - + -
165C VAL* 6.0 0.7 - - + -
174C PHE* 3.7 30.1 - - + -
178C ILE* 5.8 6.2 - - + +
191C ILE* 3.7 51.6 - - + -
193C CYS* 4.5 8.5 - - - -
197C ARG* 3.4 19.1 - - + +
198C ILE* 3.1 8.7 + - - +
200C THR* 1.3 77.6 - - - +
202C LEU* 1.3 59.9 + - + +
204C GLN* 3.1 21.3 + - - +
205C VAL* 3.3 22.8 - - + +
217C TYR* 5.5 4.7 - - + -
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Residues in contact with LEU 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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191C ILE* 4.8 2.9 - - + -
198C ILE* 3.3 38.8 - - + +
199C ASN 3.2 5.0 + - - +
201C ILE* 1.3 81.5 - - + +
203C GLU* 1.3 63.4 + - - +
204C GLN 3.3 0.2 - - - -
205C VAL* 3.5 13.0 + - + +
217C TYR* 4.7 21.8 - - + -
219C LEU* 4.5 13.2 - - + -
227C ILE* 4.6 4.3 - - + -
228C LEU 3.6 25.6 - - - +
229C LEU* 4.6 5.2 - - + -
231C ARG* 5.1 6.6 - - + +
232C VAL* 3.3 49.4 - - + +
239C ILE* 4.8 8.1 - - + -
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Residues in contact with GLU 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 ASN 2.8 15.1 + - - +
200C THR* 3.4 15.0 - - + +
201C ILE 3.2 0.2 - - - -
202C LEU* 1.3 76.4 - - - +
204C GLN* 1.3 70.8 + - - +
205C VAL 3.1 8.3 + - - -
231C ARG* 6.3 1.1 - - - -
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Residues in contact with GLN 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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171C VAL* 3.4 36.7 - - + +
172C GLN* 6.4 0.2 - - - -
174C PHE* 4.7 19.1 - - + -
175C ARG* 5.5 8.5 - - + +
178C ILE* 4.1 17.2 - - + +
200C THR* 2.7 37.3 + - - +
201C ILE* 3.1 11.4 + - - +
203C GLU* 1.3 88.2 - - - +
205C VAL* 1.3 58.9 + - - +
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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