Contacts of the helix formed by residues 196 - 205 (chain C) in PDB entry 3UO9
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 ASP 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.8 9.9 - - - -
152C GLU 4.7 7.2 - - - +
153C LYS* 5.0 5.4 - - + -
194C MET 4.9 1.4 - - - +
195C LEU* 1.3 76.3 - - - +
197C LYS* 1.3 53.9 + - - +
198C ASP* 2.6 34.1 + - - +
199C LEU* 3.1 26.8 + - - +
200C PHE* 2.9 19.9 + - - +
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Residues in contact with LYS 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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140C GLU 6.1 0.2 - - - -
141C ASP* 3.0 42.6 + - - +
144C PHE* 3.3 41.4 - - + +
145C TYR* 3.5 26.9 - - + +
152C GLU 4.8 0.8 + - - +
196C ASP* 1.3 72.0 + - - +
198C ASP* 1.3 59.4 + - + +
200C PHE* 4.4 0.7 - - - +
201C LYS* 3.2 25.3 + - - +
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Residues in contact with ASP 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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196C ASP* 2.6 18.9 + - - +
197C LYS* 1.3 78.3 + - + +
199C LEU* 1.3 65.0 + - + +
200C PHE 3.3 0.7 - - - -
201C LYS* 3.4 8.1 + - - +
202C LYS* 2.9 27.9 + - - +
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Residues in contact with LEU 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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185C THR* 4.8 20.4 - - + -
194C MET 4.6 5.6 - - - +
195C LEU* 4.4 22.2 - - + -
196C ASP* 3.1 32.6 + - - +
198C ASP* 1.3 80.9 - - + +
200C PHE* 1.3 60.6 + - - +
202C LYS* 3.3 14.1 + - + +
203C CYS* 2.9 35.6 + - - -
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Residues in contact with PHE 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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140C GLU 3.9 7.2 - - - -
143C LEU* 3.5 33.0 - - + -
144C PHE* 3.5 45.5 - + + -
147C ILE* 3.9 8.1 - - + -
154C ILE* 4.2 15.3 - - + -
159C PHE* 3.7 28.9 - + + -
195C LEU* 4.2 23.1 - - + +
196C ASP 2.9 17.0 + - - +
197C LYS 4.4 1.6 - - - +
199C LEU* 1.3 74.4 - - - +
201C LYS* 1.3 66.0 + - - +
203C CYS* 3.0 8.4 + - + +
204C VAL* 3.0 47.6 + - + +
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Residues in contact with LYS 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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138C SER* 3.3 25.3 + - - -
140C GLU* 3.8 36.0 + - + -
141C ASP* 4.4 10.5 - - - +
197C LYS 3.2 19.1 + - - +
198C ASP* 3.4 10.6 + - - +
199C LEU 3.3 0.2 - - - -
200C PHE* 1.3 79.6 - - + +
202C LYS* 1.3 64.2 + - - +
204C VAL* 4.3 7.4 - - - -
205C GLN* 3.1 46.9 + - + +
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Residues in contact with LYS 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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181C MET* 3.4 38.6 - - + +
184C LEU* 5.9 0.4 - - - +
185C THR* 4.7 14.8 - - + +
198C ASP 2.9 18.8 + - - +
199C LEU* 3.4 15.9 - - + +
200C PHE 3.2 0.2 - - - -
201C LYS* 1.3 78.4 - - - +
203C CYS* 1.3 59.9 + - - +
205C GLN* 4.3 16.5 + - - +
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Residues in contact with CYS 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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177C GLU 4.7 0.3 - - - -
178C CYS* 3.3 25.4 + - - -
181C MET* 3.7 33.5 - - + +
182C LEU* 3.7 33.7 - - + -
185C THR* 4.0 16.8 - - - -
195C LEU* 5.2 3.8 - - + -
199C LEU* 2.9 19.1 + - - +
200C PHE* 3.0 10.3 + - + +
202C LYS* 1.3 80.2 - - - +
204C VAL* 1.3 66.4 + - + +
205C GLN 3.5 0.4 + - - -
206C SER* 5.2 2.3 + - - -
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Residues in contact with VAL 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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140C GLU* 4.2 6.7 - - + -
143C LEU* 5.1 0.2 - - + -
159C PHE* 4.1 15.0 - - + -
178C CYS* 4.0 12.8 - - - -
200C PHE* 3.0 51.3 + - + +
201C LYS 4.2 3.1 - - - +
203C CYS* 1.3 81.1 - - + +
205C GLN* 1.3 65.7 + - - +
206C SER 3.2 3.5 + - - -
207C ASN 3.3 4.2 + - - -
208C ILE* 3.1 38.0 + - + -
211C LEU* 3.6 24.5 - - + -
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Residues in contact with GLN 205 (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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140C GLU* 3.6 25.3 - - + +
201C LYS* 3.1 32.9 + - - +
202C LYS* 4.3 14.3 + - - +
203C CYS 3.5 2.6 - - - -
204C VAL* 1.3 77.8 - - - +
206C SER* 1.3 60.8 + - - +
208C ILE* 3.4 21.0 - - - +
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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