Contacts of the helix formed by residues 194 - 206 (chain C) in PDB entry 5DO7
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 SER 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C ARG* 4.9 2.0 - - - +
188C TYR* 4.5 6.7 - - - -
192C GLY 3.7 2.0 + - - -
193C ILE* 1.3 74.4 - - - +
195C THR* 1.3 57.0 + - - +
196C GLY* 3.1 2.7 - - - -
197C GLU* 2.8 61.6 + - - +
198C ARG* 2.8 17.5 + - - +
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Residues in contact with THR 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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188C TYR* 3.0 66.5 - - + +
193C ILE 4.5 0.2 - - - -
194C SER* 1.3 73.8 - - - +
196C GLY* 1.3 63.6 + - - +
198C ARG* 4.4 13.0 + - - +
199C ARG* 4.3 8.1 + - - +
222C GLY 5.4 1.6 + - - -
223C LEU* 3.8 23.2 - - + +
224C ASP* 5.3 7.2 - - - +
227C THR* 5.4 2.2 - - - +
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Residues in contact with GLY 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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194C SER* 3.1 2.8 - - - -
195C THR* 1.3 82.2 - - - +
197C GLU* 1.3 59.3 + - - +
199C ARG* 2.8 31.2 + - - +
200C ARG* 3.4 4.2 + - - -
223C LEU* 4.4 1.8 - - - -
227C THR* 3.5 29.8 + - - +
231C ILE* 4.2 9.5 - - - +
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 4.2 12.1 - - + +
179C HIS* 2.5 38.6 + - - -
180C VAL* 3.1 22.4 - - - +
183C ARG* 5.1 1.4 + - - -
193C ILE* 3.4 16.7 - - + +
194C SER* 2.8 33.4 + - - +
196C GLY* 1.3 67.8 - - - +
198C ARG* 1.3 68.1 + - - +
200C ARG* 2.8 39.9 + - - +
201C VAL* 2.8 15.2 + - - +
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Residues in contact with ARG 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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136C ASP* 3.5 35.7 + - - +
137C THR* 4.8 5.3 - - - +
138C LEU* 3.9 27.2 - - + +
185C ILE* 5.6 2.2 - - + -
186C GLY 4.4 14.8 + - - -
187C ASN* 4.6 5.8 - - - +
188C TYR* 3.7 35.8 - - - +
193C ILE* 3.3 21.4 + - + +
194C SER 2.8 18.6 + - - +
195C THR* 4.7 10.6 + - - +
196C GLY 3.1 0.2 + - - -
197C GLU* 1.3 71.5 - - - +
199C ARG* 1.3 66.8 + - - +
201C VAL* 2.9 19.3 + - + +
202C SER* 3.0 8.3 + - - -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.5 20.4 - - - +
133C LEU 3.2 27.0 + - - -
134C GLN 4.1 11.5 + - - -
135C SER 4.1 2.0 + - - -
136C ASP* 2.9 38.7 + - - +
195C THR 4.3 6.7 + - - +
196C GLY* 2.8 13.8 + - - +
198C ARG* 1.3 75.5 - - - +
200C ARG* 1.3 66.6 + - - +
202C SER* 2.8 23.7 + - - -
203C ILE* 3.2 13.3 + - + +
217C ASP 3.6 3.4 + - - -
219C PRO* 3.1 48.4 + - - +
221C THR 5.5 3.2 + - - -
223C LEU* 5.3 8.3 - - + -
231C ILE* 4.5 25.4 - - + -
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Residues in contact with ARG 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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175C LEU* 3.6 21.9 - - + +
176C SER* 3.6 24.1 + - - -
177C LEU* 4.0 18.6 - - + -
179C HIS* 4.7 4.4 - - - -
196C GLY 3.4 0.8 + - - -
197C GLU* 2.8 41.1 + - - +
199C ARG* 1.3 77.4 - - - +
201C VAL* 1.3 62.9 + - - +
203C ILE* 2.8 25.8 + - + +
204C ALA 3.2 7.6 + - - -
230C GLN* 3.0 43.1 - - - +
231C ILE* 4.2 15.2 - - + +
234C LEU* 3.3 33.1 - - + +
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Residues in contact with VAL 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 LEU* 3.5 25.8 - - + -
144C VAL* 3.6 36.8 - - + -
147C THR* 5.4 7.4 - - + -
148C LEU* 4.5 9.6 - - + +
177C LEU* 3.4 26.6 - - + +
185C ILE* 5.7 2.0 - - + -
193C ILE* 4.2 11.4 - - + -
197C GLU 2.8 16.4 + - - +
198C ARG* 2.9 8.7 + - - +
200C ARG* 1.3 70.8 - - - +
202C SER* 1.3 67.3 + - - +
204C ALA* 2.8 21.6 + - - +
205C ALA* 3.3 4.8 + - + +
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Residues in contact with SER 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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132C VAL* 5.1 6.9 - - - +
133C LEU* 5.8 3.6 + - - +
135C SER 4.9 0.9 + - - -
136C ASP* 3.3 36.6 - - - +
138C LEU* 4.4 12.8 - - - +
198C ARG 3.0 2.7 + - - -
199C ARG* 2.8 23.6 + - - -
201C VAL* 1.3 78.1 - - - +
203C ILE* 1.3 61.8 + - - +
205C ALA* 3.3 19.1 + - - +
206C GLN* 3.8 7.6 + - - +
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Residues in contact with ILE 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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132C VAL* 4.6 15.5 - - + -
175C LEU* 4.0 12.1 - - + -
199C ARG* 3.5 19.1 - - + +
200C ARG* 2.8 16.8 + - + +
202C SER* 1.3 75.4 - - - +
204C ALA* 1.3 55.8 + - - +
206C GLN* 2.8 27.3 + - + +
207C LEU* 3.2 26.2 + - + +
214C MET* 4.8 2.2 - - + -
216C PHE* 3.9 39.0 - - + -
231C ILE* 5.0 16.4 - - + -
234C LEU* 5.5 6.5 - - + -
235C LEU* 5.4 3.8 - - + -
238C LEU* 4.5 12.1 - - + -
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Residues in contact with ALA 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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148C LEU* 3.5 26.2 - - + -
171C VAL* 3.4 24.4 - - + +
172C MET 5.4 0.2 - - - +
175C LEU* 3.3 19.5 - - + +
177C LEU* 4.6 4.0 - - + -
200C ARG 3.2 2.4 + - - +
201C VAL* 2.8 20.1 + - - +
203C ILE* 1.3 77.9 - - - +
205C ALA* 1.3 54.7 + - - +
207C LEU* 2.8 18.7 + - - -
208C LEU* 3.3 10.7 + - - +
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Residues in contact with ALA 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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138C LEU* 6.2 4.0 - - + -
147C THR* 6.4 0.7 - - + -
148C LEU* 3.5 12.7 - - + +
151C THR* 4.1 27.7 - - + +
201C VAL* 3.3 4.1 + - + +
202C SER* 3.3 14.7 + - - +
203C ILE 3.2 0.8 - - - -
204C ALA* 1.3 78.1 - - - +
206C GLN* 1.3 65.6 + - - +
207C LEU 3.3 0.9 + - - -
208C LEU* 3.8 20.0 + - - +
209C GLN* 3.9 13.2 + - - +
457C LEU* 6.0 1.3 - - + +
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Residues in contact with GLN 206 (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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130C SER* 2.8 28.2 + - - +
131C TYR 3.4 26.4 - - - +
132C VAL* 4.1 15.9 - - + -
202C SER 3.8 6.0 + - - +
203C ILE* 2.8 15.5 + - + +
205C ALA* 1.3 78.0 - - - +
207C LEU* 1.3 62.1 + - - +
209C GLN* 4.1 19.5 + - - +
211C PRO* 3.3 25.8 - - - +
214C MET* 4.0 5.1 - - - +
357C LYS* 4.9 2.2 - - - +
455C ASP* 3.0 34.8 + - - +
457C LEU* 4.6 7.4 - - - +
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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