Contacts of the helix formed by residues 175 - 187 (chain C) in PDB entry 2DSA
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 TRP 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C ASN* 3.5 49.3 + - - -
133C LEU* 3.8 25.1 - - + -
134C GLY* 3.6 20.3 - - - -
137C ALA* 3.6 23.8 - - + -
170C ILE* 4.7 3.1 - - + -
171C ASP 3.3 20.2 - - - -
172C LEU* 2.9 39.1 + - + +
173C SER 3.1 0.2 - - - -
174C PRO* 1.3 102.2 + - + +
176C PRO* 1.4 58.9 - - - +
177C SER 3.2 3.6 - - - +
178C LEU* 2.9 43.6 + - + +
179C GLN 3.4 3.1 + - - -
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Residues in contact with PRO 176 (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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173C SER 3.6 8.5 - - - +
174C PRO 3.3 10.5 - - - +
175C TRP* 1.4 88.4 - - - +
177C SER* 1.3 57.1 + - - +
179C GLN* 3.4 18.6 + - - +
180C ALA* 3.0 28.5 + - - +
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Residues in contact with SER 177 (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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137C ALA* 2.7 42.9 + - - +
140C LEU* 3.7 24.1 - - - +
141C GLU* 4.0 15.3 + - - +
175C TRP* 5.2 0.2 - - - -
176C PRO* 1.3 79.7 - - - +
178C LEU* 1.3 57.5 + - - +
180C ALA* 3.7 7.7 - - - +
181C PHE* 3.1 26.2 + - - +
184C ARG* 4.4 2.3 + - - -
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Residues in contact with LEU 178 (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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133C LEU* 3.7 29.6 - - + +
136C VAL* 3.9 10.1 - - + -
137C ALA* 3.8 24.7 - - + +
140C LEU* 3.9 20.9 - - + -
162C LEU* 4.2 29.0 - - + +
172C LEU* 4.6 10.1 - - + -
175C TRP* 2.9 36.8 + - + +
177C SER* 1.3 76.2 + - - +
179C GLN* 1.3 59.5 + - - +
180C ALA 3.3 0.2 - - - -
181C PHE* 3.4 6.6 + - - +
182C GLN* 2.9 33.6 + - - +
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Residues in contact with GLN 179 (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 ASP* 5.1 0.6 + - - -
172C LEU* 3.6 36.7 + - + +
173C SER* 3.9 16.0 + - - +
175C TRP 3.4 1.2 + - - -
176C PRO* 3.4 22.8 + - - +
178C LEU* 1.3 75.2 - - - +
180C ALA* 1.3 63.9 + - - +
182C GLN* 3.3 22.0 + - - +
183C GLY* 3.2 18.9 + - - -
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Residues in contact with ALA 180 (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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176C PRO 3.0 17.2 + - - +
177C SER* 3.7 9.4 - - - +
178C LEU 3.3 0.2 - - - -
179C GLN* 1.3 73.1 - - - +
181C PHE* 1.3 61.4 + - - +
183C GLY* 3.3 2.5 + - - -
184C ARG* 3.0 45.2 + - - +
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Residues in contact with PHE 181 (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 LEU* 3.7 23.3 - - + -
144C PRO 3.7 15.3 - - - -
145C TYR* 4.4 2.0 - + - -
155C ASP* 3.2 47.3 - - + -
158C LEU* 3.7 23.6 - - + -
159C PHE* 3.7 25.1 - - + -
162C LEU* 3.9 16.6 - - + -
177C SER 3.1 18.8 + - - +
178C LEU 3.5 3.4 - - - +
179C GLN 3.3 0.2 - - - -
180C ALA* 1.3 76.6 - - - +
182C GLN* 1.3 59.5 + - - +
184C ARG* 3.2 17.0 + - - +
185C VAL* 2.9 47.7 + - + +
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Residues in contact with GLN 182 (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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159C PHE* 3.4 22.6 - - + +
162C LEU* 3.8 32.5 - - + +
163C GLY* 4.2 4.7 + - - -
165C SER* 4.8 0.3 + - - -
172C LEU* 3.8 28.4 - - - +
178C LEU 2.9 14.6 + - - +
179C GLN* 3.4 28.4 + - - +
180C ALA 3.3 0.4 - - - -
181C PHE* 1.3 76.2 - - - +
183C GLY* 1.3 51.8 + - - +
186C GLY* 2.8 34.1 + - - -
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Residues in contact with GLY 183 (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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179C GLN 3.2 10.2 + - - -
180C ALA* 3.8 3.4 - - - -
182C GLN* 1.3 75.6 - - - +
184C ARG* 1.3 65.9 + - - +
186C GLY* 5.1 0.9 - - - -
187C GLY* 3.4 17.7 + - - -
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Residues in contact with ARG 184 (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 LEU* 4.5 6.9 + - - +
143C ALA 4.2 4.0 + - - -
144C PRO* 2.9 55.5 + - - +
145C TYR* 3.5 24.4 + - + +
177C SER 4.4 4.0 + - - -
180C ALA* 3.0 32.7 + - - +
181C PHE* 3.2 33.0 + - - +
183C GLY* 1.3 78.9 - - - +
185C VAL* 1.3 62.7 + - + +
187C GLY* 4.0 4.3 + - - -
188C ARG* 4.0 10.9 + - - +
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Residues in contact with VAL 185 (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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145C TYR* 4.1 6.5 - - + -
151C LEU* 4.1 26.0 - - + -
155C ASP* 4.7 3.1 - - + +
156C ILE* 5.0 7.6 - - + -
159C PHE* 3.7 31.4 - - + -
181C PHE* 2.9 47.8 + - + +
184C ARG* 1.3 72.9 - - - +
186C GLY* 1.3 62.4 + - - +
187C GLY 3.1 6.3 + - - -
188C ARG* 3.1 19.5 + - - +
191C VAL* 3.2 23.0 - - + +
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Residues in contact with GLY 186 (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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159C PHE* 3.5 22.4 - - - -
182C GLN 2.8 22.9 + - - -
183C GLY* 4.3 1.1 - - - -
185C VAL* 1.3 73.1 - - - +
187C GLY* 1.3 56.4 + - - +
188C ARG 3.3 1.0 + - - -
191C VAL* 3.8 5.3 - - - +
192C GLN* 2.6 37.9 + - - +
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Residues in contact with GLY 187 (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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183C GLY 3.4 15.6 + - - -
184C ARG 4.0 3.5 + - - -
185C VAL 3.1 1.6 - - - -
186C GLY* 1.3 76.5 - - - +
188C ARG* 1.3 63.7 + - - +
189C GLU* 3.7 1.4 + - - -
192C GLN* 5.0 4.6 - - - +
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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