Contacts of the helix formed by residues 178 - 194 (chain C) in PDB entry 3UGV
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 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ARG* 3.2 9.4 - - - +
177C ASP* 1.3 79.1 - - + +
179C PRO* 1.3 71.8 - - - +
180C ALA* 3.0 26.5 + - - +
181C VAL* 3.1 36.2 + - + +
182C ASP 3.7 2.9 + - - -
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Residues in contact with PRO 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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176C ARG 4.2 0.2 - - - -
177C ASP 3.5 8.7 - - - +
178C ASP* 1.3 91.4 - - - +
180C ALA* 1.3 62.5 + - - +
182C ASP* 3.0 22.8 + - + +
183C ILE* 3.3 9.6 + - - +
215C ARG* 3.7 41.3 - - + +
218C GLN* 3.3 30.3 - - - +
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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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178C ASP* 3.0 19.6 + - - +
179C PRO* 1.3 79.4 - - - +
181C VAL* 1.3 57.5 + - + +
183C ILE* 3.2 12.4 + - - +
184C GLU* 3.0 27.6 + - - +
218C GLN* 5.0 0.6 + - - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO* 3.7 30.7 - - + -
176C ARG* 3.6 20.4 - - + +
178C ASP* 3.1 32.4 + - + +
180C ALA* 1.3 74.7 - - + +
182C ASP* 1.3 60.2 + - - +
184C GLU* 4.0 13.7 - - - +
185C THR* 2.7 34.1 + - - -
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Residues in contact with ASP 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 5.0 0.2 - - - +
174C MET* 3.0 38.3 - - - +
175C GLY 2.8 24.6 + - - -
176C ARG* 3.0 47.1 + - - +
178C ASP 3.7 1.6 + - - -
179C PRO* 3.0 13.7 + - + +
181C VAL* 1.3 78.1 - - - +
183C ILE* 1.3 63.2 + - + +
185C THR* 3.3 4.9 + - - -
186C ALA 3.1 16.6 + - - -
203C PHE* 3.9 2.8 - - - -
215C ARG* 3.5 14.1 + - - -
219C ILE* 5.7 1.1 - - + -
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Residues in contact with ILE 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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174C MET* 4.8 0.7 - - - -
179C PRO 3.3 10.0 + - - +
180C ALA* 3.2 12.9 + - - +
181C VAL 3.2 0.4 - - - -
182C ASP* 1.3 72.7 - - - +
184C GLU* 1.3 69.7 + - - +
186C ALA* 3.0 9.2 + - - +
187C GLU* 2.9 32.8 + - + +
218C GLN* 4.1 37.2 - - + +
219C ILE* 4.0 19.1 - - + -
222C LEU* 4.3 21.1 - - + -
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Residues in contact with GLU 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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148C PRO* 3.8 25.2 - - + +
180C ALA 3.0 15.8 + - - +
181C VAL* 3.7 20.1 - - - +
183C ILE* 1.3 78.2 - - - +
185C THR* 1.3 57.3 + - - +
187C GLU* 3.3 7.0 + - - +
188C ALA* 2.8 33.1 + - + +
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Residues in contact with THR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO* 3.7 22.0 - - + +
151C VAL* 3.5 37.2 - - + -
172C LEU* 3.8 13.7 - - + -
176C ARG* 3.5 27.0 + - - +
181C VAL 2.7 22.8 + - - -
182C ASP 3.4 6.1 - - - -
183C ILE 3.1 0.2 - - - -
184C GLU* 1.3 74.1 - - - +
186C ALA* 1.3 61.3 + - - +
188C ALA* 3.7 1.8 - - - +
189C VAL* 2.8 35.9 + - + +
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Residues in contact with ALA 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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172C LEU* 3.8 22.3 - - + +
174C MET* 4.0 10.3 - - + -
182C ASP 3.1 11.7 + - - +
183C ILE 3.0 9.0 + - - +
185C THR* 1.3 77.4 - - - +
187C GLU* 1.3 61.9 + - - +
189C VAL* 3.3 2.8 + - - +
190C TRP* 3.1 41.0 + - + -
199C LEU* 3.9 4.3 - - + +
222C LEU* 4.1 17.3 - - + -
224C LEU* 4.9 2.2 - - + -
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Residues in contact with GLU 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 ILE* 2.9 29.1 + - + +
184C GLU* 3.8 6.5 - - - +
186C ALA* 1.3 75.1 - - - +
188C ALA* 1.3 57.4 + - - +
190C TRP* 3.4 18.1 + - - +
191C ASP* 2.9 38.9 + - - +
195C ARG* 3.5 32.1 + - - +
222C LEU* 4.4 14.8 - - - +
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Residues in contact with ALA 188 (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 PRO* 4.0 26.0 - - + +
149C ALA* 5.5 0.9 - - - -
152C ALA* 3.5 16.6 - - + +
184C GLU* 2.8 23.7 + - + +
185C THR* 3.8 3.6 - - - +
187C GLU* 1.3 71.4 - - - +
189C VAL* 1.3 64.4 + - - +
191C ASP* 3.5 11.9 + - - +
192C ALA* 3.2 16.8 + - - +
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Residues in contact with VAL 189 (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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143C LEU* 4.9 3.1 - - + -
151C VAL* 3.6 38.8 - - + +
152C ALA* 4.1 9.6 - - - +
155C ALA* 3.8 17.7 - - + -
170C LEU* 4.5 3.1 - - + -
172C LEU* 4.4 6.3 - - + -
185C THR* 2.8 22.8 + - + +
186C ALA 3.7 3.8 - - - +
188C ALA* 1.3 76.5 - - + +
190C TRP* 1.3 58.5 + - - +
192C ALA* 3.4 3.1 + - - +
193C VAL* 3.1 34.3 + - + +
199C LEU* 3.9 29.8 - - + -
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Residues in contact with TRP 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 ALA* 3.1 25.3 + - + +
187C GLU* 3.7 21.1 - - - +
188C ALA 3.2 0.2 - - - -
189C VAL* 1.3 75.6 - - - +
191C ASP* 1.3 61.4 + - - +
193C VAL* 4.5 2.2 - - + -
194C GLY* 2.8 52.0 + - - -
195C ARG* 3.5 44.8 + - + +
197C THR* 2.8 27.4 + - - -
198C ALA* 5.6 0.2 - - - -
199C LEU* 3.7 29.9 - - + +
222C LEU* 3.3 31.2 - - + -
223C GLY 3.5 23.8 - - - -
224C LEU* 3.8 16.4 - - + -
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Residues in contact with ASP 191 (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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187C GLU* 2.9 29.7 + - - +
188C ALA* 3.7 10.5 - - - +
189C VAL 3.4 0.2 - - - -
190C TRP* 1.3 76.4 - - - +
192C ALA* 1.3 59.3 + - - +
194C GLY* 4.3 2.4 + - - -
195C ARG* 4.1 13.1 + - - +
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Residues in contact with ALA 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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152C ALA* 3.8 27.4 - - + +
156C VAL* 4.0 17.1 - - + +
188C ALA 3.2 13.3 + - - +
189C VAL 3.7 4.0 - - - +
190C TRP 3.1 0.6 - - - -
191C ASP* 1.3 81.8 - - - +
193C VAL* 1.3 60.7 + - + +
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Residues in contact with VAL 193 (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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155C ALA* 3.8 35.0 - - + +
156C VAL* 4.0 10.3 - - + +
159C LYS* 4.2 24.0 - - + -
170C LEU* 4.5 3.4 - - + -
189C VAL* 3.1 31.1 + - + +
190C TRP* 4.5 2.2 - - + -
192C ALA* 1.3 80.5 - - - +
194C GLY* 1.3 61.2 + - - +
196C ASP* 5.4 1.7 - - - +
197C THR* 3.3 40.8 + - + +
199C LEU* 5.8 0.2 - - + -
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Residues in contact with GLY 194 (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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190C TRP* 2.8 24.2 + - - -
191C ASP 4.3 2.3 + - - -
192C ALA 3.7 1.2 - - - -
193C VAL* 1.3 77.6 - - - +
195C ARG* 1.3 58.0 + - - -
196C ASP* 2.9 13.6 + - - -
197C THR* 3.1 18.4 + - - -
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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