Contacts of the helix formed by residues 178 - 194 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.0 10.0 - - + +
177A ASP* 1.3 80.7 - - + +
179A PRO* 1.3 74.2 - - - +
180A ALA* 3.0 20.9 + - - +
181A VAL* 3.1 37.1 + - + +
182A ASP 3.7 2.8 + - - -
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG 4.2 0.2 - - - -
177A ASP 3.7 8.1 - - - +
178A ASP* 1.3 90.7 - - - +
180A ALA* 1.3 61.6 + - - +
182A ASP* 3.0 19.4 + - + +
183A ILE* 3.3 13.7 + - - +
215A ARG* 3.8 37.2 - - + +
218A GLN* 3.7 33.9 - - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 3.0 16.7 + - - +
179A PRO* 1.3 78.8 - - - +
181A VAL* 1.3 58.2 + - + +
183A ILE* 3.6 12.4 + - - +
184A GLU* 2.9 30.3 + - - +
218A GLN* 4.9 1.9 + - - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO* 3.8 28.9 - - + -
176A ARG* 3.6 22.2 - - + +
178A ASP* 3.1 29.8 + - + +
179A PRO 3.1 1.0 - - - -
180A ALA* 1.3 77.0 - - + +
182A ASP* 1.3 52.8 + - - +
184A GLU* 3.3 13.9 - - - +
185A THR* 2.6 42.3 + - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MET* 3.5 33.0 - - - +
175A GLY 3.0 25.0 + - - -
176A ARG* 2.6 56.6 + - - +
178A ASP 3.7 1.0 + - - -
179A PRO* 3.0 12.2 + - + +
181A VAL* 1.3 78.0 - - - +
183A ILE* 1.3 57.0 + - + +
185A THR* 3.2 4.3 + - - -
186A ALA 2.9 23.4 + - - -
203A PHE* 4.4 2.3 - - - -
215A ARG* 3.4 15.8 + - - -
219A ILE* 5.8 1.3 - - + -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MET* 4.8 0.7 - - - -
179A PRO 3.3 9.5 + - - +
180A ALA* 3.8 10.5 - - - +
182A ASP* 1.3 73.2 - - + +
184A GLU* 1.3 58.7 + - - +
186A ALA* 2.9 7.9 + - - +
187A GLU* 2.8 47.0 + - + +
218A GLN* 4.0 39.3 - - + +
219A ILE* 3.9 18.6 - - + -
222A LEU* 4.4 18.2 - - + -
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO* 4.0 21.9 - - + +
180A ALA* 2.9 18.4 + - - +
181A VAL* 3.3 21.1 - - - +
183A ILE* 1.3 76.9 - - - +
185A THR* 1.3 59.2 + - - +
187A GLU* 3.3 6.3 + - - +
188A ALA* 2.8 31.7 + - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO* 3.5 25.3 - - + +
151A VAL* 3.7 31.4 - - + -
172A LEU* 4.0 11.2 - - + -
176A ARG* 3.3 36.5 + - - +
181A VAL 2.6 26.8 + - - -
182A ASP 3.5 5.2 - - - -
184A GLU* 1.3 73.2 - - - +
186A ALA* 1.3 62.4 + - - +
188A ALA* 3.3 1.9 + - - +
189A VAL* 3.0 23.9 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.7 24.1 - - + +
174A MET* 3.9 10.3 - - + -
182A ASP 2.9 12.7 + - - +
183A ILE 3.3 7.9 - - - +
185A THR* 1.3 75.6 - - - +
187A GLU* 1.3 63.3 + - - +
189A VAL* 3.2 3.9 + - - +
190A TRP* 3.2 31.3 + - + -
199A LEU* 4.0 9.9 - - + +
222A LEU* 4.1 18.2 - - + -
224A LEU* 5.1 1.8 - - + -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ILE* 2.8 33.0 + - + +
184A GLU* 3.7 7.4 - - - +
186A ALA* 1.3 74.1 - - - +
188A ALA* 1.3 60.6 + - - +
190A TRP* 3.5 6.7 + - - +
191A ASP* 3.2 33.4 + - - +
195A ARG* 2.8 36.7 + - - -
222A LEU* 3.7 21.5 - - + +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO* 4.0 28.3 - - + +
149A ALA* 5.6 0.4 - - - -
152A ALA* 3.8 12.3 - - + +
184A GLU* 2.8 18.1 + - + +
185A THR 3.7 4.7 - - - +
187A GLU* 1.3 74.3 - - - +
189A VAL* 1.3 65.7 + - - +
191A ASP* 3.2 12.6 + - - +
192A ALA* 3.1 17.3 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.9 2.5 - - + -
151A VAL* 3.8 27.1 - - + -
152A ALA* 4.1 16.6 - - - +
155A ALA* 3.6 21.5 - - + -
170A LEU* 4.4 3.8 - - + -
172A LEU* 4.3 9.4 - - + -
185A THR 3.0 22.8 + - - +
186A ALA 3.2 4.7 + - - +
188A ALA* 1.3 75.5 - - - +
190A TRP* 1.3 58.3 + - - +
192A ALA* 3.1 4.6 + - - +
193A VAL* 3.0 33.8 + - + +
199A LEU* 4.1 26.5 - - + -
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Residues in contact with TRP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ALA* 3.2 19.8 + - + +
187A GLU* 3.9 7.4 - - - +
189A VAL* 1.3 77.7 - - - +
191A ASP* 1.3 59.0 + - - +
193A VAL* 4.4 1.6 - - + -
194A GLY* 2.7 51.6 + - - -
195A ARG* 3.0 61.4 + - + +
197A THR* 2.9 25.5 + - - -
199A LEU* 3.5 36.3 - - + +
222A LEU* 3.2 38.8 - - + -
223A GLY 3.6 19.5 - - - -
224A LEU* 3.8 17.5 - - + -
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.2 22.4 + - - +
188A ALA* 3.2 10.9 + - - +
190A TRP* 1.3 77.4 - - - +
192A ALA* 1.3 61.1 + - - +
194A GLY 4.4 1.6 + - - -
195A ARG* 3.7 15.6 + - - -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA* 3.7 28.7 - - + +
156A VAL* 3.8 18.4 - - + +
188A ALA 3.1 11.4 + - - +
189A VAL 3.1 7.1 + - - +
191A ASP* 1.3 79.5 - - - +
193A VAL* 1.3 60.6 + - + +
194A GLY 3.7 0.2 - - - -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 3.8 36.3 - - + +
156A VAL* 3.9 9.9 - - + +
159A LYS* 4.0 27.6 - - + +
170A LEU* 4.5 1.8 - - + -
189A VAL* 3.0 30.5 + - + +
190A TRP* 4.4 2.5 - - + -
192A ALA* 1.3 81.1 - - + +
194A GLY* 1.3 72.2 + - - +
196A ASP* 4.7 3.5 - - - +
197A THR* 3.7 26.9 + - + +
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A TRP* 2.7 28.2 + - - -
191A ASP 4.4 1.6 + - - -
192A ALA 3.7 0.8 - - - -
193A VAL* 1.3 77.9 - - - +
195A ARG* 1.3 65.1 + - - -
196A ASP* 3.2 11.4 - - - -
197A THR* 3.3 17.7 + - - -
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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