Contacts of the helix formed by residues 184 - 195 (chain A) in PDB entry 3VLG
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ILE* 3.5 8.2 - - - +
183A ASN* 1.3 80.2 - - - +
185A THR* 1.3 65.6 + - - +
186A ALA* 3.6 10.8 + - - +
187A ASP* 3.2 30.2 + - - +
188A LEU* 3.1 17.5 + - - +
224A MET* 5.3 0.7 - - - -
227A LEU* 3.5 13.2 - - - +
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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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184A SER* 1.3 74.2 - - - +
186A ALA* 1.4 53.8 + - - +
188A LEU* 3.2 13.1 + - + +
189A ASP* 2.9 43.9 + - - +
226A HIS 4.3 9.0 + - - -
227A LEU* 3.5 17.0 + - - +
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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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151A HIS* 3.8 16.6 - - + +
184A SER* 3.2 9.9 + - - +
185A THR* 1.4 73.2 - - - +
187A ASP* 1.3 56.6 + - - +
189A ASP* 2.9 11.6 - - - +
190A PHE* 2.7 37.4 + - - +
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Residues in contact with ASP 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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151A HIS* 2.9 31.0 + - - -
154A ASN* 5.8 1.6 + - - -
156A TYR* 4.2 9.5 + - + -
180A LEU* 6.1 1.6 - - + -
181A LYS 3.8 7.4 - - - +
182A ILE* 4.0 9.9 - - + -
183A ASN* 2.9 29.4 + - - +
184A SER* 3.2 24.4 + - - +
186A ALA* 1.3 74.1 - - - +
188A LEU* 1.3 66.6 + - - +
190A PHE* 3.3 2.4 + - - +
191A ILE* 3.0 30.6 + - + +
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Residues in contact with LEU 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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182A ILE* 3.9 23.8 - - + +
184A SER 3.1 10.4 + - - +
185A THR* 3.2 14.8 + - + +
187A ASP* 1.3 80.1 - - - +
189A ASP* 1.3 57.4 + - + +
191A ILE* 3.2 3.6 + - + +
192A GLN* 2.8 55.6 + - - +
227A LEU* 3.8 25.1 - - + +
228A PHE* 4.4 16.2 - - + -
246A ILE* 4.3 17.9 - - + -
249A GLY 4.9 1.3 - - - +
251A VAL* 5.1 3.8 - - + -
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Residues in contact with ASP 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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185A THR* 2.9 34.3 + - - +
186A ALA* 2.9 26.1 - - - +
188A LEU* 1.3 74.1 - - - +
190A PHE* 1.3 67.4 + - - +
192A GLN* 3.8 14.7 - - + +
193A GLN* 3.0 24.1 + - - +
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Residues in contact with PHE 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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149A ILE* 3.5 34.1 - - + -
150A ALA 3.9 3.4 - - - -
151A HIS* 3.6 40.8 - + + +
156A TYR* 3.3 44.2 - + + -
158A PHE* 6.2 0.2 - + - -
186A ALA 2.7 22.1 + - - +
187A ASP* 3.7 2.2 - - - +
189A ASP* 1.3 76.2 + - - +
191A ILE* 1.3 84.7 + - + +
193A GLN* 3.2 29.8 + - - +
194A ALA* 2.9 25.4 + - + +
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Residues in contact with ILE 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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156A TYR* 4.2 5.6 - - + -
158A PHE* 5.4 1.6 - - + -
180A LEU* 3.7 39.7 - - + -
182A ILE* 4.8 5.6 - - + -
187A ASP* 3.0 23.0 + - + +
188A LEU* 3.6 4.9 - - - +
190A PHE* 1.3 101.1 - - + +
192A GLN* 1.3 63.9 + - - +
194A ALA* 3.1 7.2 + - + +
195A ILE* 3.0 41.9 + - + +
246A ILE* 4.3 13.2 - - + -
263A ILE* 4.0 22.4 - - + -
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Residues in contact with GLN 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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188A LEU* 2.8 43.0 + - - +
189A ASP* 3.8 15.5 - - + +
191A ILE* 1.3 77.9 - - - +
193A GLN* 1.3 60.8 + - - +
195A ILE* 3.6 16.3 + - - +
196A SER* 3.8 3.3 + - - -
197A TYR 5.0 1.7 + - - -
246A ILE* 4.2 8.3 - - + -
249A GLY* 2.6 44.1 + - - +
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Residues in contact with GLN 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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149A ILE* 5.6 1.0 - - - +
189A ASP 3.0 15.8 + - - +
190A PHE* 3.3 38.2 - - - +
192A GLN* 1.3 76.9 - - - +
194A ALA* 1.3 67.7 + - - +
196A SER* 3.0 23.0 + - - -
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Residues in contact with ALA 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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149A ILE* 4.6 11.2 - - + +
158A PHE* 3.7 29.6 - - + -
190A PHE* 2.9 28.2 + - + +
191A ILE* 3.1 8.3 + - + +
193A GLN* 1.3 86.5 - - - +
195A ILE* 1.3 57.9 + - - +
196A SER* 2.9 15.3 + - - -
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Residues in contact with ILE 195 (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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158A PHE* 3.8 25.1 - - + -
191A ILE* 3.0 32.3 + - + +
192A GLN* 3.7 8.7 - - - +
194A ALA* 1.3 75.8 - - - +
196A SER* 1.3 67.6 + - - +
197A TYR* 4.2 2.7 - - - +
198A SER* 2.9 43.0 + - - +
200A PHE 5.7 0.2 - - - +
202A PHE* 4.0 23.1 - - + -
246A ILE* 4.0 23.6 - - + +
247A GLN* 6.1 0.9 - - - -
248A ARG 5.8 1.3 - - - +
249A GLY 5.7 7.9 - - - +
263A ILE* 4.5 1.6 - - + -
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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