Contacts of the helix formed by residues 186 - 202 (chain A) in PDB entry 3Q29
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 ASN 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A GLY* 2.7 28.9 + - - +
167A GLY* 3.6 0.2 - - - -
168A TYR* 3.7 17.0 - - - -
183A GLY* 3.2 18.2 + - - -
184A VAL 3.6 0.4 - - - -
185A ASP* 1.3 82.4 - - - +
187A ALA* 1.3 64.9 + - - +
188A GLY 3.2 4.0 + - - -
189A ALA* 2.8 34.0 + - - +
190A LYS* 3.0 23.3 + - - +
394A SO4 3.4 24.7 - - - +
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Residues in contact with ALA 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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165A ASP* 4.7 2.5 - - - +
186A ASN* 1.3 75.4 - - - +
188A GLY* 1.3 56.9 + - - +
190A LYS* 3.4 10.7 + - - +
191A ALA* 2.9 30.4 + - - +
394A SO4 3.1 27.0 + - - +
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Residues in contact with GLY 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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162A ILE 3.5 10.8 - - - +
165A ASP* 3.3 44.2 + - - +
166A GLY* 4.1 0.6 - - - -
167A GLY 4.0 1.6 - - - -
186A ASN* 3.2 6.8 + - - -
187A ALA* 1.3 76.9 - - - +
189A ALA* 1.3 64.2 + - - +
191A ALA* 3.4 1.9 + - - +
192A GLY* 3.2 17.8 + - - -
394A SO4 4.5 0.8 + - - -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 3.5 28.6 - - + +
167A GLY* 3.8 2.7 - - - +
183A GLY 4.0 4.7 - - - +
184A VAL* 3.4 31.0 - - - +
186A ASN* 2.8 24.8 + - - +
188A GLY* 1.3 70.5 - - - +
190A LYS* 1.3 63.8 + - - +
192A GLY* 3.3 1.9 + - - -
193A LEU* 3.0 26.2 + - - +
362A LEU* 3.8 4.5 - - + -
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Residues in contact with LYS 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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185A ASP* 3.3 32.6 + - - +
186A ASN 3.0 20.5 + - - +
187A ALA* 3.7 8.5 - - - +
189A ALA* 1.3 77.1 - - - +
191A ALA* 1.3 55.0 + - - +
194A THR* 2.7 40.0 + - - +
358A VAL* 3.7 4.2 - - + +
359A ASP* 3.4 41.7 + - - +
362A LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 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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165A ASP* 3.9 5.8 - - - +
187A ALA 2.9 18.1 + - - +
188A GLY 3.7 4.9 - - - +
189A ALA 3.3 0.2 - - - -
190A LYS* 1.3 76.4 - - - +
192A GLY* 1.3 58.2 + - - +
194A THR* 3.6 6.6 + - - -
195A PHE* 3.1 20.4 + - - +
251A PHE* 3.4 14.2 - - + -
252A LYS* 3.6 31.9 - - - +
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Residues in contact with GLY 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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161A LEU* 3.5 32.8 - - - +
162A ILE* 4.5 2.7 - - - -
188A GLY 3.2 12.3 + - - -
189A ALA 3.8 1.8 - - - -
191A ALA* 1.3 75.0 - - - +
193A LEU* 1.3 65.3 + - - +
195A PHE* 3.1 4.9 + - - +
196A LEU 3.1 17.8 + - - -
251A PHE* 3.7 17.2 - - - -
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Residues in contact with LEU 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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162A ILE* 4.4 21.2 - - + +
189A ALA 3.0 16.5 + - - +
192A GLY* 1.3 74.6 - - - +
194A THR* 1.3 58.6 + - - +
196A LEU* 3.2 26.6 + - + -
197A VAL* 2.9 40.2 + - + +
347A ALA 4.5 6.3 - - - +
348A VAL* 4.6 15.3 - - + +
351A ALA* 3.8 20.9 - - + -
358A VAL* 3.9 19.5 - - + +
361A ALA* 5.0 0.4 - - + -
362A LEU* 3.7 35.0 - - + -
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Residues in contact with THR 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 LYS* 2.7 27.0 + - - +
191A ALA* 3.6 7.0 - - - -
193A LEU* 1.3 76.6 - - - +
195A PHE* 1.3 57.5 + - - +
197A VAL* 3.4 1.9 + - - +
198A ASP* 2.9 45.0 + - - +
358A VAL* 3.6 23.9 - - + +
359A ASP* 5.4 0.7 + - - -
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Residues in contact with PHE 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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130A TRP* 3.2 46.7 - + + -
131A GLU* 3.8 19.5 - - + -
134A PRO* 4.3 15.7 - - + -
161A LEU* 4.2 12.6 - - + -
191A ALA 3.1 13.8 + - - +
192A GLY* 3.1 9.9 + - - +
194A THR* 1.3 77.0 - - - +
196A LEU* 1.3 61.8 + - - +
198A ASP* 3.2 10.8 + - + +
199A LEU* 3.0 44.6 + - + +
251A PHE* 3.8 22.2 - + + -
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Residues in contact with LEU 196 (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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130A TRP* 5.3 0.2 - - + -
150A PHE* 3.9 20.2 - - + -
152A LEU* 4.2 8.5 - - + -
158A THR* 3.5 33.4 - - + +
161A LEU* 3.9 17.5 - - + +
192A GLY 3.1 11.9 + - - +
193A LEU* 3.4 23.3 - - + +
195A PHE* 1.3 76.4 - - - +
197A VAL* 1.3 63.4 + - + +
199A LEU* 3.3 11.3 + - + +
200A ILE* 3.2 34.5 + - + +
205A MET* 3.8 22.8 - - + +
348A VAL* 4.2 9.6 - - + -
352A ALA* 5.2 3.6 - - + -
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Residues in contact with VAL 197 (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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193A LEU* 2.9 26.0 + - + +
194A THR* 3.8 4.5 - - - +
196A LEU* 1.3 77.3 - - + +
198A ASP* 1.3 58.7 + - - +
200A ILE* 3.1 9.5 + - + +
201A LYS* 2.8 53.4 + - + +
351A ALA* 3.6 36.8 - - + +
352A ALA* 4.3 6.3 - - - +
358A VAL* 3.7 22.9 - - + -
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Residues in contact with ASP 198 (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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194A THR* 2.9 36.4 + - - +
195A PHE* 3.7 10.5 - - + +
197A VAL* 1.3 76.8 - - - +
199A LEU* 1.3 65.7 + - - +
201A LYS* 3.9 22.2 + - - +
202A ASN* 2.9 39.2 + - - +
204A HIS* 5.4 0.2 - - - -
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Residues in contact with LEU 199 (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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130A TRP* 4.0 20.9 - - + -
133A ILE* 4.5 10.3 - - + -
134A PRO* 3.9 31.6 - - + -
148A LEU* 5.1 2.7 - - + -
195A PHE* 3.0 40.8 + - + +
196A LEU* 3.4 10.8 - - - +
198A ASP* 1.3 74.4 - - - +
200A ILE* 1.3 58.8 + - - +
202A ASN 3.7 0.5 + - - -
203A LYS 3.3 2.1 + - - -
204A HIS* 2.7 53.0 + - + +
205A MET* 3.2 32.2 + - + -
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Residues in contact with ILE 200 (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 LEU* 4.0 17.9 - - + -
196A LEU* 3.2 24.0 + - + +
197A VAL* 3.1 8.6 + - + +
198A ASP 3.1 0.6 - - - -
199A LEU* 1.3 75.0 - - - +
201A LYS* 1.3 67.5 + - + +
203A LYS* 2.9 19.9 + - - +
205A MET* 3.4 30.2 - - + +
206A ASN* 4.6 0.4 - - - -
207A ALA* 3.8 20.2 - - + +
352A ALA* 3.7 47.1 - - + +
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Residues in contact with LYS 201 (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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197A VAL* 2.8 40.9 + - + +
198A ASP* 3.3 23.1 + - - +
200A ILE* 1.3 76.3 - - + +
202A ASN* 1.3 64.3 + - - +
203A LYS* 3.2 20.3 - - - +
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Residues in contact with ASN 202 (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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198A ASP* 2.9 29.2 + - - +
201A LYS* 1.3 81.7 + - - +
203A LYS* 1.3 70.5 + - - +
204A HIS* 3.2 34.0 + - + +
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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