Contacts of the helix formed by residues 187 - 203 (chain B) in PDB entry 3NZG
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASP 3.7 1.6 + - - -
186B TRP* 1.3 77.7 - - - +
188B THR* 1.3 59.8 + - - +
189B LYS* 3.4 10.9 + - - +
190B GLU* 2.9 34.5 + - - +
191B VAL* 2.9 26.0 + - - +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B SER* 1.3 74.9 - - - +
189B LYS* 1.3 70.5 + - - +
191B VAL* 3.2 9.1 + - - +
192B ALA* 3.1 20.1 + - - +
216B PHE* 3.7 21.3 - - + -
221B GLU* 3.4 45.3 + - + +
225B LEU* 3.5 27.8 + - + +
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B SER* 3.1 10.4 + - - +
188B THR* 1.3 92.0 + - - +
190B GLU* 1.3 61.0 + - + +
192B ALA* 3.6 14.2 + - - +
193B TYR* 3.3 19.1 + - - +
225B LEU* 6.2 0.4 - - - -
228B SER* 4.6 16.7 + - - -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.7 28.9 - - + +
185B ASP 4.3 1.2 - - - +
186B TRP* 3.1 23.0 - - + -
187B SER* 2.9 34.5 + - - +
189B LYS* 1.3 78.7 - - + +
191B VAL* 1.3 58.9 + - - +
193B TYR* 3.5 8.4 - - + +
194B TYR* 2.9 28.8 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL* 4.1 22.4 - - + -
186B TRP* 4.2 14.4 - - + +
187B SER 2.9 19.2 + - - +
188B THR* 3.2 13.2 + - - +
190B GLU* 1.3 77.6 - - - +
192B ALA* 1.3 62.9 + - - +
194B TYR* 3.1 9.1 + - + +
195B LEU* 2.9 28.0 + - + +
212B TYR* 4.0 20.2 - - + -
215B ARG* 4.3 21.1 - - - +
216B PHE* 4.8 3.1 - - + -
225B LEU* 3.9 18.8 - - + -
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B THR 3.1 12.7 + - - +
189B LYS* 3.7 20.4 - - - +
191B VAL* 1.3 77.5 - - - +
193B TYR* 1.3 56.3 + - - +
195B LEU* 3.2 5.9 + - - +
196B ARG* 2.9 40.4 + - - +
225B LEU* 3.8 11.4 - - + +
228B SER* 4.3 6.7 - - - +
229B ILE* 3.8 25.6 - - + +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.0 30.3 - - + -
158B ILE* 4.1 14.2 - - + +
189B LYS 3.3 10.4 + - - +
190B GLU* 3.5 8.1 - - - +
191B VAL 3.3 0.2 - - - -
192B ALA* 1.3 77.0 - - - +
194B TYR* 1.3 67.4 + - - +
196B ARG* 3.0 15.3 + - + +
197B GLU* 2.9 58.5 + - + +
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Residues in contact with TYR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.7 11.4 - - + -
157B ALA* 3.7 15.3 - - + +
158B ILE* 3.8 24.2 - - + -
161B TYR* 3.0 21.5 - - - -
178B VAL* 5.5 0.2 - - + -
179B CYS 2.7 28.8 + - - -
180B VAL* 4.1 13.7 - - + -
181B PRO* 4.0 4.2 - - - +
186B TRP* 3.5 37.7 - + + -
190B GLU 2.9 13.5 + - - +
191B VAL* 3.3 9.9 - - - +
193B TYR* 1.3 82.8 - - - +
195B LEU* 1.3 76.9 + - + +
197B GLU* 3.2 4.2 + - - +
198B LEU* 3.1 48.0 + - + +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B VAL* 4.5 4.9 - - + -
180B VAL* 4.7 1.8 - - + -
191B VAL* 2.9 24.4 + - + +
192B ALA* 3.7 4.3 - - - +
194B TYR* 1.3 94.2 - - + +
196B ARG* 1.3 60.8 + - - +
198B LEU* 3.4 2.4 + - + +
199B ARG* 2.9 31.5 + - - +
208B MSE 3.8 14.4 - - + +
210B VAL* 3.8 27.4 - - + -
212B TYR* 3.3 35.4 - - + +
229B ILE* 3.6 18.6 - - + -
232B LEU* 3.9 13.8 - - + +
234B LEU* 4.2 5.2 - - + -
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA* 2.9 30.0 + - - +
193B TYR* 3.4 13.9 - - + +
195B LEU* 1.3 76.7 - - - +
197B GLU* 1.3 61.2 + - + +
199B ARG* 3.8 1.6 - - - +
200B GLY* 2.8 26.3 + - - -
228B SER* 2.9 29.3 + - - -
229B ILE* 4.0 9.0 - - + +
231B ASP* 2.9 33.9 + - - -
232B LEU* 3.7 24.6 - - + +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 3.5 28.1 - - + +
193B TYR* 2.9 54.5 + - + +
194B TYR 3.5 7.6 - - - +
196B ARG* 1.3 77.1 - - - +
198B LEU* 1.3 60.5 + - - +
200B GLY* 3.2 2.6 + - - -
201B ILE* 3.0 35.0 + - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 4.2 26.0 - - + -
161B TYR* 3.7 32.3 - - + -
165B LEU* 3.7 14.5 - - + +
178B VAL* 4.0 24.9 - - + -
194B TYR* 3.1 49.0 + - + +
195B LEU* 3.9 5.8 - - + +
197B GLU* 1.3 72.5 - - - +
199B ARG* 1.3 61.9 + - - +
201B ILE* 3.0 7.6 + - + +
202B LEU* 2.8 30.3 + - - +
208B MSE 4.3 10.8 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU 2.9 17.9 + - - +
196B ARG 3.8 3.6 - - - +
198B LEU* 1.3 76.8 - - - +
200B GLY* 1.3 57.6 + - - +
202B LEU* 4.0 2.7 - - - +
203B GLY* 2.9 45.3 + - - -
204B HIS* 3.5 33.9 + - + +
206B THR 2.8 29.3 + - - -
207B ASP* 4.9 2.6 + - - +
208B MSE 3.8 37.1 - - + +
232B LEU* 2.8 51.5 + - + -
233B GLU* 3.1 19.4 + - - +
234B LEU* 4.2 4.2 - - - +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG 2.8 16.4 + - - -
197B GLU* 3.2 5.4 + - - -
198B LEU 3.0 0.6 - - - -
199B ARG* 1.3 80.4 - - - +
201B ILE* 1.3 60.9 + - - +
203B GLY* 3.9 5.9 + - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ILE* 3.9 23.6 - - + +
162B ALA* 3.9 42.4 - - + +
165B LEU* 4.0 12.3 - - + -
166B GLU* 3.7 21.1 - - - +
169B LYS* 3.1 22.5 + - - -
197B GLU* 3.0 21.2 + - - +
198B LEU* 3.0 13.9 + - + +
200B GLY* 1.3 79.4 - - - +
202B LEU* 1.3 58.4 + - - +
203B GLY* 4.6 0.2 - - - -
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 4.3 20.4 - - + +
168B ALA* 5.2 1.8 - - + -
169B LYS* 2.9 43.8 + - + +
176B VAL* 3.8 25.6 - - + -
198B LEU 2.8 19.7 + - - +
199B ARG* 4.0 5.6 - - - +
201B ILE* 1.3 76.6 - - - +
203B GLY* 1.3 61.7 + - - +
205B ASP* 5.2 0.7 + - - +
206B THR* 3.8 39.0 + - + +
207B ASP 4.2 0.2 - - - +
208B MSE 3.7 36.1 - - + -
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LYS* 5.3 1.3 - - - -
199B ARG* 2.9 36.3 + - - -
200B GLY 3.9 5.1 + - - -
201B ILE 3.4 2.4 - - - -
202B LEU* 1.3 85.7 - - - +
204B HIS* 1.3 64.2 + - - -
205B ASP* 3.4 3.1 + - - -
206B THR 4.0 0.9 - - - +
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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