Contacts of the helix formed by residues 187 - 203 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ASP 3.6 2.3 + - - -
186C TRP* 1.3 76.7 - - - +
188C THR* 1.3 65.6 + - - +
189C LYS* 3.4 10.6 + - - +
190C GLU* 2.8 36.9 + - - +
191C VAL* 2.9 20.3 + - - +
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Residues in contact with THR 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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187C SER* 1.3 74.5 - - - +
189C LYS* 1.3 67.7 + - - +
191C VAL* 3.1 11.4 + - - +
192C ALA* 3.0 19.1 + - - +
216C PHE* 3.7 21.3 - - + -
221C GLU* 3.6 43.6 + - + +
225C LEU* 3.6 24.3 - - + +
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Residues in contact with LYS 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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233B GLU* 5.5 10.1 - - - +
187C SER* 3.1 9.7 + - - +
188C THR* 1.3 87.0 + - - +
190C GLU* 1.3 61.8 + - + +
192C ALA* 3.3 24.0 + - - +
193C TYR* 3.1 21.8 + - - +
196C ARG* 5.5 5.1 - - - +
225C LEU* 6.1 0.2 - - - -
228C SER* 4.4 14.5 + - - -
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Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 3.7 28.7 - - + +
185C ASP* 4.2 3.3 - - - +
186C TRP* 2.9 25.3 - - + +
187C SER* 2.8 39.5 + - - +
189C LYS* 1.3 77.8 - - + +
191C VAL* 1.3 58.1 + - - +
193C TYR* 3.4 8.6 + - - +
194C TYR* 2.8 29.3 + - - +
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Residues in contact with VAL 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 4.0 26.5 - - + -
186C TRP* 4.2 22.7 - - + +
187C SER 2.9 23.3 + - - +
188C THR* 3.5 11.0 - - - +
190C GLU* 1.3 76.5 - - - +
192C ALA* 1.3 59.2 + - - +
194C TYR* 3.4 7.0 + - + +
195C LEU* 3.0 33.2 + - + +
212C TYR* 4.1 19.3 - - + -
215C ARG* 4.3 16.8 - - - +
216C PHE* 5.0 3.4 - - + -
225C LEU* 4.2 9.9 - - + -
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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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188C THR 3.0 11.9 + - - +
189C LYS* 3.3 30.0 + - - +
191C VAL* 1.3 73.5 - - - +
193C TYR* 1.3 60.5 + - - +
195C LEU* 3.5 3.1 + - - +
196C ARG* 2.9 38.9 + - - +
225C LEU* 3.8 13.0 - - + +
228C SER* 4.2 2.0 - - - +
229C ILE* 3.7 24.5 - - + +
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Residues in contact with TYR 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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154C LEU* 3.8 33.9 - - + -
155C ASP* 5.4 4.3 + - - -
158C ILE* 4.2 15.1 - - + +
189C LYS 3.1 13.5 + - - +
190C GLU* 3.5 8.1 - - - +
192C ALA* 1.3 76.0 - - - +
194C TYR* 1.3 74.0 + - - +
196C ARG* 3.0 13.1 + - + +
197C GLU* 2.8 61.2 + - + +
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Residues in contact with TYR 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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154C LEU* 3.9 10.3 - - + -
157C ALA* 3.8 14.1 - - + +
158C ILE* 3.8 22.2 - - + -
161C TYR* 3.2 22.4 - + - -
178C VAL* 5.5 0.2 - - + -
179C CYS 2.9 27.9 + - - -
180C VAL* 4.0 14.1 - - + -
181C PRO* 3.9 4.0 - - - +
186C TRP* 3.6 36.6 - + + -
190C GLU 2.8 17.9 + - - +
191C VAL* 3.4 6.7 - - + +
193C TYR* 1.3 82.0 - - - +
195C LEU* 1.3 70.3 + - + +
197C GLU* 3.2 7.1 + - - +
198C LEU* 3.0 53.5 + - + +
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Residues in contact with LEU 195 (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 VAL* 4.4 5.4 - - + -
180C VAL* 4.7 1.1 - - + -
191C VAL* 3.0 26.6 + - + +
192C ALA* 3.9 3.1 - - - +
194C TYR* 1.3 95.3 - - + +
196C ARG* 1.3 60.9 + - - +
198C LEU* 3.8 3.7 - - + +
199C ARG* 2.9 31.9 + - - +
208C MSE 3.9 11.2 - - + +
210C VAL* 3.9 30.3 - - + -
212C TYR* 3.4 37.2 - - + +
225C LEU* 5.6 0.2 - - + -
229C ILE* 3.8 16.6 - - + -
232C LEU* 3.7 14.4 - - + +
234C LEU* 4.4 0.7 - - + -
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Residues in contact with ARG 196 (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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189C LYS* 5.5 4.6 - - - +
192C ALA* 2.9 29.7 + - - +
193C TYR* 3.3 12.3 - - + +
195C LEU* 1.3 75.5 - - - +
197C GLU* 1.3 61.3 + - - +
199C ARG* 3.8 1.9 - - - +
200C GLY* 2.9 24.9 + - - -
228C SER 2.8 29.3 + - - -
229C ILE* 4.4 7.5 - - + +
231C ASP* 2.7 36.7 + - - -
232C LEU* 3.6 24.6 - - + +
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Residues in contact with GLU 197 (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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158C ILE* 3.6 24.2 - - + +
193C TYR* 2.8 54.3 + - + +
194C TYR 3.4 7.6 - - - +
195C LEU 3.2 0.2 - - - -
196C ARG* 1.3 77.6 - - - +
198C LEU* 1.3 65.1 + - - +
200C GLY* 3.3 2.5 + - - +
201C ILE* 3.2 29.5 + - - +
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Residues in contact with LEU 198 (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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158C ILE* 4.3 25.1 - - + -
161C TYR* 3.8 26.2 - - + -
165C LEU* 3.6 18.7 - - + +
178C VAL* 3.9 29.4 - - + -
194C TYR* 3.0 54.8 + - + +
195C LEU* 3.8 6.1 - - + +
197C GLU* 1.3 73.0 - - - +
199C ARG* 1.3 66.6 + - - +
201C ILE* 3.2 6.6 + - + +
202C LEU* 3.0 21.1 + - - +
208C MSE 4.2 11.7 - - + -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LEU 2.9 17.1 + - - +
196C ARG 3.8 3.8 - - - +
198C LEU* 1.3 76.8 - - - +
200C GLY* 1.3 57.6 + - - +
202C LEU* 4.4 2.5 - - - +
203C GLY* 2.9 52.3 + - - -
204C HIS* 3.6 36.5 + - + +
206C THR 2.9 21.2 + - - -
207C ASP* 5.0 2.4 + - - +
208C MSE 3.9 37.4 - - + +
232C LEU* 2.9 49.4 + - + -
233C GLU* 3.2 21.8 + - - +
234C LEU* 4.1 4.8 - - - +
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Residues in contact with GLY 200 (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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196C ARG 2.9 17.4 + - - -
197C GLU* 3.3 3.3 + - - -
198C LEU 3.1 0.8 - - - -
199C ARG* 1.3 80.4 - - - +
201C ILE* 1.3 61.8 + - - +
203C GLY* 3.7 6.6 + - - -
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Residues in contact with ILE 201 (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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158C ILE* 3.9 26.7 - - + +
162C ALA* 4.1 27.8 - - + +
165C LEU* 3.7 27.8 - - + -
166C GLU* 4.0 20.2 - - + +
169C LYS* 3.2 18.7 + - - +
197C GLU* 3.2 16.5 + - - +
198C LEU* 3.2 7.8 + - + +
200C GLY* 1.3 78.4 - - - +
202C LEU* 1.3 62.7 + - - +
203C GLY 3.5 0.2 + - - -
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Residues in contact with LEU 202 (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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165C LEU* 4.0 26.2 - - + +
168C ALA* 5.0 3.4 - - + -
169C LYS* 3.3 44.8 - - + +
176C VAL* 3.9 19.5 - - + -
198C LEU 3.0 16.1 + - - +
199C ARG* 4.1 3.4 - - - +
201C ILE* 1.3 80.0 - - - +
203C GLY* 1.3 65.5 + - - +
206C THR* 3.9 35.3 + - + +
208C MSE 3.9 33.0 - - + -
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Residues in contact with GLY 203 (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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169C LYS* 5.3 1.1 - - - -
199C ARG* 2.9 38.4 + - - -
200C GLY 3.7 5.1 + - - -
201C ILE 3.4 2.6 - - - -
202C LEU* 1.3 82.3 - - - +
204C HIS* 1.3 64.4 + - - -
205C ASP* 3.4 4.1 + - - -
206C THR 3.8 1.8 + - - +
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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