Contacts of the helix formed by residues 187 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASP 3.8 1.8 + - - -
186A TRP* 1.3 77.2 - - - +
188A THR* 1.3 66.2 + - - +
189A LYS* 3.5 9.0 + - - +
190A GLU* 3.0 33.6 + - - +
191A VAL* 2.9 21.1 + - - +
216A PHE* 6.2 0.2 - - - -
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Residues in contact with THR 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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187A SER* 1.3 75.0 - - - +
189A LYS* 1.3 69.6 + - - +
191A VAL* 3.3 7.8 + - - +
192A ALA* 3.0 18.9 + - - +
216A PHE* 3.9 22.2 - - + -
221A GLU* 3.5 44.2 + - + +
225A LEU* 3.5 27.1 - - + +
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Residues in contact with LYS 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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187A SER* 3.1 9.4 + - - +
188A THR* 1.3 87.4 + - - +
190A GLU* 1.3 63.7 + - + +
192A ALA* 3.4 23.7 + - - +
193A TYR* 3.1 21.3 + - - +
196A ARG* 5.6 4.4 - - - +
225A LEU* 5.9 0.4 - - - -
228A SER* 4.3 16.4 + - - -
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Residues in contact with GLU 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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154A LEU* 3.7 28.1 - - + +
185A ASP 3.9 4.3 - - - +
186A TRP* 3.0 23.7 - - + +
187A SER* 3.0 36.8 + - - +
189A LYS* 1.3 77.4 - - + +
191A VAL* 1.3 60.7 + - - +
193A TYR* 3.3 7.3 + - - +
194A TYR* 2.9 28.6 + - - +
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Residues in contact with VAL 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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180A VAL* 3.9 25.6 - - + -
186A TRP* 4.0 22.7 - - + +
187A SER 2.9 18.7 + - - +
188A THR* 3.7 10.1 - - - +
190A GLU* 1.3 75.0 - - - +
192A ALA* 1.3 57.5 + - - +
194A TYR* 3.2 8.7 - - + +
195A LEU* 3.0 31.6 + - + +
212A TYR* 4.2 10.8 - - + -
215A ARG* 4.0 22.9 - - - +
216A PHE* 5.0 2.9 - - + -
225A LEU* 4.1 19.1 - - + -
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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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188A THR 3.0 16.2 + - - +
189A LYS* 3.6 26.5 - - - +
190A GLU 3.2 0.2 - - - -
191A VAL* 1.3 76.0 - - - +
193A TYR* 1.3 64.0 + - - +
195A LEU* 3.3 4.8 + - - +
196A ARG* 3.0 32.5 + - - +
225A LEU* 3.7 18.6 - - + +
228A SER* 4.3 0.9 - - - +
229A ILE* 3.8 19.9 - - + +
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Residues in contact with TYR 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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154A LEU* 3.7 33.7 - - + -
158A ILE* 4.1 20.4 - - + +
189A LYS* 3.1 11.5 + - - +
190A GLU* 3.3 8.0 + - - +
192A ALA* 1.3 77.7 - - - +
194A TYR* 1.3 67.7 + - - +
196A ARG* 3.1 13.0 + - + +
197A GLU* 2.9 58.3 + - + +
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Residues in contact with TYR 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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154A LEU* 3.9 11.0 - - + -
157A ALA* 3.7 15.4 - - + +
158A ILE* 3.9 22.0 - - + -
161A TYR* 3.2 20.8 - - - -
179A CYS 2.9 29.4 + - - -
180A VAL* 4.2 12.8 - - + -
181A PRO* 3.9 5.4 - - - +
186A TRP* 3.6 35.2 - + + -
190A GLU 2.9 14.2 + - - +
191A VAL* 3.2 12.3 - - - +
193A TYR* 1.3 84.7 - - - +
195A LEU* 1.3 75.5 + - + +
197A GLU* 3.3 5.9 + - - +
198A LEU* 3.1 47.0 + - + +
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Residues in contact with LEU 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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178A VAL* 4.2 8.3 - - + -
180A VAL* 4.9 1.8 - - + -
191A VAL* 3.0 24.2 + - + +
192A ALA* 3.8 4.5 - - - +
193A TYR 3.3 0.2 - - - -
194A TYR* 1.3 90.6 - - + +
196A ARG* 1.3 60.5 + - - +
198A LEU* 3.3 5.1 + - + +
199A ARG* 2.9 30.7 + - - +
208A MSE 3.8 12.4 - - + +
210A VAL* 3.8 27.8 - - + -
212A TYR* 3.4 35.9 - - + +
225A LEU* 5.5 0.4 - - + -
229A ILE* 3.7 17.9 - - + -
232A LEU* 3.7 12.9 - - + +
234A LEU* 4.2 5.2 - - + -
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Residues in contact with ARG 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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189A LYS* 5.6 4.0 - - - +
192A ALA* 3.0 22.9 + - - +
193A TYR* 3.1 12.3 + - + +
195A LEU* 1.3 74.6 - - - +
197A GLU* 1.3 64.1 + - - +
199A ARG* 3.3 3.1 + - - +
200A GLY* 2.9 26.2 + - - -
228A SER 2.8 21.8 + - - -
229A ILE* 4.0 10.0 - - + +
231A ASP* 2.6 44.4 + - - -
232A LEU* 3.6 23.9 - - + +
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Residues in contact with GLU 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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158A ILE* 3.6 25.0 - - + +
193A TYR* 2.9 55.8 + - + +
194A TYR 3.5 8.3 - - - +
195A LEU 3.3 0.2 - - - -
196A ARG* 1.3 80.8 - - - +
198A LEU* 1.3 62.6 + - - +
200A GLY* 3.3 2.2 + - - -
201A ILE* 3.1 27.9 + - + +
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Residues in contact with LEU 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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158A ILE* 4.2 26.9 - - + -
161A TYR* 4.1 25.4 - - + -
165A LEU* 3.9 13.1 - - + +
178A VAL* 4.0 28.3 - - + -
194A TYR* 3.1 49.2 + - + +
195A LEU* 3.7 7.6 - - + +
196A ARG 3.3 0.2 - - - -
197A GLU* 1.3 73.7 - - - +
199A ARG* 1.3 60.4 + - - +
201A ILE* 3.1 6.0 + - + +
202A LEU* 2.9 30.1 + - - +
208A MSE 4.1 13.5 - - + -
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Residues in contact with ARG 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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195A LEU 2.9 17.0 + - - +
196A ARG 3.6 4.7 - - - +
198A LEU* 1.3 77.5 - - - +
200A GLY* 1.3 57.1 + - - +
202A LEU* 4.2 2.7 - - - +
203A GLY* 2.8 44.2 + - - -
204A HIS* 3.5 41.4 + - - +
206A THR 2.7 28.7 + - - -
207A ASP* 4.8 4.6 + - - +
208A MSE 3.9 36.9 - - + +
232A LEU* 2.9 48.8 + - + -
233A GLU* 3.4 16.2 + - - +
234A LEU* 4.5 2.8 - - - +
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Residues in contact with GLY 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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196A ARG 2.9 14.1 + - - -
197A GLU* 3.8 4.3 - - - -
198A LEU 3.1 0.4 - - - -
199A ARG* 1.3 80.1 - - - +
201A ILE* 1.3 61.8 + - - +
203A GLY* 3.7 6.6 + - - -
204A HIS* 6.2 0.2 - - - -
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Residues in contact with ILE 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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158A ILE* 3.8 34.3 - - + +
162A ALA* 4.4 19.5 - - + +
165A LEU* 3.7 23.3 - - + -
166A GLU* 4.1 20.0 - - + +
169A LYS* 3.3 18.2 + - - -
197A GLU 3.1 17.7 + - - +
198A LEU* 3.1 13.2 + - + +
200A GLY* 1.3 77.4 - - - +
202A LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 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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165A LEU* 4.0 31.0 - - + +
168A ALA* 4.9 2.7 - - + -
169A LYS* 2.8 49.6 + - + +
176A VAL* 3.6 26.2 - - + -
198A LEU 2.9 15.8 + - - +
199A ARG* 4.2 3.8 - - - +
201A ILE* 1.3 80.1 - - - +
203A GLY* 1.3 62.8 + - - +
206A THR* 4.0 31.3 + - + +
208A MSE 3.9 28.5 - - + -
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Residues in contact with GLY 203 (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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169A LYS* 4.9 2.2 - - - -
199A ARG* 2.8 40.6 + - - -
200A GLY 3.7 5.1 + - - -
201A ILE 3.5 1.6 - - - -
202A LEU* 1.3 80.0 - - - +
204A HIS* 1.3 64.9 + - - -
205A ASP* 3.4 2.9 + - - -
206A THR 3.6 4.6 + - - +
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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