Contacts of the helix formed by residues 214 - 228 (chain E) in PDB entry 1NZB
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 214 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169E ASN* 3.1 8.9 - - - +
192E ARG* 5.2 2.7 - - - -
213E LEU* 1.3 74.0 - - - +
215E LEU* 1.3 57.5 + - - +
216E GLY* 3.2 9.5 + - - -
217E VAL* 3.1 24.2 - - - +
218E THR* 2.6 37.2 + - - -
336F VAL* 4.7 10.5 - - - +
339F LEU* 3.8 26.4 - - - +
340F GLU* 4.3 17.1 - - - +
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E GLY 4.7 9.6 - - - +
191E GLY 3.9 19.5 - - - +
192E ARG* 4.7 13.2 - - + +
214E SER* 1.3 76.8 + - - +
216E GLY* 1.3 66.0 + - - +
218E THR* 3.3 4.6 - - - +
219E LYS* 2.7 25.9 + - - +
340F GLU* 3.9 25.1 + - + +
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Residues in contact with GLY 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG* 4.0 16.4 - - - -
214E SER* 3.2 5.2 + - - -
215E LEU* 1.3 78.4 - - - +
217E VAL* 1.3 61.1 + - - +
219E LYS* 3.0 20.7 - - - +
220E LEU* 2.9 25.5 - - - +
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Residues in contact with VAL 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E PHE* 4.8 11.9 - - + -
146E ARG* 4.5 0.4 - - - +
162E ALA* 5.9 0.7 - - - +
165E GLY* 3.6 32.8 - - - +
166E ILE 3.7 1.6 - - - +
169E ASN* 4.1 3.1 - - + +
213E LEU* 3.3 27.8 - - + -
214E SER* 3.1 23.1 - - - +
215E LEU 3.2 0.2 - - - -
216E GLY* 1.3 70.9 - - - +
218E THR* 1.3 67.5 - - - +
219E LYS 3.2 0.2 + - - -
220E LEU* 3.2 10.9 + - + +
221E VAL* 2.8 29.6 + - + +
339F LEU* 3.5 24.9 - - + -
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Residues in contact with THR 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG* 4.1 3.6 - - - +
191E GLY 4.2 13.7 - - - +
192E ARG* 3.8 1.1 - - - -
193E MET* 2.9 52.6 + - + +
213E LEU* 3.4 9.2 + - - +
214E SER 2.6 26.0 + - - -
215E LEU* 2.8 5.4 + - - +
217E VAL* 1.3 70.2 - - - +
219E LYS* 1.3 70.9 + - - +
221E VAL* 2.9 4.6 + - - +
222E GLU* 2.8 42.0 + - - +
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Residues in contact with LYS 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU 2.7 15.1 + - - +
216E GLY* 3.0 16.8 - - - +
218E THR* 1.3 78.1 - - - +
220E LEU* 1.3 77.1 + - + +
222E GLU* 2.8 30.0 + - - +
223E ARG* 3.1 12.3 + - + +
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Residues in contact with LEU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E PHE* 4.5 13.5 - - + -
146E ARG* 3.1 32.8 - - - +
150E GLU* 6.1 4.7 - - + -
158E ILE* 5.0 1.4 - - - +
161E LEU* 4.6 25.4 - - + +
162E ALA* 3.6 24.5 - - + +
165E GLY* 5.8 0.7 - - - -
216E GLY* 2.9 16.6 + - - +
217E VAL* 3.2 7.6 + - + +
219E LYS* 1.3 88.7 - - + +
221E VAL* 1.3 60.2 + - - +
223E ARG* 3.7 15.7 - - - +
224E TRP* 3.4 14.4 + - - +
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ALA* 4.4 14.4 - - + +
166E ILE* 4.3 23.6 - - + -
185E ILE* 3.8 29.4 - - + -
193E MET* 3.8 7.6 - - - -
213E LEU* 4.4 9.0 - - + -
217E VAL* 2.8 23.1 - - + +
218E THR* 2.9 8.0 + - - +
219E LYS 2.9 0.2 + - - -
220E LEU* 1.3 74.8 - - + +
222E GLU* 1.3 68.8 + - - +
224E TRP* 2.9 13.7 + - + +
225E ILE* 2.8 20.4 + - + +
238E LEU* 4.5 13.5 - - + -
239E PHE* 5.7 0.7 - - + -
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Residues in contact with GLU 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG* 2.7 41.2 + - - +
193E MET* 4.0 2.9 - - + -
218E THR* 2.8 33.0 + - + +
219E LYS* 2.8 33.2 + - - +
221E VAL* 1.3 69.3 - - - +
223E ARG* 1.3 57.0 + - - +
225E ILE* 2.7 42.6 + - - +
226E SER* 3.3 7.0 + - - -
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Residues in contact with ARG 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLU 5.9 1.2 + - - -
152E SER 3.4 14.3 + - - -
153E ASP* 3.8 18.2 + - - +
158E ILE* 3.1 43.8 - - + +
219E LYS* 3.1 7.4 + - + +
220E LEU* 3.7 18.8 - - - +
221E VAL 3.3 0.2 - - - -
222E GLU* 1.3 77.9 - - - +
224E TRP* 1.3 61.5 + - - +
226E SER* 3.0 21.9 + - - -
227E VAL* 3.3 23.8 + - + +
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Residues in contact with TRP 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E CYS* 3.7 22.7 - - + -
158E ILE* 3.4 27.1 - - + -
159E ARG* 3.1 53.6 - - + -
162E ALA* 4.1 9.4 - - + -
220E LEU 3.4 7.9 + - - +
221E VAL* 2.9 12.1 + - + +
223E ARG* 1.3 77.2 - - - +
225E ILE* 1.3 64.1 + - + +
227E VAL* 4.7 1.8 - - + +
228E SER* 2.7 67.3 + - - -
230E VAL* 4.5 0.8 - - + +
238E LEU* 3.3 39.5 + - + +
239E PHE* 4.2 6.0 - + - -
240E CYS* 4.2 20.4 - - - -
242E VAL* 4.0 7.9 - - + -
248E ALA* 4.0 10.8 - - + -
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Residues in contact with ILE 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E VAL* 4.5 17.0 - - + -
185E ILE* 4.7 7.4 - - + -
187E ARG* 4.5 5.4 - - - +
193E MET* 3.4 26.0 - - + -
221E VAL* 2.8 21.2 + - + +
222E GLU* 2.7 35.2 + - + +
224E TRP* 1.3 78.5 - - + +
226E SER* 1.3 53.8 + - - +
228E SER* 3.6 3.3 + - - -
229E GLY* 3.0 23.2 + - - -
230E VAL* 3.4 8.0 + - + +
231E ALA* 4.3 23.2 + - + +
238E LEU* 5.9 4.0 - - + -
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Residues in contact with SER 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E GLU 3.3 4.9 + - - -
223E ARG* 3.0 13.9 + - - -
225E ILE* 1.3 76.5 - - - +
227E VAL* 1.3 74.4 + - - +
228E SER 3.0 1.6 - - - -
229E GLY* 2.8 22.7 + - - -
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ASP 5.5 2.9 - - - +
155E CYS* 3.8 33.2 - - + +
158E ILE* 5.1 7.0 - - + -
223E ARG* 3.3 38.5 + - + +
224E TRP* 4.3 4.5 - - + +
226E SER* 1.3 86.4 + - - +
228E SER* 1.3 57.3 + - - +
248E ALA* 4.5 5.2 + - - +
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Residues in contact with SER 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E TRP* 2.7 61.6 + - - -
225E ILE 3.6 1.2 + - - -
227E VAL* 1.3 77.9 - - - +
229E GLY* 1.3 68.2 + - - +
230E VAL* 2.8 22.7 - - - +
248E ALA* 3.4 17.0 - - - +
250E PRO* 3.2 16.0 - - - +
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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