Contacts of the helix formed by residues 216 - 228 (chain F) 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 GLY 216 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A GLU* 5.4 0.8 - - - +
146F ARG* 5.1 13.5 - - - -
214F SER* 3.2 4.7 + - - -
215F LEU* 1.3 78.4 - - - +
217F VAL* 1.3 63.9 + - - +
218F THR 3.2 1.6 - - - -
219F LYS* 3.0 19.1 + - - +
220F LEU* 3.1 14.9 + - - +
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 4.2 7.0 - - + -
142F PHE* 4.3 18.4 - - + -
146F ARG* 5.4 1.8 - - - +
162F ALA 4.9 0.2 - - - +
165F GLY* 3.6 36.1 - - - +
166F ILE* 3.9 3.6 - - - +
169F ASN* 3.8 19.3 - - + +
213F LEU* 4.0 17.3 - - + -
214F SER* 3.0 20.2 + - - +
216F GLY* 1.3 72.0 - - - +
218F THR* 1.3 68.3 + - - +
220F LEU* 2.7 24.0 + - + +
221F VAL* 2.8 17.1 + - + +
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Residues in contact with THR 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F ARG* 3.5 23.6 + - - -
191F GLY 4.1 7.1 + - - +
192F ARG* 4.6 0.9 - - - -
193F MET* 3.9 32.4 + - - +
213F LEU* 4.3 11.8 - - - +
214F SER 2.7 27.9 + - - +
215F LEU* 3.0 26.7 - - + +
217F VAL* 1.3 75.0 - - - +
219F LYS* 1.3 55.2 + - + +
221F VAL* 3.8 3.5 - - - +
222F GLU* 2.9 31.9 + - - +
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Residues in contact with LYS 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F LEU* 4.0 17.0 - - - +
216F GLY* 3.0 13.1 + - - +
217F VAL 2.9 0.6 - - - -
218F THR* 1.3 79.1 - - + +
220F LEU* 1.3 66.4 + - + +
222F GLU* 3.0 33.5 + - + +
223F ARG* 3.0 15.2 + - - +
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Residues in contact with LEU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F PHE* 4.0 27.1 - - + -
146F ARG* 4.3 16.2 - - + +
150F GLU* 5.5 5.4 - - + -
158F ILE* 4.6 4.0 - - - +
161F LEU* 3.5 48.5 - - + +
162F ALA* 3.4 21.9 - - - +
165F GLY* 4.7 2.0 - - - -
216F GLY 3.1 11.4 + - - +
217F VAL* 2.7 19.9 + - + +
219F LYS* 1.3 77.9 - - + +
221F VAL* 1.3 60.4 + - - +
223F ARG* 3.8 12.0 + - + +
224F TRP* 3.5 9.5 + - - +
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Residues in contact with VAL 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F ALA* 3.8 17.9 - - + +
166F ILE* 3.8 29.6 - - + -
193F MET* 3.1 29.8 - - + -
213F LEU* 3.9 11.9 - - + -
217F VAL* 2.8 19.0 + - + +
218F THR 3.8 4.0 - - - +
220F LEU* 1.3 72.5 - - - +
222F GLU* 1.3 58.1 + - - +
224F TRP* 2.7 25.0 + - + +
225F ILE* 2.8 25.9 + - + +
238F LEU* 4.5 13.7 - - + -
239F PHE* 5.5 0.4 - - + -
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Residues in contact with GLU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ARG* 2.6 45.4 + - - +
193F MET* 4.8 3.4 - - - -
218F THR* 2.9 23.5 + - - +
219F LYS* 3.2 41.8 + - + +
221F VAL* 1.3 75.6 - - - +
223F ARG* 1.3 64.6 + - - +
225F ILE* 3.0 23.3 + - + +
226F SER* 3.1 15.2 + - - -
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Residues in contact with ARG 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F MET 5.3 1.6 + - - -
150F GLU 4.2 14.4 + - - -
151F ASN 4.2 2.8 + - - -
152F SER 2.8 24.9 + - - -
153F ASP* 3.2 18.4 + - - -
158F ILE* 2.9 48.6 - - + +
161F LEU* 5.8 4.6 - - - +
219F LYS 3.0 15.0 + - - +
220F LEU* 3.9 12.2 - - + +
222F GLU* 1.3 76.5 - - - +
224F TRP* 1.3 58.2 + - - +
226F SER* 3.1 17.6 + - - +
227F VAL* 3.2 20.3 + - + +
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Residues in contact with TRP 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F CYS* 4.3 15.0 - - - -
158F ILE* 3.7 15.0 - - + +
159F ARG* 3.5 48.2 - - + -
162F ALA* 4.1 10.5 - - + -
220F LEU 3.5 8.7 + - - +
221F VAL* 2.7 18.3 + - + +
223F ARG* 1.3 73.0 - - - +
225F ILE* 1.3 60.8 + - - +
226F SER 3.2 0.2 - - - -
227F VAL 5.1 0.7 - - - -
228F SER* 2.7 63.2 + - - -
230F VAL* 5.0 0.4 - - - +
238F LEU* 2.9 36.8 + - + -
239F PHE* 3.9 18.9 - + - -
240F CYS* 3.6 25.1 - - - -
242F VAL* 4.2 6.3 - - + -
248F ALA* 3.8 16.6 - - + -
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Residues in contact with ILE 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F VAL* 5.2 6.1 - - + -
185F ILE* 4.5 13.2 - - + -
187F ARG* 6.2 0.7 - - - +
193F MET* 4.7 6.7 - - - -
221F VAL* 2.8 27.3 + - + +
222F GLU* 3.0 15.2 + - + +
224F TRP* 1.3 79.8 - - + +
226F SER* 1.3 66.1 + - - +
228F SER* 3.3 2.6 + - - -
229F GLY* 3.2 16.1 + - - -
230F VAL* 3.7 18.8 + - + -
231F ALA* 4.1 22.6 + - + +
238F LEU* 4.0 25.4 - - + -
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Residues in contact with SER 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F GLU 3.1 8.6 + - - -
223F ARG* 3.1 15.2 + - - +
225F ILE* 1.3 80.1 - - - +
227F VAL* 1.3 70.6 + - - +
228F SER 2.8 11.2 + - - -
229F GLY* 3.1 11.8 + - - +
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ASP 5.3 2.2 - - - +
155F CYS* 3.2 33.0 - - - -
158F ILE* 3.8 32.8 - - + -
223F ARG* 3.2 24.4 + - + +
224F TRP* 3.6 3.1 + - + +
226F SER* 1.3 82.9 + - - +
228F SER* 1.3 56.4 + - - +
248F ALA* 5.1 0.2 - - - +
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Residues in contact with SER 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F TRP* 2.7 59.1 + - - -
225F ILE 3.3 3.1 + - - -
226F SER 2.8 2.0 + - - -
227F VAL* 1.3 74.9 - - - +
229F GLY* 1.3 69.0 + - - +
230F VAL* 3.3 18.0 + - - +
248F ALA* 3.5 12.7 - - - +
250F PRO* 3.8 15.9 - - - +
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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