Contacts of the helix formed by residues 154 - 171 (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 ARG 154 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F SER* 3.1 14.0 + - - +
153F ASP* 1.3 77.9 - - - +
155F CYS* 1.3 65.2 + - - +
156F GLN* 3.8 25.4 + - - +
157F ASP* 3.7 28.7 + - + +
158F ILE* 2.9 25.3 + - - +
105G A 3.4 24.9 + - - -
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Residues in contact with CYS 155 (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 3.5 3.3 + - - -
154F ARG* 1.3 69.3 - - - +
156F GLN* 1.3 69.2 + - - +
158F ILE* 2.8 9.0 + - - +
159F ARG* 2.7 25.2 + - - +
224F TRP* 4.3 12.0 - - - -
227F VAL* 3.2 41.7 - - - -
242F VAL* 4.4 8.7 - - + -
246F GLY* 3.6 30.6 + - - +
247F VAL* 5.3 0.2 - - - -
248F ALA* 4.6 11.0 - - - -
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Residues in contact with GLN 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ARG* 3.8 28.1 + - - +
155F CYS* 1.3 78.5 - - - +
157F ASP* 1.3 70.1 + - - +
159F ARG* 3.2 6.3 + - - +
160F ASN* 2.9 44.6 + - - +
242F VAL* 3.7 31.5 - - + +
246F GLY* 5.8 1.7 - - - -
105G A 3.5 32.9 + - - -
106G C 4.0 11.5 + - - -
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Residues in contact with ASP 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F MET* 3.7 38.3 - - - +
152F SER* 3.3 38.1 - - - +
154F ARG* 3.4 30.8 + - + +
155F CYS 3.1 0.6 - - - -
156F GLN* 1.3 83.9 - - - +
158F ILE* 1.3 64.3 + - - +
160F ASN* 3.7 4.4 + - - +
161F LEU* 3.3 23.7 + - - +
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Residues in contact with ILE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F MET 6.0 0.4 - - - -
152F SER 4.1 4.3 - - - +
153F ASP* 4.0 8.7 - - - +
154F ARG 2.9 18.9 + - - +
155F CYS* 2.8 14.6 + - - +
157F ASP* 1.3 74.4 - - - +
159F ARG* 1.3 62.5 + - - +
161F LEU* 3.5 6.3 + - - +
162F ALA* 3.5 16.3 + - - +
220F LEU 4.6 2.4 - - - +
223F ARG* 2.9 57.2 - - + +
224F TRP* 3.7 31.4 - - + +
227F VAL* 3.8 29.8 - - + -
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Residues in contact with ARG 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F CYS 2.7 12.2 + - - +
156F GLN* 3.5 9.8 - - - +
158F ILE* 1.3 69.3 - - - +
160F ASN* 1.3 86.8 + - - +
161F LEU 3.0 4.7 - - - -
162F ALA* 2.8 22.7 + - - +
163F PHE* 2.9 10.5 + - + +
224F TRP* 3.5 44.8 - - + -
239F PHE* 3.8 25.0 - - + -
240F CYS 2.8 27.8 + - - -
241F ARG* 3.8 2.4 - - - +
242F VAL* 3.9 14.1 - - - +
256F LEU* 4.2 7.1 - - - +
260F ALA* 6.1 0.8 - - - +
264F ILE* 3.6 20.0 - - - +
106G C 2.9 38.8 + - - -
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Residues in contact with ASN 160 (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* 4.7 10.3 - - + -
156F GLN* 2.9 30.8 + - - +
157F ASP* 4.3 4.3 - - - +
159F ARG* 1.3 114.5 + - - +
161F LEU* 1.3 60.7 + - - +
163F PHE* 3.8 5.2 - - - +
164F LEU* 3.2 28.8 + - - +
264F ILE* 3.2 36.9 + - + +
267F ALA* 5.7 4.4 - - - +
268F THR* 5.2 4.5 + - - +
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Residues in contact with LEU 161 (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* 4.7 7.4 - - + -
145F VAL* 3.8 15.5 - - + +
146F ARG* 3.9 15.5 - - + -
149F MET* 3.6 28.5 - - + +
150F GLU* 4.1 28.5 - - - +
157F ASP 3.3 16.7 + - - +
158F ILE* 3.8 5.8 - - - +
159F ARG 2.8 1.4 + - - -
160F ASN* 1.3 74.5 - - - +
162F ALA* 1.3 60.8 + - - +
164F LEU* 3.4 4.5 + - + +
165F GLY* 2.8 26.0 + - - -
220F LEU* 3.5 38.2 - - + +
223F ARG* 5.8 4.7 - - - +
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Residues in contact with ALA 162 (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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158F ILE 3.5 5.6 + - - +
159F ARG 2.8 8.8 + - - +
161F LEU* 1.3 77.0 - - - +
163F PHE* 1.3 65.2 + - - +
165F GLY* 3.6 1.2 - - - +
166F ILE* 3.0 28.6 + - - +
220F LEU* 3.4 34.0 - - - +
221F VAL* 3.8 19.3 - - + +
224F TRP* 4.1 10.3 - - + -
239F PHE* 4.1 8.1 - - + -
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Residues in contact with PHE 163 (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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159F ARG 2.9 10.0 + - - +
160F ASN* 3.8 11.0 - - - +
162F ALA* 1.3 76.9 - - - +
164F LEU* 1.3 83.3 + - + +
166F ILE* 3.0 5.4 + - - +
167F ALA* 2.8 35.1 + - + +
174F ILE* 4.3 7.6 - - + -
177F ILE* 4.3 23.5 - - + +
239F PHE* 3.5 23.9 - + + -
261F LEU* 3.3 56.1 - - + -
264F ILE* 4.0 16.4 - - + -
265F PHE* 3.3 41.5 - + - -
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Residues in contact with LEU 164 (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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137F PHE* 4.3 23.0 - - + -
142F PHE* 4.3 7.7 - - + -
145F VAL* 4.1 14.8 - - + -
149F MET* 4.8 2.9 - - + -
160F ASN 3.2 18.0 + - - +
161F LEU* 3.8 5.6 - - + +
163F PHE* 1.3 90.0 - - + +
165F GLY* 1.3 62.5 + - - +
167F ALA* 3.7 3.2 - - + +
168F TYR* 3.1 26.3 + - - +
264F ILE* 4.6 5.4 - - + -
265F PHE* 3.5 43.1 - - + -
268F THR* 3.6 35.9 - - + +
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Residues in contact with GLY 165 (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* 3.6 21.0 - - - -
161F LEU 2.8 17.0 + - - -
162F ALA* 3.6 3.1 - - - -
163F PHE 3.0 0.4 - - - -
164F LEU* 1.3 78.0 - - - +
166F ILE* 1.3 55.4 - - - +
168F TYR* 4.2 1.6 - - - +
169F ASN* 3.0 31.5 + - - +
217F VAL* 3.6 19.6 - - - +
220F LEU* 4.7 0.9 - - - -
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Residues in contact with ILE 166 (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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162F ALA 3.0 13.0 + - - +
163F PHE* 3.7 6.7 - - - +
165F GLY* 1.3 72.8 - - - +
167F ALA* 1.3 67.0 + - - +
169F ASN* 4.4 4.7 - - - -
170F THR* 2.9 43.9 + - + +
172F LEU* 4.5 1.6 - - + -
177F ILE* 3.5 26.0 - - + -
180F ILE* 4.9 1.8 - - + -
195F ILE* 3.5 25.6 - - + -
213F LEU* 3.7 20.0 - - + -
217F VAL* 4.5 0.7 - - - -
221F VAL* 3.8 19.7 - - + -
238F LEU* 4.0 19.5 - - + -
239F PHE* 4.1 11.7 - - + -
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Residues in contact with ALA 167 (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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163F PHE* 2.8 30.8 + - + +
164F LEU* 3.7 6.7 - - + +
165F GLY 3.4 0.2 - - - -
166F ILE* 1.3 74.0 - - - +
168F TYR* 1.3 57.5 + - - +
170F THR* 4.7 0.2 - - - -
171F LEU* 3.1 26.5 + - - -
172F LEU 4.2 5.7 + - - +
174F ILE* 6.4 0.4 - - + -
177F ILE* 4.6 11.2 - - + +
265F PHE* 4.1 18.6 - - + -
291F ALA* 3.4 20.9 - - + +
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Residues in contact with TYR 168 (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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335A MET* 3.1 37.1 - - + +
338A LEU* 5.3 4.0 - - - +
339A LEU* 3.7 28.0 - - + -
137F PHE* 3.8 33.9 - + + -
138F GLU 4.0 1.3 - - - -
139F ARG* 3.1 32.1 + - - +
142F PHE* 4.2 14.4 - + + -
164F LEU 3.1 15.5 + - - +
165F GLY 4.3 0.9 - - - +
167F ALA* 1.3 75.6 - - - +
169F ASN* 1.3 66.7 + - + +
170F THR 3.5 0.3 + - - -
171F LEU* 3.7 2.9 - - - +
291F ALA* 3.6 10.5 - - + -
295F ALA* 3.7 27.5 - - + +
298F ASP* 2.7 37.0 + - - +
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Residues in contact with ASN 169 (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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335A MET* 3.5 30.1 + - - +
336A VAL* 4.3 1.2 - - - +
339A LEU* 3.3 31.4 - - + +
165F GLY 3.0 21.4 + - - +
166F ILE 4.1 1.8 - - - +
168F TYR* 1.3 79.7 - - - +
170F THR* 1.3 57.5 + - - +
171F LEU* 4.5 0.9 - - - -
212F ALA 4.1 8.3 + - - +
213F LEU* 3.0 20.7 - - + +
214F SER* 2.6 31.8 + - - +
217F VAL* 3.8 6.4 - - + +
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Residues in contact with THR 170 (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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166F ILE* 2.9 25.3 + - + +
169F ASN* 1.3 78.2 - - - +
171F LEU* 1.3 74.7 + - - +
172F LEU* 3.0 36.4 + - + +
195F ILE* 5.0 1.3 - - + -
211F LYS* 3.2 44.3 - - + -
212F ALA 4.8 2.9 - - - +
213F LEU* 3.4 31.4 - - + -
312F ALA 3.6 2.4 - - - +
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Residues in contact with LEU 171 (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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335A MET* 3.7 29.2 - - + -
167F ALA 3.1 15.3 + - - -
168F TYR 3.7 4.3 - - - +
170F THR* 1.3 81.6 + - - +
172F LEU* 1.3 61.5 + - - +
211F LYS* 5.6 0.2 - - - -
291F ALA 4.6 0.2 - - - +
292F ARG* 2.5 62.8 + - + +
295F ALA* 3.7 20.0 - - + -
296F ALA 4.6 0.9 - - - +
299F MET* 3.9 17.7 - - + -
312F ALA 4.3 6.7 - - - +
313F GLY* 3.8 13.0 - - - +
315F TRP* 3.8 29.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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