Contacts of the helix formed by residues 154 - 171 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 3.1 19.1 + - - +
153A ASP* 1.3 75.9 - - - +
155A CYS* 1.3 63.2 + - - +
156A GLN* 2.6 40.8 + - - +
157A ASP* 3.4 29.4 + - + +
158A ILE* 2.9 27.9 + - - +
246A GLY* 6.3 2.1 - - - -
105D A 4.4 11.1 + - - -
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Residues in contact with CYS 155 (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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153A ASP 3.4 3.4 + - - +
154A ARG* 1.3 72.0 - - - +
156A GLN* 1.3 65.2 + - - +
158A ILE* 3.6 6.6 + - - +
159A ARG* 3.2 16.8 + - - +
224A TRP* 3.6 25.9 - - - -
227A VAL* 3.4 34.1 - - + -
242A VAL* 4.3 5.2 - - + -
246A GLY* 3.2 33.2 - - - +
248A ALA* 4.3 13.0 - - - -
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 2.6 38.4 + - - +
155A CYS* 1.3 78.7 - - - +
157A ASP* 1.3 67.2 + - - +
159A ARG* 3.3 19.2 + - - +
160A ASN* 3.1 32.0 + - - +
242A VAL* 4.1 21.2 + - + +
246A GLY* 5.7 0.4 - - - -
105D A 4.0 30.0 + - - +
106D C 3.6 10.9 + - - +
5304D MG 3.2 21.4 - - - -
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 3.4 36.8 - - + +
152A SER* 3.0 37.4 + - - +
154A ARG* 3.4 35.3 + - + +
155A CYS 3.4 0.2 - - - -
156A GLN* 1.3 80.9 - - - +
158A ILE* 1.3 65.4 + - - +
160A ASN* 4.1 1.4 + - - +
161A LEU* 3.2 24.6 + - - +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET 5.7 1.1 - - - +
152A SER 3.9 13.5 - - - +
153A ASP* 3.7 11.4 - - - +
154A ARG 2.9 24.4 + - - +
155A CYS* 3.9 4.3 - - - +
156A GLN 3.2 0.2 - - - -
157A ASP* 1.3 75.6 - - - +
159A ARG* 1.3 66.0 + - - +
161A LEU* 3.6 4.7 + - - +
162A ALA* 3.3 18.4 + - - +
220A LEU 4.7 2.5 - - - +
223A ARG* 3.6 45.3 - - + +
224A TRP* 3.6 29.8 - - + +
227A VAL* 3.9 25.8 - - + -
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A CYS 3.2 5.6 + - - +
156A GLN* 3.3 14.6 + - - +
158A ILE* 1.3 79.7 - - - +
160A ASN* 1.3 80.7 + - - +
162A ALA* 3.0 7.3 + - - +
163A PHE* 2.9 24.1 + - - +
224A TRP* 3.4 46.4 - - + -
239A PHE* 3.9 17.1 - - + -
240A CYS 3.0 29.9 + - - +
241A ARG* 4.1 4.6 - - - +
242A VAL* 4.3 6.0 - - + +
256A LEU* 4.3 11.3 - - - +
260A ALA* 6.4 0.2 - - - +
264A ILE* 3.7 16.8 - - + +
106D C 3.0 40.0 + - - -
5304D MG 3.5 11.3 - - - -
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Residues in contact with ASN 160 (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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149A MET* 4.2 17.4 - - + +
156A GLN* 3.1 21.9 + - - +
157A ASP* 4.1 3.7 + - - +
159A ARG* 1.3 100.9 + - - +
161A LEU* 1.3 66.5 + - - +
162A ALA 3.0 0.2 + - - -
163A PHE* 3.0 5.3 + - - +
164A LEU* 2.9 29.4 + - - +
264A ILE* 3.2 29.0 + - + +
267A ALA* 5.7 3.8 - - - +
268A THR* 4.8 5.1 + - - +
5304D MG 3.6 19.4 - - - -
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Residues in contact with LEU 161 (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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142A PHE* 4.1 10.5 - - + -
145A VAL* 4.7 9.0 - - + -
146A ARG* 3.8 34.1 - - + +
149A MET* 3.9 23.9 - - + +
150A GLU* 4.1 26.0 - - + +
157A ASP 3.2 17.3 + - - +
158A ILE* 4.1 4.9 - - - +
160A ASN* 1.3 78.6 - - - +
162A ALA* 1.3 59.9 + - - +
164A LEU* 4.6 4.5 - - + -
165A GLY 3.2 13.7 + - - -
220A LEU* 3.2 36.2 - - + +
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Residues in contact with ALA 162 (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 3.3 10.5 + - - +
159A ARG 3.0 10.5 + - - +
160A ASN 3.0 0.6 - - - -
161A LEU* 1.3 77.8 - - - +
163A PHE* 1.3 59.8 + - - +
165A GLY* 3.3 1.7 + - - -
166A ILE* 2.9 33.3 + - - +
217A VAL* 5.2 0.2 - - - +
220A LEU* 3.9 27.3 - - - +
221A VAL* 4.1 11.2 - - + +
224A TRP* 4.1 11.4 - - + -
239A PHE* 4.2 12.1 - - + -
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Residues in contact with PHE 163 (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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159A ARG 2.9 12.4 + - - +
160A ASN* 3.0 8.0 + - - +
162A ALA* 1.3 73.8 - - - +
164A LEU* 1.3 65.5 - - + +
166A ILE* 3.3 1.6 + - - +
167A ALA* 2.8 32.1 + - + +
174A ILE* 4.2 6.3 - - + -
177A ILE* 3.8 35.2 - - + -
239A PHE* 3.7 20.8 - + + -
261A LEU* 3.7 50.9 - - + -
264A ILE* 3.6 31.6 - - + -
265A PHE* 3.6 35.9 - + - -
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Residues in contact with LEU 164 (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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137A PHE* 4.4 17.3 - - + -
142A PHE* 4.4 7.9 - - + -
145A VAL* 3.7 18.8 - - + -
149A MET* 5.1 1.3 - - - -
160A ASN 2.9 21.9 + - - +
161A LEU* 4.0 6.5 - - + +
163A PHE* 1.3 88.5 - - + +
165A GLY* 1.3 65.2 + - - +
167A ALA* 2.9 5.1 + - - +
168A TYR* 2.8 24.9 + - - +
264A ILE* 4.4 6.5 - - + -
265A PHE* 3.6 38.8 - - + -
268A THR* 3.7 33.9 - - + +
291A ALA* 5.3 0.2 - - - +
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Residues in contact with GLY 165 (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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142A PHE* 3.5 28.8 - - - -
161A LEU 3.2 11.9 + - - -
162A ALA* 3.3 3.3 + - - -
164A LEU* 1.3 78.4 - - - +
166A ILE* 1.3 56.6 + - - +
168A TYR* 3.4 1.7 + - - +
169A ASN* 2.9 33.1 + - - +
217A VAL* 3.7 14.8 - - - +
220A LEU* 5.1 0.9 - - - -
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Residues in contact with ILE 166 (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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162A ALA 2.9 18.8 + - - +
163A PHE* 3.9 3.6 - - - +
165A GLY* 1.3 72.4 - - - +
167A ALA* 1.3 58.5 + - - +
169A ASN* 4.6 0.2 - - - -
170A THR* 2.8 56.9 + - + +
172A LEU* 4.7 7.6 - - + -
177A ILE* 4.8 11.2 - - + -
180A ILE* 4.8 4.0 - - + -
195A ILE* 4.0 18.8 - - + -
213A LEU* 4.1 8.5 - - + -
217A VAL* 4.0 2.9 - - + +
221A VAL* 3.6 31.0 - - + -
238A LEU* 3.7 27.8 - - + -
239A PHE* 3.9 13.2 - - + -
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Residues in contact with ALA 167 (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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163A PHE* 2.8 23.5 + - + +
164A LEU* 2.9 4.5 + - - +
166A ILE* 1.3 78.0 - - - +
168A TYR* 1.3 60.9 + - - +
170A THR* 4.6 0.9 - - - -
171A LEU* 3.3 21.3 + - - -
172A LEU 4.7 3.9 - - - +
174A ILE* 6.3 0.2 - - + -
177A ILE* 3.9 23.1 - - + +
265A PHE* 4.0 26.5 - - + -
291A ALA* 3.2 13.0 - - + +
292A ARG* 5.5 0.2 - - - +
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Residues in contact with TYR 168 (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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137A PHE* 3.6 31.4 - + + -
138A GLU 4.6 0.7 - - - -
139A ARG* 3.2 31.1 + - - +
142A PHE* 4.5 13.9 - + + -
164A LEU 2.8 17.5 + - - +
165A GLY* 4.0 3.4 - - - +
167A ALA* 1.3 74.9 - - - +
169A ASN* 1.3 66.9 + - + +
171A LEU* 4.0 3.6 - - - +
291A ALA* 3.5 16.8 - - + +
295A ALA* 3.7 29.6 - - + +
298A ASP* 2.5 32.2 + - - +
335B MET* 3.3 28.9 - - + +
338B LEU* 4.9 1.7 - - - +
339B LEU* 3.6 28.5 - - + -
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Residues in contact with ASN 169 (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 GLY 2.9 19.0 + - - +
166A ILE 4.3 0.9 - - - +
168A TYR* 1.3 84.4 - - + +
170A THR* 1.3 60.2 + - + +
171A LEU* 3.6 1.1 - - - +
212A ALA 3.8 14.1 + - - +
213A LEU* 3.2 11.8 - - - +
214A SER 3.0 28.2 + - - -
217A VAL* 3.6 9.4 - - + +
335B MET* 3.3 35.2 + - - +
336B VAL* 4.3 3.6 - - - +
339B LEU* 3.4 25.8 - - + +
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Residues in contact with THR 170 (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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166A ILE* 2.8 29.1 + - + +
167A ALA* 4.6 0.3 - - - -
169A ASN* 1.3 77.8 - - - +
171A LEU* 1.3 67.4 + - - +
172A LEU* 2.9 39.1 + - + +
195A ILE* 4.4 3.8 - - + -
211A LYS* 3.3 43.8 + - + +
212A ALA 5.2 1.3 - - - +
213A LEU* 3.4 32.5 - - + -
312A ALA 4.0 1.0 - - - +
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Residues in contact with LEU 171 (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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167A ALA 3.3 16.9 + - - -
168A TYR 4.0 1.8 - - - +
169A ASN 3.6 1.8 - - - +
170A THR* 1.3 79.1 - - - +
172A LEU* 1.3 58.4 + - - +
211A LYS* 5.2 1.5 + - - -
291A ALA 4.6 0.2 - - - +
292A ARG* 2.4 53.8 + - + +
295A ALA* 3.8 33.0 - - + -
296A ALA 4.6 1.8 - - - +
299A MET* 4.9 3.8 - - + -
312A ALA* 4.1 15.9 - - + +
313A GLY* 3.8 14.3 - - - +
315A TRP* 3.5 38.1 - - + -
335B MET* 3.9 25.6 - - + -
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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