Contacts of the helix formed by residues 224 - 241 (chain A) in PDB entry 2ZOQ
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 LYS 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 2.8 62.8 + - + +
161A ASN* 3.6 21.5 + - - +
163A LEU* 3.5 20.9 - - + +
191A ALA* 5.2 8.9 - - + +
223A THR* 1.3 71.6 - - - +
225A SER* 1.3 61.9 + - - +
226A ILE 3.1 0.2 - - - -
227A ASP* 3.0 16.0 + - - +
228A ILE* 3.3 16.6 + - + +
321A VAL* 6.2 1.1 - - + -
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 4.4 1.9 + - - -
223A THR* 2.5 32.1 + - - -
224A LYS* 1.3 75.1 - - - +
226A ILE* 1.3 62.1 + - - +
228A ILE* 3.2 19.7 + - - +
229A TRP 3.2 5.7 + - - -
315A PRO* 3.6 36.0 + - - +
318A ARG* 3.0 32.5 + - - -
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 5.0 2.0 - - + -
165A ARG* 4.2 26.7 - - + +
210A TYR 5.3 0.5 - - - +
211A ARG* 6.3 0.2 - - - -
212A ALA* 3.6 19.4 + - + +
214A GLU* 3.9 8.0 + - - +
215A ILE* 3.4 39.0 - - + -
219A SER* 5.0 0.2 - - - +
221A GLY* 3.8 21.5 - - - +
223A THR* 2.9 16.6 + - - +
225A SER* 1.3 82.5 + - - +
227A ASP* 1.3 80.9 + - - +
229A TRP* 3.5 3.3 + - - +
230A SER* 3.5 22.2 + - - +
318A ARG* 4.5 1.8 - - - +
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Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.1 4.9 - - + +
158A HIS* 3.0 35.2 + - + +
163A LEU* 3.5 6.6 - - - -
164A HIS* 3.0 24.6 + - - +
165A ARG* 2.9 25.5 + - - -
167A LEU* 3.9 20.9 - - + +
224A LYS 3.0 4.2 + - - +
226A ILE* 1.3 90.0 - - - +
228A ILE* 1.3 65.0 + - - +
230A SER* 3.5 5.1 + - - -
231A VAL* 3.2 27.0 + - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.3 5.4 - - + -
154A LEU* 4.1 16.2 - - + -
158A HIS* 4.7 2.7 - - + -
224A LYS* 3.5 14.4 - - + +
225A SER* 3.2 11.5 + - - +
227A ASP* 1.3 77.6 - - - +
229A TRP* 1.3 62.2 + - - +
231A VAL* 3.4 7.4 + - + +
232A GLY* 2.9 19.1 + - - -
310A MET* 4.0 20.8 - - + +
318A ARG* 3.6 20.6 - - + -
319A ILE* 3.3 33.2 - - + +
320A THR* 3.9 2.5 - - - +
321A VAL* 3.7 28.9 - - + +
324A ALA* 5.6 0.9 - - + -
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Residues in contact with TRP 229 (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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209A TRP 5.4 0.2 + - - -
210A TYR 3.7 13.4 - - - -
211A ARG 3.4 10.5 + - - -
212A ALA* 3.5 28.0 - - + -
213A PRO* 3.6 15.5 - - + -
225A SER 3.2 5.9 + - - -
226A ILE 3.9 4.7 - - - +
227A ASP 3.3 0.2 - - - -
228A ILE* 1.3 76.3 - - - +
230A SER* 1.3 55.9 + - - +
232A GLY* 2.6 22.2 + - - -
233A CYS* 2.9 24.9 + - - -
245A PHE* 3.5 24.5 - + - -
257A ILE* 3.6 18.4 - - + +
261A LEU* 3.7 22.9 - - + -
310A MET 3.8 8.5 - - - -
311A LEU* 3.3 39.2 - - + +
312A THR 3.1 29.2 - - - -
318A ARG* 3.8 19.9 - - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG 5.1 6.2 + - - -
167A LEU* 3.5 38.3 + - - -
210A TYR* 3.3 24.2 + - - +
226A ILE* 3.5 11.1 + - - +
227A ASP* 3.5 10.6 + - - -
228A ILE 3.4 0.4 - - - -
229A TRP* 1.3 78.6 - - - +
231A VAL* 1.3 55.8 + - - +
233A CYS* 2.7 27.9 + - - +
234A ILE* 2.9 16.8 + - - +
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Residues in contact with VAL 231 (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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147A LEU* 3.9 24.5 - - + -
150A ILE* 4.1 22.4 - - + -
151A LEU* 4.2 12.6 - - + -
154A LEU* 4.3 13.0 - - + -
167A LEU* 3.8 20.4 - - + -
227A ASP 3.2 14.2 + - - +
228A ILE* 3.6 9.2 - - + +
230A SER* 1.3 76.4 - - - +
232A GLY* 1.3 57.7 + - - +
234A ILE* 3.7 11.2 - - + +
235A LEU* 2.9 27.7 + - - +
310A MET* 4.0 11.9 - - - -
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE 2.9 10.4 + - - -
229A TRP 2.6 16.7 + - - -
231A VAL* 1.3 72.8 - - - +
233A CYS* 1.3 60.2 + - - -
236A ALA* 3.2 6.6 + - - +
307A LEU* 2.9 29.6 - - - +
310A MET* 3.8 22.4 - - - -
311A LEU* 4.0 12.4 - - - +
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Residues in contact with CYS 233 (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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209A TRP 3.9 13.9 - - - +
210A TYR* 3.7 22.4 - - + -
229A TRP* 2.9 40.7 + - - -
230A SER 2.7 9.6 + - - +
232A GLY* 1.3 74.6 - - - +
234A ILE* 1.3 58.9 + - - +
236A ALA* 3.4 3.6 + - - +
237A GLU* 2.9 29.2 + - - +
244A ILE* 4.1 15.8 + - + +
245A PHE* 3.8 22.0 - - - -
311A LEU* 4.4 1.1 - - - -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.7 28.5 - - + -
150A ILE* 4.6 11.0 - - + -
167A LEU* 3.9 10.8 - - + -
168A LYS* 3.6 31.6 - - - +
169A PRO* 4.2 8.1 - - + -
172A LEU* 3.5 27.1 - - + -
210A TYR* 4.4 3.1 - - + -
230A SER 2.9 17.7 + - - +
231A VAL* 3.7 18.8 - - + +
233A CYS* 1.3 77.5 - - - +
235A LEU* 1.3 56.5 + - - +
237A GLU* 3.1 8.8 + - - +
238A MET* 2.9 31.4 + - + +
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Residues in contact with LEU 235 (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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143A ILE* 4.0 17.9 - - + -
147A LEU* 3.9 25.8 - - + +
231A VAL 2.9 16.2 + - - +
232A GLY 3.7 5.2 - - - +
234A ILE* 1.3 75.1 - - - +
236A ALA* 1.3 66.8 + - - +
238A MET* 3.1 10.5 + - + +
239A LEU* 3.0 39.9 + - + +
303A ALA* 3.8 24.5 - - + +
306A LEU* 4.7 0.9 - - + -
307A LEU* 3.7 11.2 - - + +
310A MET* 3.0 29.8 - - + -
329A TYR* 5.4 0.4 - - + -
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Residues in contact with ALA 236 (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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232A GLY 3.2 11.4 + - - +
233A CYS 3.7 7.4 - - - +
234A ILE 3.3 0.2 - - - -
235A LEU* 1.3 77.6 - - - +
237A GLU* 1.3 62.6 + - - +
239A LEU* 3.0 13.3 + - - +
240A SER* 3.0 26.5 + - - -
242A ARG 4.5 1.7 - - - +
244A ILE* 4.1 22.7 - - + -
296A PHE* 3.8 22.6 - - + -
307A LEU* 3.7 12.9 - - + +
311A LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 237 (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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130A TYR* 5.8 4.5 - - - -
133A LEU* 3.2 23.9 - - + +
169A PRO* 3.3 14.7 - - + +
210A TYR* 2.7 31.5 + - - -
233A CYS 2.9 13.5 + - - +
234A ILE* 3.3 10.8 - - - +
235A LEU 3.1 0.2 - - - -
236A ALA* 1.3 77.8 - - - +
238A MET* 1.3 54.9 + - - +
239A LEU 3.0 0.2 - - - -
241A ASN* 2.6 36.6 + - - -
242A ARG* 3.5 18.4 + - - +
243A PRO* 3.2 40.0 - - + +
244A ILE* 5.8 0.2 - - - +
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Residues in contact with MET 238 (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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129A LEU* 3.9 25.8 - - + -
133A LEU* 3.6 11.9 - - + +
138A LEU* 3.9 31.9 + - + +
143A ILE* 3.3 46.1 - - + +
146A PHE* 3.8 23.1 - - + -
147A LEU* 4.1 22.7 - - + +
150A ILE* 4.4 8.5 - - + -
234A ILE* 2.9 20.2 + - + +
235A LEU* 3.1 20.8 + - - +
237A GLU* 1.3 72.7 - - - +
239A LEU* 1.3 59.6 + - - +
240A SER 3.4 0.4 + - - -
241A ASN* 4.4 6.9 + - - -
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Residues in contact with LEU 239 (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 GLN* 5.6 1.6 - - - +
140A ASN* 5.2 2.5 - - - +
143A ILE* 3.5 32.2 - - + +
235A LEU* 3.0 37.7 + - + +
236A ALA* 3.3 16.6 - - - +
237A GLU 3.0 0.6 - - - -
238A MET* 1.3 80.2 - - - +
240A SER* 1.3 62.4 + - - +
241A ASN* 5.2 1.8 + - - -
296A PHE* 4.3 9.4 - - + -
299A SER* 4.3 26.1 + - - +
300A ASP 5.6 0.7 - - - +
303A ALA* 4.9 12.3 - - + +
304A LEU* 3.8 29.2 - - + -
307A LEU* 5.0 3.8 - - + -
329A TYR* 5.2 0.9 - - - +
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA 3.0 7.0 + - - -
239A LEU* 1.3 78.3 + - - +
241A ASN* 1.3 76.2 + - - +
242A ARG* 3.3 29.0 + - - +
295A LEU 4.8 0.2 + - - -
296A PHE* 2.5 44.3 - - - -
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Residues in contact with ASN 241 (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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133A LEU* 2.6 45.0 - - - +
134A LYS* 5.5 7.4 + - - +
136A GLN 3.0 16.4 - - - +
137A GLN* 3.8 31.6 + - - +
138A LEU 4.6 2.8 - - - +
237A GLU* 2.6 22.1 + - - -
238A MET 4.4 4.9 + - - -
239A LEU 5.2 1.4 + - - -
240A SER* 1.3 78.5 + - - +
242A ARG* 1.3 57.3 + - - +
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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