Contacts of the helix formed by residues 229 - 246 (chain A) in PDB entry 2WZJ
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 PRO 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A HIS* 3.3 45.3 - - + +
172A VAL* 4.0 16.1 - - + -
228A GLY* 1.3 81.3 - - - +
230A GLU* 1.3 71.5 - - - +
231A VAL 3.1 0.4 - - - -
232A ASP 3.0 12.9 + - - +
233A VAL* 3.1 16.7 + - + +
91B SER* 4.0 13.5 - - - +
95B GLN* 4.5 1.6 - - - +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLU* 4.3 2.9 - - - +
228A GLY* 3.6 20.1 + - - +
229A PRO* 1.3 83.4 - - - +
231A VAL* 1.3 66.6 + - + +
233A VAL* 3.3 10.4 + - - +
234A TRP 3.1 19.2 + - - -
289A PRO* 3.6 41.6 - - + +
290A SER* 6.1 0.7 - - - -
292A ARG* 3.1 26.2 + - + +
91B SER* 5.0 3.5 + - - -
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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
----------------------------------------------------------
172A VAL* 5.1 0.2 - - + -
174A ARG* 4.1 13.9 - - + -
217A ALA* 4.4 4.5 - - + +
219A GLU* 3.9 13.2 - - - +
225A LYS 5.1 0.2 - - - +
226A TYR* 3.3 72.2 - - + +
227A ASP 4.5 0.7 - - - +
228A GLY 3.1 16.7 + - - +
230A GLU* 1.3 81.9 - - + +
232A ASP* 1.3 73.9 + - - +
234A TRP* 3.5 4.5 + - - +
235A SER* 3.3 21.6 + - - +
292A ARG* 4.3 4.3 - - - +
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 4.1 4.3 - - + +
167A HIS* 2.9 27.8 + - + +
172A VAL* 3.4 7.9 - - - +
173A HIS* 2.7 34.1 + - - +
174A ARG* 3.0 26.6 + - - -
175A ASP 4.7 0.5 + - - -
176A LEU* 4.0 15.9 - - + +
229A PRO 3.0 9.2 + - - +
231A VAL* 1.3 76.9 - - - +
233A VAL* 1.3 60.9 + - - +
235A SER* 3.0 7.7 + - - +
236A LEU* 2.8 35.0 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A HIS* 4.7 2.2 - - + -
229A PRO* 3.1 17.4 + - + +
230A GLU* 3.3 13.7 + - + +
232A ASP* 1.3 76.1 - - - +
234A TRP* 1.3 62.1 + - - +
236A LEU* 3.5 5.1 + - - -
237A GLY 3.3 2.6 + - - -
283A LYS 4.6 0.4 - - - +
284A PHE* 2.8 54.4 - - + +
292A ARG* 4.6 9.9 - - + -
293A GLY 3.5 26.7 - - - +
294A THR* 5.1 1.1 - - - -
295A LEU* 4.1 21.3 - - + +
298A ILE* 3.9 9.0 - - + -
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Residues in contact with TRP 234 (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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214A PRO 5.2 0.2 + - - -
215A TYR 3.4 19.5 - - - -
216A ALA 3.3 12.9 + - - -
217A ALA* 3.4 21.1 - - + -
218A PRO* 3.7 26.2 - - + -
230A GLU 3.1 11.0 + - - +
231A VAL 3.6 8.3 - - - +
232A ASP 3.2 0.2 - - - -
233A VAL* 1.3 75.4 - - - +
235A SER* 1.3 63.9 + - - +
237A GLY* 3.0 13.3 + - - -
238A VAL* 3.1 20.3 + - + +
250A PHE* 3.6 31.9 - + - -
262A VAL* 4.3 9.4 - - + +
265A GLY* 5.0 2.0 - - - -
284A PHE 4.0 6.3 - - - -
285A LEU* 3.5 25.7 - - + +
286A ILE 3.5 47.1 - - - -
287A LEU* 3.9 14.4 - - + -
292A ARG* 3.7 11.8 - - - +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG 6.1 0.7 - - - -
176A LEU* 4.2 29.2 + - - -
215A TYR* 2.5 32.0 + - - +
226A TYR* 4.6 5.2 + - - -
231A VAL* 3.3 12.2 + - - +
232A ASP* 3.0 10.1 + - - -
234A TRP* 1.3 77.2 - - - +
236A LEU* 1.3 51.1 + - - +
238A VAL* 3.0 7.6 + - - +
239A ILE* 2.8 37.9 + - - +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.6 11.2 - - + -
159A ILE* 3.3 33.7 - - + -
160A VAL* 4.7 7.9 - - + -
163A VAL* 4.1 14.8 - - + -
176A LEU* 4.2 12.3 - - + -
232A ASP 2.8 24.1 + - - +
233A VAL 3.7 0.2 - - - +
235A SER* 1.3 73.1 - - - +
237A GLY* 1.3 51.7 + - - +
239A ILE* 3.0 17.7 + - + +
240A LEU* 2.7 35.3 + - - +
284A PHE* 3.5 19.5 - - + -
295A LEU* 3.7 40.2 - - + -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL 3.3 4.8 + - - -
234A TRP 3.0 8.9 + - - -
236A LEU* 1.3 78.2 - - - +
238A VAL* 1.3 61.8 + - - +
240A LEU* 3.3 1.0 + - - -
241A TYR* 3.0 20.8 + - - +
281A LEU* 3.4 13.1 - - - +
284A PHE* 3.4 29.6 - - - -
285A LEU* 4.2 10.5 - - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PRO* 3.3 29.6 - - + +
215A TYR* 3.4 25.4 - - + +
234A TRP* 3.1 36.5 + - + +
235A SER 3.0 7.2 + - - +
237A GLY* 1.3 75.3 - - - +
239A ILE* 1.3 63.8 + - - +
241A TYR* 3.5 2.4 + - - +
242A THR* 3.1 28.7 + - + +
248A LEU* 5.2 0.7 - - + -
249A PRO* 4.0 23.8 - - + -
250A PHE* 4.4 8.5 - - + -
285A LEU* 3.9 8.5 - - + -
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.4 9.0 - - + -
159A ILE* 4.5 2.7 - - + -
176A LEU* 4.1 27.4 - - + -
177A LYS* 4.1 8.3 - - - +
178A ALA* 4.8 1.3 - - - +
181A LEU* 3.8 34.5 - - + -
215A TYR* 3.7 18.8 - - + -
235A SER 2.8 17.8 + - - +
236A LEU* 3.4 22.7 - - + +
238A VAL* 1.3 76.1 - - - +
240A LEU* 1.3 64.6 + - - +
242A THR* 2.8 26.9 + - - +
243A LEU* 2.9 25.2 + - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.5 33.9 - - + -
236A LEU 2.7 13.6 + - - +
237A GLY* 3.3 4.0 + - - +
239A ILE* 1.3 72.4 - - - +
241A TYR* 1.3 64.1 + - - +
243A LEU* 2.9 20.3 + - + +
244A VAL* 3.2 22.2 + - + +
277A CYS* 4.7 7.2 - - - +
280A LEU* 3.2 33.2 - - + -
281A LEU* 3.5 26.7 - - + +
284A PHE* 4.6 3.8 - - + -
303A TRP* 3.9 29.6 - - + -
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Residues in contact with TYR 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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237A GLY 3.0 12.4 + - - +
238A VAL 3.6 8.7 - - - +
240A LEU* 1.3 78.3 - - - +
242A THR* 1.3 59.8 + - - +
244A VAL* 3.5 4.9 + - - +
245A SER* 2.7 48.8 + - - -
247A SER* 3.2 20.4 + - - -
248A LEU 3.7 3.7 + - - -
249A PRO* 3.5 41.4 - - + +
267A TYR* 4.0 16.8 - + + -
268A ARG* 2.6 42.0 + - - +
269A ILE* 5.2 0.2 - - - -
270A PRO* 4.2 6.9 - - + +
273A MET* 4.5 12.1 - - + -
281A LEU* 3.7 27.5 - - + +
285A LEU* 5.1 1.3 - - + -
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Residues in contact with THR 242 (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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141A LEU* 3.7 23.1 - - - +
178A ALA* 4.9 2.9 - - - +
215A TYR* 4.0 17.3 + - + +
238A VAL* 3.1 16.8 - - + +
239A ILE* 2.8 22.6 + - - +
241A TYR* 1.3 72.4 - - - +
243A LEU* 1.3 67.4 + - - +
246A GLY* 2.9 23.0 + - - +
247A SER 3.7 22.2 - - - +
248A LEU* 3.9 25.8 - - + -
249A PRO* 4.5 1.6 - - + -
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Residues in contact with LEU 243 (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 VAL* 3.9 21.8 - - + -
141A LEU* 4.3 7.5 - - + +
146A ARG* 3.9 0.3 - - - -
147A MET* 3.0 56.1 + - + +
152A ALA* 3.8 34.8 - - + +
155A LYS* 4.6 4.9 - - + -
156A PHE* 4.1 26.2 - - + +
159A ILE* 4.4 11.2 - - + -
239A ILE* 2.9 25.2 + - + +
240A LEU* 2.9 10.1 + - + +
242A THR* 1.3 81.0 + - - +
244A VAL* 1.3 59.6 + - + +
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Residues in contact with VAL 244 (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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146A ARG* 3.4 11.9 + - - +
147A MET 3.8 9.8 - - - +
149A GLU* 4.6 14.6 - - + +
152A ALA* 3.9 18.8 - - + -
240A LEU* 3.2 28.3 + - + +
241A TYR* 4.3 4.0 - - - +
243A LEU* 1.3 78.0 - - - +
245A SER* 1.3 59.3 + - - +
272A TYR* 3.3 17.8 - - + -
273A MET* 3.3 38.4 - - + -
277A CYS* 4.0 14.8 - - - -
303A TRP* 4.6 5.8 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 3.4 11.4 + - - +
241A TYR* 2.7 38.1 + - - -
244A VAL* 1.3 81.0 - - - +
246A GLY* 1.3 63.0 + - - +
247A SER* 2.9 30.9 + - - -
270A PRO* 4.5 7.6 - - - -
272A TYR* 3.1 22.9 + - - -
273A MET* 5.4 0.2 - - - -
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Residues in contact with GLY 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.8 14.6 - - - +
145A GLY* 4.5 5.3 - - - -
146A ARG* 3.6 19.5 - - - +
242A THR* 2.9 17.9 + - - -
245A SER* 1.3 78.6 - - - +
247A SER* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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