Contacts of the helix formed by residues 235 - 256 (chain A) in PDB entry 3ZXR
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 LEU 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 3.8 28.5 - - + +
115A ALA* 4.2 6.5 - - + -
116A GLU* 3.2 14.6 + - + +
128A ALA* 3.1 11.6 + - + +
130A PHE* 3.7 35.7 - - + -
234A SER* 1.3 72.6 - - - +
236A LEU* 1.3 66.4 + - - +
238A ALA* 3.1 3.6 + - - +
239A ALA* 2.9 21.5 + - + +
377A TYR 4.6 1.3 - - - +
380A PHE* 3.9 30.9 - - + +
381A SER* 3.9 12.6 - - - +
384A LEU* 3.7 27.4 - - + -
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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
----------------------------------------------------------
74A ASP* 4.6 4.3 - - - +
94A PHE* 4.4 19.5 - - + -
109A ARG* 4.1 19.7 - - - +
112A ALA* 3.7 24.5 - - + -
113A ARG* 4.6 14.8 - - + -
116A GLU* 3.0 27.1 + - - +
235A LEU* 1.3 82.1 - - - +
237A HIS* 1.3 76.6 + - + +
239A ALA* 3.2 3.3 + - - +
240A ASP* 3.0 35.0 + - - +
377A TYR* 4.1 11.7 - - + -
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 6.1 0.4 - - - -
76A GLU* 3.4 39.7 + - + +
77A THR* 6.3 0.4 - - - +
116A GLU* 4.7 0.4 + - - -
233A ASN* 3.6 26.9 - - - +
234A SER* 3.0 26.0 + - - +
236A LEU* 1.3 88.8 - - + +
238A ALA* 1.3 57.9 + - - +
240A ASP* 3.3 10.9 + - - +
241A ASP* 2.8 36.1 + - - +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.9 17.5 - - + +
132A ALA* 6.5 0.2 - - + -
230A TYR* 4.4 5.2 + - + -
233A ASN* 3.6 20.3 - - + +
234A SER 2.8 12.3 + - - +
235A LEU 3.3 8.5 - - - +
237A HIS* 1.3 77.1 - - - +
239A ALA* 1.3 55.8 + - - +
241A ASP* 3.4 10.9 + - - +
242A MET* 2.9 26.9 + - - +
380A PHE* 3.7 17.2 - - + -
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 2.9 14.5 + - + +
236A LEU* 3.2 6.0 + - - +
238A ALA* 1.3 73.3 - - - +
240A ASP* 1.3 65.6 + - - +
242A MET* 3.3 2.8 + - - +
243A GLN* 3.2 26.7 + - - +
376A PRO* 4.0 4.2 - - - +
377A TYR* 3.3 48.0 - - + +
380A PHE* 3.6 17.0 - - + -
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 4.6 0.2 - - - +
77A THR* 3.6 13.3 - - + +
92A ASN* 3.0 17.6 + - - +
109A ARG* 2.9 36.7 + - - -
236A LEU* 3.0 23.1 + - - +
237A HIS* 3.6 13.5 + - - +
239A ALA* 1.3 75.9 - - - +
241A ASP* 1.3 63.3 + - - +
242A MET 3.3 0.3 + - - -
243A GLN* 3.3 3.5 + - - +
244A LEU* 3.1 24.2 + - - +
377A TYR* 2.5 30.1 + - - -
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Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.9 10.4 + - - -
211A PHE* 3.4 22.2 - - + -
230A TYR* 3.7 26.4 - - + -
231A GLN 4.6 3.1 - - - +
233A ASN* 4.3 20.4 + - - +
237A HIS* 2.8 25.3 + - - +
238A ALA* 3.4 10.6 - - - +
240A ASP* 1.3 75.1 - - - +
242A MET* 1.3 55.4 - - - +
244A LEU* 4.7 2.6 - - - +
245A TYR* 2.9 30.7 + - - +
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Residues in contact with MET 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.4 33.2 - - + -
134A ALA* 3.6 32.5 - - + +
230A TYR* 3.3 18.4 + - + +
238A ALA 2.9 14.2 + - - +
239A ALA* 3.5 9.4 - - - +
240A ASP 3.2 0.2 - - - -
241A ASP* 1.3 76.3 - - - +
243A GLN* 1.3 58.6 - - - +
245A TYR* 3.2 10.4 + - - +
246A LYS* 3.0 47.1 + - + +
275A MET* 3.9 18.8 - - + +
372A SER* 5.3 0.2 - - - -
376A PRO* 4.0 25.6 - - + -
380A PHE* 4.8 2.9 - - + -
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Residues in contact with GLN 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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26A CYS* 3.6 12.5 - - - -
30A GLY 3.0 27.4 + - - +
32A MET* 3.4 42.8 - - + +
92A ASN* 5.6 0.9 - - - +
239A ALA 3.2 8.2 + - - +
240A ASP 3.7 7.0 - - - +
242A MET* 1.3 77.1 - - - +
244A LEU* 1.3 63.7 + - - +
246A LYS* 3.3 20.7 + - - +
247A TYR* 3.1 21.1 + - - +
376A PRO* 3.5 23.8 - - + +
377A TYR* 3.5 28.4 - - + +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 4.9 6.3 - - - +
77A THR 5.8 0.2 - - - +
79A ARG* 3.8 36.1 - - + +
82A PRO* 6.0 2.0 - - + -
90A ASN* 4.9 9.0 - - + +
209A SER* 4.6 5.2 - - - -
211A PHE* 3.6 26.2 - - + -
240A ASP 3.1 16.6 + - - +
241A ASP* 3.9 4.7 - - - +
243A GLN* 1.3 77.3 - - - +
245A TYR* 1.3 55.7 + - - +
247A TYR* 3.2 24.1 + - + +
248A ILE* 2.9 36.8 + - + +
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Residues in contact with TYR 245 (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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134A ALA* 2.9 41.2 + - + -
136A PHE* 3.3 15.9 - - - -
206A LEU* 3.9 17.9 - - + -
211A PHE* 3.7 9.8 - - + -
228A ILE* 3.3 38.3 + - + -
230A TYR* 3.5 26.9 - + + -
241A ASP 2.9 18.6 + - - +
242A MET* 3.4 19.7 - - - +
244A LEU* 1.3 75.9 - - - +
246A LYS* 1.3 62.0 + - + +
248A ILE* 3.3 1.4 + - - +
249A ILE* 2.8 52.4 + - + +
262A PHE* 3.8 12.3 - + - -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY 5.3 3.2 + - - -
31A ILE* 6.0 4.2 - - - +
242A MET* 3.0 35.8 + - + +
243A GLN* 3.7 26.2 + - - +
245A TYR* 1.3 75.6 - - + +
247A TYR* 1.3 58.4 + - - +
249A ILE* 3.8 0.5 - - - +
250A LYS* 2.9 52.8 + - + +
262A PHE* 4.0 47.2 - - + +
372A SER* 2.7 33.1 + - - +
374A GLY 4.4 9.7 + - - -
376A PRO* 5.7 1.4 - - + +
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Residues in contact with TYR 247 (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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24A ARG* 3.0 40.6 + - - +
32A MET* 6.5 1.3 - - + -
81A ASP* 2.4 33.3 + - - -
82A PRO* 4.8 2.5 - - + -
83A PHE* 3.8 22.4 - + - +
84A ARG* 4.9 5.0 - - - +
90A ASN* 4.1 4.3 - - - -
243A GLN 3.1 13.0 + - - +
244A LEU* 3.4 22.7 - - + +
246A LYS* 1.3 76.2 - - - +
248A ILE* 1.3 60.3 + - + +
250A LYS* 4.8 3.6 - - - -
251A ASN* 2.8 62.1 + - - +
189B VAL* 4.0 16.4 - - + -
190B ALA* 3.6 23.3 - - + +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 4.3 6.3 - - + -
83A PHE* 3.5 16.6 - - + -
202A MET 4.4 2.5 - - - +
205A ASN* 3.7 29.4 - - + +
206A LEU* 3.9 31.4 - - + -
209A SER* 3.3 35.0 - - - +
211A PHE* 3.9 9.0 - - + -
244A LEU* 2.9 28.4 + - + +
245A TYR 3.8 3.4 - - - +
247A TYR* 1.3 75.1 - - + +
249A ILE* 1.3 60.1 + - + +
252A THR* 2.7 38.3 + - - +
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.5 39.0 - - + -
202A MET* 3.7 37.3 - - + +
206A LEU* 4.1 10.8 - - + -
228A ILE* 4.1 9.9 - - + -
245A TYR* 2.8 58.5 + - + +
246A LYS 3.8 2.9 - - - +
248A ILE* 1.3 74.7 - - - +
250A LYS* 1.3 63.8 + - - +
253A ALA* 3.1 23.4 + - - +
260A VAL* 4.0 6.7 - - + -
262A PHE* 4.0 8.7 - - + -
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Residues in contact with LYS 250 (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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31A ILE* 5.1 13.9 - - - +
246A LYS* 2.9 39.3 + - - +
247A TYR* 4.0 4.0 - - - +
249A ILE* 1.3 74.1 - - - +
251A ASN* 1.3 59.4 + - - +
253A ALA* 3.6 3.3 + - - +
254A TRP* 3.0 26.9 + - - +
259A THR* 5.8 0.2 - - - -
260A VAL* 4.2 22.4 + - + +
262A PHE* 3.7 27.3 - - + +
178B TYR* 3.3 38.3 + - + +
190B ALA 5.4 0.7 - - - +
191B PRO* 3.9 22.2 - - + +
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Residues in contact with ASN 251 (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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83A PHE* 3.6 26.0 - - + -
247A TYR* 2.8 45.6 + - - +
250A LYS* 1.3 74.6 - - - +
252A THR* 1.3 65.8 - - - +
253A ALA 3.3 0.2 - - - -
254A TRP* 3.7 7.0 - - + +
255A GLN* 3.0 30.9 + - + +
190B ALA* 3.1 36.2 + - - +
191B PRO* 3.4 23.7 - - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.4 9.6 - - - -
198A LEU* 4.2 3.4 - - + -
201A LYS* 4.0 8.1 - - + -
202A MET* 3.7 35.9 - - + +
205A ASN* 2.8 31.6 + - - +
248A ILE* 2.7 28.8 + - - +
249A ILE 3.9 0.2 - - - -
251A ASN* 1.3 76.8 - - - +
253A ALA* 1.3 63.5 + - - +
255A GLN* 3.4 1.5 + - - +
256A ASN* 2.7 42.7 + - - +
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Residues in contact with ALA 253 (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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138A ILE* 5.0 0.4 - - + -
198A LEU* 4.5 6.1 - - + -
202A MET* 4.1 10.4 - - + +
249A ILE 3.1 10.0 + - - +
250A LYS 3.6 4.0 - - - +
252A THR* 1.3 78.2 - - - +
254A TRP* 1.3 60.0 - - - +
256A ASN* 3.1 8.8 + - - +
257A GLY 3.4 0.2 + - - -
258A LYS* 2.9 44.7 + - + +
260A VAL* 3.4 34.8 - - + +
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Residues in contact with TRP 254 (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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250A LYS 3.0 17.2 + - - +
251A ASN* 3.7 12.1 - - - +
252A THR 3.2 0.6 - - - -
253A ALA* 1.3 76.2 - - - +
255A GLN* 1.3 68.3 + - + +
256A ASN 3.1 1.2 + - - -
257A GLY 3.2 2.9 + - - -
258A LYS 3.6 11.4 - - - -
259A THR* 4.4 4.3 - - - -
158B ILE* 6.1 3.6 - - + -
176B ARG* 2.7 84.7 + - + +
177B GLY 3.7 17.3 - - - -
178B TYR* 3.9 19.1 - + + -
191B PRO* 3.7 28.8 + - + +
194B GLN* 4.0 26.3 - - + +
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Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO 5.1 1.2 - - - +
83A PHE* 3.4 54.9 + - + +
205A ASN* 5.7 0.3 + - - -
251A ASN* 3.0 19.6 + - + +
252A THR* 3.9 4.9 - - - +
254A TRP* 1.3 81.3 - - + +
256A ASN* 1.3 65.3 + - - +
257A GLY 3.5 0.8 + - - -
197B ASP* 5.1 5.9 + - - -
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Residues in contact with ASN 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.8 26.1 - - + +
201A LYS* 3.1 34.5 + - - +
252A THR* 2.7 35.1 + - - +
253A ALA 3.1 3.9 + - - +
255A GLN* 1.3 86.9 - - - +
257A GLY* 1.3 58.4 + - - +
258A LYS* 3.3 14.3 + - - +
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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