Contacts of the helix formed by residues 253 - 273 (chain A) in PDB entry 5OIV
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 VAL 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ARG* 4.8 5.8 - - - +
186A ARG* 4.6 1.3 - - - +
251A GLU 3.7 1.8 + - - +
252A ASP* 1.3 73.4 - - - +
254A PHE* 1.3 60.4 + - - +
256A SER* 3.4 5.2 + - - -
257A ALA* 2.9 27.4 + - - +
294A VAL* 3.7 26.2 - - + +
297A THR* 3.6 31.9 - - + +
305A ALA* 3.7 22.7 - - + +
306A ARG 3.7 18.2 - - - +
307A ASP* 2.9 21.7 + - - +
322A ALA* 4.1 11.7 - - + +
325A ALA* 3.6 1.5 - - + +
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 5.0 4.9 - + - -
116A PRO* 6.2 0.4 - - + -
179A SER 5.5 4.5 - - - -
181A MET* 3.6 23.1 - - + -
186A ARG* 3.7 12.8 - - - +
252A ASP* 2.9 7.2 + - - +
253A VAL* 1.3 78.3 - - - +
255A PHE* 1.3 67.0 + - - +
257A ALA* 3.2 2.9 + - - +
258A ILE* 2.9 48.6 + - + +
321A ALA 4.2 4.5 - - - -
322A ALA* 3.7 29.2 - - + -
325A ALA* 3.9 12.3 - - + -
328A LEU* 3.7 25.4 - - + -
384A LEU* 3.9 23.6 - - + -
387A LEU* 4.1 6.5 - - + -
388A PHE* 3.7 24.7 - + - -
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 4.2 9.0 - - + -
115A GLN* 3.4 30.1 - - - -
116A PRO* 3.8 11.4 - - + -
117A PRO* 3.3 19.9 - - + +
159A LEU* 3.8 23.6 - - + -
171A ILE* 3.8 28.0 - - + -
173A LEU* 3.7 20.0 - - + -
178A GLU 3.4 26.7 - - - -
179A SER 5.7 0.2 - - - +
252A ASP* 2.8 32.2 + - + +
254A PHE* 1.3 73.3 - - - +
256A SER* 1.3 56.5 + - - +
258A ILE* 3.3 11.5 + - - +
259A PHE* 2.9 25.7 + - + +
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Residues in contact with SER 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY 4.3 3.8 - - - -
170A ARG* 3.3 18.2 - - - +
171A ILE* 2.9 32.1 + - - -
252A ASP 2.6 23.2 + - - -
253A VAL* 3.5 8.3 - - - -
254A PHE 3.2 0.2 - - - -
255A PHE* 1.3 76.8 - - - +
257A ALA* 1.3 58.1 + - - +
259A PHE* 3.3 4.6 + - - +
260A SER* 3.0 26.0 + - - -
290A PHE* 3.7 8.3 - - - +
294A VAL* 3.8 14.4 - - - -
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL 2.9 16.9 + - - +
254A PHE 3.2 4.5 + - - +
256A SER* 1.3 72.5 - - - +
258A ILE* 1.3 66.6 + - - +
260A SER* 3.2 3.7 + - - -
261A VAL* 3.0 28.2 + - - +
294A VAL* 3.5 8.5 - - + +
325A ALA* 3.4 34.3 - - + +
328A LEU* 4.4 7.0 - - + -
329A CYS* 3.8 16.0 - - + +
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Residues in contact with ILE 258 (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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42A TRP* 4.4 7.4 - - + -
116A PRO* 4.0 18.4 - - + -
117A PRO* 3.9 22.4 - - + +
118A VAL* 3.8 23.6 - - + -
121A ILE* 5.2 6.5 - - + +
254A PHE* 2.9 43.2 + - + +
255A PHE* 3.6 7.0 - - - +
257A ALA* 1.3 75.5 - - - +
259A PHE* 1.3 58.2 + - - +
261A VAL* 3.3 8.2 + - - +
262A ALA* 2.8 27.8 + - + +
328A LEU* 4.1 17.3 - - + -
387A LEU* 4.0 15.7 - - + -
391A CYS* 6.5 0.2 - - - -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.6 25.8 - - + -
156A HIS* 3.3 45.1 - + + -
159A LEU* 3.8 19.5 - - + -
160A ALA* 4.2 8.7 - - + -
171A ILE* 4.2 9.0 - - + -
255A PHE 2.9 17.6 + - - +
256A SER* 3.6 6.7 - - - +
258A ILE* 1.3 75.1 - - - +
260A SER* 1.3 58.1 + - - +
262A ALA* 4.3 0.7 - - - -
263A CYS* 2.9 54.4 + - - -
286A TRP* 4.5 2.2 - + + -
290A PHE* 3.5 50.3 - + - -
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Residues in contact with SER 260 (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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256A SER 3.0 12.7 + - - -
257A ALA* 3.2 8.9 + - - -
259A PHE* 1.3 77.4 - - - +
261A VAL* 1.3 62.4 + - - +
263A CYS* 3.3 3.0 + - - +
264A GLN* 3.1 19.5 + - - +
287A ALA* 2.8 36.4 + - - +
290A PHE* 4.0 5.8 - - - +
291A ARG* 3.5 28.9 + - - +
329A CYS* 3.7 13.4 + - - +
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Residues in contact with VAL 261 (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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121A ILE* 4.3 10.8 - - + -
257A ALA 3.0 14.3 + - - +
258A ILE* 3.6 8.1 - - - +
260A SER* 1.3 76.0 - - - +
262A ALA* 1.3 58.6 + - - +
264A GLN* 3.1 4.0 + - - +
265A VAL* 2.9 41.7 + - + +
328A LEU* 3.3 37.7 - - + +
329A CYS* 3.8 6.5 - - - -
390A TRP* 4.1 17.3 - - + -
391A CYS* 4.6 7.6 - - - -
394A ARG* 4.0 27.8 - - - +
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Residues in contact with ALA 262 (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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117A PRO* 3.1 28.9 - - + +
120A ALA* 3.5 15.1 - - + +
121A ILE* 5.1 6.5 - - + +
156A HIS* 3.7 15.3 - - + -
258A ILE* 2.8 18.7 + - + +
259A PHE* 3.8 6.1 - - - +
261A VAL* 1.3 73.9 - - - +
263A CYS* 1.3 58.2 + - - +
265A VAL* 4.4 3.1 - - - -
266A LEU* 2.8 32.6 + - - +
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Residues in contact with CYS 263 (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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156A HIS* 3.4 24.0 - - - -
259A PHE* 2.9 46.6 + - - +
260A SER 3.6 4.3 - - - +
261A VAL 3.2 0.2 - - - -
262A ALA* 1.3 73.3 - - - +
264A GLN* 1.3 60.0 + - - +
267A ALA* 2.9 30.5 + - - +
283A LEU* 3.4 25.2 - - - +
286A TRP* 3.7 23.8 - - - -
287A ALA 3.7 7.0 - - - +
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Residues in contact with GLN 264 (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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260A SER 3.1 11.9 + - - +
261A VAL* 3.1 5.6 + - - +
263A CYS* 1.3 76.0 - - - +
265A VAL* 1.3 63.1 + - - +
267A ALA* 3.4 5.9 + - - +
268A GLU* 3.1 42.0 + - - +
284A TYR* 3.9 14.7 - - + -
287A ALA* 3.8 9.8 - - + +
291A ARG* 3.5 27.0 + - - +
394A ARG* 3.1 29.8 + - - +
506A GOL 3.6 22.2 + - - -
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Residues in contact with VAL 265 (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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120A ALA 3.5 27.4 - - - +
121A ILE* 4.4 3.1 - - + +
124A GLN* 3.1 33.7 - - + +
261A VAL* 2.9 25.1 + - + +
262A ALA* 3.7 6.7 - - - +
264A GLN* 1.3 75.8 - - - +
266A LEU* 1.3 63.2 + - - +
268A GLU* 3.2 12.0 + - - +
269A ILE* 3.0 25.6 + - + +
390A TRP* 4.0 12.3 - - + -
394A ARG* 3.9 22.4 - - - +
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Residues in contact with LEU 266 (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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120A ALA* 4.0 14.8 - - + -
123A VAL* 5.3 1.8 - - + -
145A LEU* 5.9 0.2 - - + -
149A TRP* 3.3 39.4 - - + -
152A LEU* 4.1 38.4 - - + +
153A MET* 4.6 2.9 - - - -
156A HIS* 3.9 26.5 - - + +
262A ALA 2.8 21.4 + - - +
263A CYS 4.0 2.7 - - - +
265A VAL* 1.3 74.5 - - - +
267A ALA* 1.3 57.8 + - - +
269A ILE* 3.4 16.6 + - + +
270A GLY 2.9 22.9 + - - -
283A LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 267 (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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263A CYS 2.9 18.9 + - - +
264A GLN 3.6 2.5 - - - +
266A LEU* 1.3 76.6 - - - +
268A GLU* 1.3 56.6 + - - +
270A GLY* 3.1 2.4 + - - -
271A GLU* 2.9 31.4 + - - +
280A VAL* 3.9 8.1 - - + +
283A LEU* 3.6 22.4 - - + +
284A TYR* 3.6 38.4 - - + -
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Residues in contact with GLU 268 (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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124A GLN* 4.6 9.4 + - - +
264A GLN* 3.1 36.5 + - + +
265A VAL* 3.2 12.8 + - - +
267A ALA* 1.3 71.9 - - - +
269A ILE* 1.3 65.0 + - + +
271A GLU* 3.3 11.7 + - - +
272A ASP* 3.0 32.5 + - - +
284A TYR* 3.5 14.7 - - + +
394A ARG* 4.4 8.8 + - - -
334B HIS* 5.6 2.0 - - + -
338B ARG* 4.3 4.4 + - - +
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Residues in contact with ILE 269 (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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120A ALA 4.0 8.3 - - - +
123A VAL* 3.8 24.0 - - + -
124A GLN* 3.9 20.9 - - + +
127A LEU* 3.7 24.5 - - + -
145A LEU* 4.0 24.9 - - + -
149A TRP* 4.3 9.0 - - + -
265A VAL* 3.0 25.5 + - + +
266A LEU* 3.6 15.7 - - + +
268A GLU* 1.3 76.0 - - + +
270A GLY* 1.3 57.9 + - - +
272A ASP* 3.2 6.9 + - - -
273A TYR* 2.9 31.6 + - + +
275A ARG* 5.8 0.2 - - + -
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Residues in contact with GLY 270 (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 TRP* 3.5 24.0 - - - -
266A LEU 2.9 11.9 + - - -
267A ALA 3.1 3.1 + - - -
269A ILE* 1.3 76.7 - - - +
271A GLU* 1.3 61.6 + - - +
274A LYS* 3.1 3.3 + - - -
275A ARG* 2.8 39.1 + - - +
280A VAL* 3.8 9.4 - - - -
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Residues in contact with GLU 271 (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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267A ALA 2.9 12.9 + - - +
268A GLU* 3.6 9.5 - - - +
269A ILE 3.2 0.2 - - - -
270A GLY* 1.3 77.3 - - - +
272A ASP* 1.3 62.4 + - - +
274A LYS* 3.3 15.6 + - - +
280A VAL* 3.7 16.7 - - + +
284A TYR* 2.5 34.2 + - - -
506A GOL 5.4 0.2 - - - -
334B HIS* 2.8 29.8 + - - -
335B ASP* 4.7 2.8 - - - +
338B ARG* 3.5 36.2 + - - +
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Residues in contact with ASP 272 (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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131A ARG* 4.8 11.9 + - - +
268A GLU* 3.0 22.3 + - - +
269A ILE* 3.7 6.1 - - - +
271A GLU* 1.3 77.6 - - - +
273A TYR* 1.3 78.6 + - + +
274A LYS* 3.4 7.9 + - - +
338B ARG* 3.0 31.1 + - - +
400B ARG* 5.5 6.1 + - - -
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Residues in contact with TYR 273 (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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127A LEU* 3.9 25.1 - - + +
131A ARG* 2.9 45.9 + - - +
142A GLU* 3.8 37.1 + - + +
145A LEU* 3.5 28.0 - - + -
269A ILE* 2.9 25.4 + - + +
272A ASP* 1.3 90.9 - - + +
274A LYS* 1.3 64.4 + - - +
275A ARG* 2.8 47.1 + - + +
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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