Contacts of the helix formed by residues 253 - 273 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 5.0 3.6 - - - +
186B ARG* 4.5 1.3 - - - +
251B GLU 3.7 2.6 + - - +
252B ASP* 1.3 70.3 - - - +
254B PHE* 1.3 63.6 + - - +
256B SER* 3.6 5.6 - - - -
257B ALA* 3.0 22.3 + - - +
294B VAL* 3.7 21.7 - - + +
297B THR* 3.5 32.8 - - + +
305B ALA* 3.8 25.6 - - + +
306B ARG 3.7 18.2 - - - +
307B ASP* 3.0 21.6 + - - +
322B ALA 4.0 12.6 - - - +
325B ALA* 3.6 6.4 - - + +
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Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 5.2 4.5 - + - -
116B PRO* 6.3 0.7 - - + -
179B SER 5.5 3.6 - - - -
181B MET* 3.6 26.9 - - + -
186B ARG* 3.6 12.6 - - - +
252B ASP* 2.9 7.4 + - - +
253B VAL* 1.3 78.7 - - - +
255B PHE* 1.3 65.7 + - - +
257B ALA* 3.1 3.8 + - - +
258B ILE* 2.9 47.8 + - + +
321B ALA 4.3 4.7 - - - -
322B ALA* 3.8 21.8 - - + -
325B ALA* 3.9 16.8 - - - -
328B LEU* 3.6 26.0 - - + -
384B LEU* 3.9 22.9 - - + -
387B LEU* 4.2 7.9 - - + -
388B PHE* 3.8 24.2 - + - -
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 4.2 8.1 - - + -
115B GLN* 3.4 31.6 - - - -
116B PRO* 3.5 13.7 - - + -
117B PRO* 3.4 18.2 - - + -
159B LEU* 3.9 24.0 - - + -
171B ILE* 3.7 30.7 - - + -
173B LEU* 3.8 17.7 - - + -
178B GLU 3.4 26.0 - - - -
252B ASP* 2.8 32.3 + - + +
254B PHE* 1.3 72.8 - - - +
256B SER* 1.3 56.3 + - - +
258B ILE* 3.2 12.8 + - - +
259B PHE* 2.8 25.0 + - + +
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Residues in contact with SER 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLY 4.2 0.7 - - - -
170B ARG* 3.2 18.1 - - - +
171B ILE* 2.9 32.5 + - - -
252B ASP 2.7 23.7 + - - -
253B VAL* 3.6 7.4 - - - -
254B PHE 3.2 0.4 - - - -
255B PHE* 1.3 76.6 - - - +
257B ALA* 1.3 57.3 + - - +
259B PHE* 3.3 3.9 + - - +
260B SER* 2.9 27.4 + - - -
290B PHE* 3.8 11.2 - - - +
294B VAL* 3.8 14.8 - - - -
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL 3.0 18.6 + - - +
254B PHE 3.1 4.2 + - - +
256B SER* 1.3 72.6 - - - +
258B ILE* 1.3 66.8 + - - +
260B SER* 3.3 3.0 + - - -
261B VAL* 3.0 28.1 + - - +
294B VAL* 3.5 8.2 - - + +
325B ALA* 3.3 33.2 - - + +
328B LEU* 4.4 7.0 - - + -
329B CYS* 3.7 17.8 - - + +
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 4.5 4.9 - - + -
116B PRO* 4.1 18.2 - - + -
117B PRO* 3.9 23.6 - - + +
118B VAL* 3.7 25.1 - - + -
121B ILE* 5.3 5.1 - - + +
254B PHE* 2.9 44.1 + - + +
255B PHE* 3.5 7.2 - - - +
257B ALA* 1.3 75.4 - - - +
259B PHE* 1.3 58.9 + - - +
261B VAL* 3.3 7.6 + - - +
262B ALA* 2.8 28.2 + - + +
328B LEU* 4.2 10.8 - - + -
387B LEU* 4.0 22.9 - - + -
391B CYS* 6.5 0.2 - - - -
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.6 26.9 - - + +
156B HIS* 3.2 45.3 - + + -
159B LEU* 3.8 17.5 - - + -
160B ALA* 4.1 12.3 - - + -
171B ILE* 4.2 9.0 - - + -
255B PHE 2.8 17.1 + - - +
256B SER* 3.5 7.4 - - - +
258B ILE* 1.3 77.0 - - - +
260B SER* 1.3 57.6 + - - +
262B ALA* 3.2 0.6 + - - +
263B CYS* 2.8 54.0 + - - -
286B TRP* 4.6 1.8 - + + -
290B PHE* 3.6 47.8 - + - -
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Residues in contact with SER 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B SER 2.9 14.1 + - - -
257B ALA* 3.3 9.2 + - - -
259B PHE* 1.3 76.8 - - - +
261B VAL* 1.4 62.5 + - - +
263B CYS* 3.3 0.8 + - - -
264B GLN* 3.1 20.3 + - - +
287B ALA* 2.8 37.5 + - - +
290B PHE* 3.9 8.4 - - - +
291B ARG* 3.5 28.3 + - - +
329B CYS* 3.7 13.1 - - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 4.3 10.3 - - + -
257B ALA 3.0 17.3 + - - +
258B ILE* 3.7 9.6 - - - +
260B SER* 1.4 74.6 - - - +
262B ALA* 1.3 59.4 + - - +
264B GLN* 3.2 6.9 + - - +
265B VAL* 2.9 31.0 + - + +
328B LEU* 3.2 38.4 - - + +
329B CYS* 3.7 5.8 - - - -
390B TRP* 4.0 23.1 - - + -
391B CYS* 4.6 7.2 - - - -
394B ARG* 3.6 24.7 - - - +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.1 27.8 - - + +
118B VAL* 5.3 1.1 - - - -
120B ALA* 3.5 15.5 - - + +
121B ILE* 5.1 4.7 - - + -
156B HIS* 3.7 14.4 - - + -
258B ILE* 2.8 18.8 + - + +
259B PHE* 3.2 6.7 + - - +
261B VAL* 1.3 76.4 - - - +
263B CYS* 1.3 56.5 + - - +
265B VAL* 3.4 3.8 + - - -
266B LEU* 2.8 31.7 + - - +
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Residues in contact with CYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B HIS* 3.5 23.8 - - - -
259B PHE* 2.8 43.8 + - - +
260B SER 3.6 4.7 - - - +
262B ALA* 1.3 77.3 - - - +
264B GLN* 1.3 57.1 + - - +
266B LEU 3.8 0.3 - - - -
267B ALA* 2.8 30.1 + - - +
283B LEU* 3.4 25.2 - - + +
286B TRP* 3.7 23.8 - - - -
287B ALA 3.7 7.2 - - - +
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Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A HIS* 5.8 0.8 - - - -
505A GOL 3.5 18.8 + - - -
260B SER 3.1 13.8 + - - +
261B VAL* 3.5 4.7 - - - +
263B CYS* 1.3 72.9 - - - +
265B VAL* 1.3 65.7 + - - +
267B ALA* 3.3 5.3 + - - +
268B GLU* 3.1 41.8 + - - +
284B TYR* 3.2 29.8 - - - -
287B ALA* 3.5 13.5 - - + +
291B ARG* 2.9 28.8 + - - +
394B ARG* 3.3 25.4 - - - +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA 3.5 29.4 - - - +
121B ILE* 4.4 3.1 - - + +
124B GLN* 3.3 33.1 - - + +
261B VAL* 2.9 25.0 + - + +
262B ALA* 3.7 6.3 - - - +
264B GLN* 1.3 73.9 - - - +
266B LEU* 1.3 64.3 + - - +
268B GLU* 3.3 12.1 + - - +
269B ILE* 3.1 25.6 + - + +
390B TRP* 3.8 13.5 - - + -
394B ARG* 3.8 22.0 - - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 4.1 15.9 - - + -
123B VAL* 5.3 2.7 - - + -
145B LEU* 5.7 0.2 - - + -
149B TRP* 3.4 37.1 - - + -
152B LEU* 4.1 35.0 - - + +
153B MET* 4.5 4.9 - - - -
156B HIS* 3.8 25.4 - - + +
262B ALA 2.8 18.0 + - - +
263B CYS 3.9 1.3 - - - +
265B VAL* 1.3 79.3 - - - +
267B ALA* 1.3 58.3 + - - +
269B ILE* 3.4 15.6 + - + +
270B GLY 2.8 24.8 + - - -
283B LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B CYS 2.8 19.1 + - - +
264B GLN 3.6 1.3 - - - +
265B VAL 3.3 0.2 - - - -
266B LEU* 1.3 77.2 - - - +
268B GLU* 1.3 57.6 + - - +
270B GLY* 3.0 3.6 + - - -
271B GLU* 2.9 31.4 + - - +
280B VAL* 4.0 6.4 - - + +
283B LEU* 3.7 22.8 - - + +
284B TYR* 3.5 40.6 - - + -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A HIS* 5.5 3.6 - - + -
338A ARG* 4.4 4.4 + - - +
124B GLN* 4.6 9.2 + - - +
264B GLN* 3.1 37.8 + - - +
265B VAL* 3.7 10.4 - - - +
267B ALA* 1.3 71.7 - - - +
269B ILE* 1.3 68.0 + - + +
271B GLU* 3.3 7.0 + - - +
272B ASP* 2.9 33.6 + - - +
284B TYR* 3.7 18.2 - - + +
394B ARG* 4.2 10.1 + - - -
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA 4.2 2.2 - - - +
123B VAL* 3.8 23.8 - - + -
124B GLN* 3.9 21.5 - - + +
127B LEU* 3.9 26.2 - - + -
145B LEU* 3.9 26.7 - - + -
149B TRP* 4.3 8.3 - - + -
265B VAL* 3.1 24.7 + - + +
266B LEU* 3.6 14.6 - - + +
268B GLU* 1.3 75.5 - - + +
270B GLY* 1.3 63.4 + - - +
272B ASP* 3.2 6.1 + - - -
273B TYR* 2.9 27.2 + - + +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TRP* 3.5 23.3 - - - -
266B LEU 2.8 11.5 + - - -
267B ALA 3.0 4.7 + - - -
269B ILE* 1.3 77.4 - - - +
271B GLU* 1.3 61.0 + - - +
274B LYS* 3.1 4.7 + - - -
275B ARG* 2.9 34.0 + - - +
280B VAL* 3.8 13.4 - - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A HIS* 2.9 31.1 + - - -
335A ASP* 4.2 5.9 - - - +
338A ARG* 3.7 31.7 + - - +
267B ALA 2.9 14.7 + - - +
268B GLU* 3.7 7.7 - - - +
270B GLY* 1.3 76.4 - - - +
272B ASP* 1.3 63.9 + - - +
273B TYR 3.4 0.5 + - - -
274B LYS* 3.4 12.2 + - - +
280B VAL* 3.6 17.1 - - + +
284B TYR* 2.4 35.9 + - - -
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 2.8 32.1 + - - +
400A ARG* 5.5 1.0 + - - -
512A GLY* 3.6 23.5 - - - +
131B ARG* 5.0 10.4 + - - +
268B GLU* 2.9 21.6 + - - +
269B ILE* 3.2 5.2 + - - +
271B GLU* 1.3 77.5 - - - +
273B TYR* 1.3 77.1 + - + +
274B LYS* 3.4 6.6 + - - +
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.8 25.1 - - + +
131B ARG* 3.0 45.7 + - - +
138B ARG* 6.1 0.2 - - - -
142B GLU* 3.7 37.1 + - + +
145B LEU* 3.5 28.3 - - + -
269B ILE* 2.9 24.2 + - + +
270B GLY 3.7 0.2 - - - -
272B ASP* 1.3 89.5 - - + +
274B LYS* 1.3 72.0 + - - +
275B ARG* 3.2 19.3 + - + -
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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