Contacts of the helix formed by residues 265 - 280 (chain B) in PDB entry 2RIO
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 ASP 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 4.6 0.9 - - - +
264B HIS* 1.3 74.3 - - - +
266B ARG* 1.3 58.6 + - - +
267B SER* 2.6 31.6 + - - -
268B LEU* 3.2 37.1 + - + +
269B ILE* 3.1 28.2 + - - +
302B LYS* 4.2 18.2 + - - -
400B TYR* 6.0 1.0 - - - -
401B ASP* 4.5 5.5 - - - +
404B THR* 5.0 5.6 + - - +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS 3.2 11.5 + - - +
265B ASP* 1.3 71.0 + - - +
267B SER* 1.3 61.2 + - - +
269B ILE* 3.3 45.3 - - + +
270B ALA* 3.2 20.9 + - - +
404B THR 5.7 0.9 - - - +
405B LYS 5.9 1.3 - - - +
408B PRO* 3.6 30.2 - - + +
409B ASN* 5.1 2.8 + - - -
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 2.6 33.6 + - - -
266B ARG* 1.3 69.0 - - - +
268B LEU* 1.3 60.4 + - - +
270B ALA* 2.9 6.2 + - - +
271B GLU* 2.9 44.8 + - - +
305B LYS* 5.2 0.3 + - - -
400B TYR* 5.1 5.3 - - - -
404B THR* 3.9 24.4 + - - +
408B PRO* 3.2 31.9 - - - +
411B LEU* 5.6 1.3 - - - -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 3.8 26.0 - - + -
263B LEU* 4.2 18.2 - - + -
264B HIS 6.2 0.2 - - - +
265B ASP* 3.2 37.8 + - + +
267B SER* 1.3 82.0 + - - +
269B ILE* 1.3 54.3 + - - +
271B GLU* 3.2 6.4 + - - +
272B ALA* 2.8 36.9 + - - +
298B LEU* 3.5 9.0 - - + +
302B LYS* 5.8 8.1 - - - -
305B LYS* 3.5 26.5 - - - +
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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
----------------------------------------------------------
257B LEU 5.7 1.8 - - - +
260B MET* 4.2 25.1 - - + +
263B LEU* 3.6 47.3 - - + +
264B HIS 4.8 2.5 - - - +
265B ASP 3.1 15.6 + - - +
266B ARG* 3.3 52.3 - - + +
268B LEU* 1.3 76.8 - - - +
270B ALA* 1.3 53.4 + - - +
272B ALA* 4.1 0.7 - - - +
273B THR* 2.6 44.2 + - - +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 3.2 21.4 + - - +
267B SER 2.9 9.2 + - - +
269B ILE* 1.3 78.0 - - - +
271B GLU* 1.3 57.0 + - - +
273B THR* 3.6 6.9 - - - -
274B ASP* 3.2 27.5 + - - +
337B PHE* 5.7 0.7 - - + -
408B PRO 3.9 9.4 - - - +
409B ASN* 3.7 23.3 - - - +
412B ILE* 4.1 13.7 - - + +
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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
----------------------------------------------------------
267B SER* 2.9 28.9 + - - +
268B LEU* 3.6 13.2 - - - +
270B ALA* 1.3 74.3 - - - +
272B ALA* 1.3 63.5 + - - +
274B ASP* 3.5 1.0 + - - +
275B LEU* 3.1 18.7 + - - +
296B HIS* 3.2 13.4 - - + -
297B PRO 4.5 1.6 - - - -
298B LEU* 3.7 24.5 - - + +
305B LYS* 2.5 38.2 + - - -
400B TYR* 4.4 0.5 + - - -
408B PRO 5.1 0.2 - - - +
411B LEU* 3.7 27.1 - - + +
412B ILE* 4.0 28.8 + - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.6 31.6 - - + -
260B MET* 3.9 13.0 - - - -
263B LEU* 4.5 1.1 - - + -
268B LEU 2.8 20.7 + - - +
271B GLU* 1.3 71.4 - - - +
273B THR* 1.3 65.3 + - - +
275B LEU* 4.6 1.3 - - - +
276B ILE* 2.9 31.3 + - + +
298B LEU* 3.8 23.2 - - + +
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.8 22.2 + - + +
260B MET* 4.0 15.7 - - - +
269B ILE* 2.6 29.9 + - - +
270B ALA* 3.6 7.4 - - - -
272B ALA* 1.3 74.0 - - - +
274B ASP* 1.3 62.0 + - - +
277B SER* 2.8 39.2 + - - +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 3.2 15.2 + - - +
271B GLU 3.7 3.6 - - - +
273B THR* 1.3 84.0 - - - +
275B LEU* 1.3 61.9 + - - +
277B SER* 3.4 13.5 + - - -
278B GLN* 3.3 28.5 + - - +
296B HIS* 3.0 24.4 + - - -
412B ILE* 3.3 24.1 - - + +
415B TYR* 5.0 2.8 - - - -
416B MET* 4.1 20.3 - - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 4.2 16.2 - - + -
271B GLU 3.1 11.6 + - - +
272B ALA 4.0 1.6 - - - +
274B ASP* 1.3 73.5 - - - +
276B ILE* 1.3 68.8 + - + +
278B GLN* 3.0 9.0 + - - +
279B MET* 3.0 42.0 + - + +
288B PRO* 4.4 10.1 - - + -
292B LYS 5.3 0.4 - - - +
293B VAL* 4.1 16.8 - - + -
296B HIS* 3.5 44.0 - - + +
298B LEU* 3.9 25.6 - - + -
299B PHE* 4.0 19.3 - - + -
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 5.3 0.7 - - + -
226B GLY 3.6 20.9 - - - +
229B PHE* 3.8 24.0 - - + -
230B TYR* 3.8 23.3 - - + +
233B LEU* 3.8 25.4 - - + -
239B PRO* 5.1 0.2 - - + -
257B LEU* 3.8 26.9 - - + -
260B MET* 3.9 11.9 - - + -
272B ALA* 2.9 23.5 + - + +
273B THR 4.1 0.7 - - - +
275B LEU* 1.3 79.4 - - + +
277B SER* 1.3 64.7 + - - +
278B GLN 3.0 1.0 + - - -
279B MET* 3.1 16.1 + - - -
280B ILE* 3.1 17.2 + - + +
298B LEU* 6.0 0.2 - - + -
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 3.8 24.0 - - - -
257B LEU* 3.7 17.8 - - - +
273B THR* 2.8 25.8 + - - +
274B ASP* 3.4 10.0 + - - -
276B ILE* 1.3 73.0 - - - +
278B GLN* 1.3 63.8 + - - +
280B ILE* 3.9 4.0 + - - +
281B ASP* 3.5 21.1 + - - +
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASP* 3.3 41.7 + - - +
275B LEU* 3.0 10.7 + - - +
277B SER* 1.3 79.7 + - - +
279B MET* 1.3 66.1 + - - +
280B ILE 3.2 0.2 - - - -
281B ASP* 3.2 18.6 + - - +
286B LYS 4.4 8.3 - - - +
287B ARG* 3.4 17.0 - - - -
288B PRO* 3.6 16.2 - - + +
292B LYS* 3.5 26.0 + - - +
296B HIS* 4.7 4.8 + - - -
415B TYR* 6.3 0.6 - - - -
419B LYS* 4.6 8.2 + - - +
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Residues in contact with MET 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 3.6 25.5 - - + +
223B PHE* 3.2 11.6 + - - -
225B MET* 3.9 16.4 - - + -
226B GLY* 3.6 24.2 - - - +
229B PHE* 3.6 34.8 - - + -
275B LEU* 3.0 42.0 + - + +
276B ILE* 3.1 7.1 + - - +
278B GLN* 1.3 75.1 - - - +
280B ILE* 1.3 59.2 + - - +
281B ASP 3.4 0.2 - - - -
287B ARG* 3.2 22.2 - - - -
288B PRO* 3.9 15.5 - - + -
293B VAL* 4.1 15.5 - - + -
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 3.5 47.4 - - + +
226B GLY* 3.8 7.9 - - - +
227B CYS* 3.8 21.8 - - - +
239B PRO* 3.6 23.8 - - + -
240B PHE* 3.7 10.1 - - + -
255B PHE* 3.5 43.2 - - + -
257B LEU* 4.2 7.0 - - + -
276B ILE* 3.1 14.1 + - + +
277B SER* 4.0 5.6 - - - +
279B MET* 1.3 78.7 - - - +
281B ASP* 1.3 64.4 + - - +
282B HIS* 3.4 2.6 + - - -
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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