Contacts of the helix formed by residues 255 - 273 (chain B) in PDB entry 1OE5
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 ASN 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B MET* 3.8 19.8 - - - +
250B HIS* 3.7 13.3 + - + +
252B SER* 3.1 14.8 + - - +
253B PRO 3.1 3.6 - - - -
254B ARG* 1.3 78.0 - - - +
256B PRO* 1.4 65.8 - - - +
257B GLN* 3.6 22.3 + - - +
258B ALA* 2.8 43.4 + - - +
259B ASN* 3.2 9.7 + - - -
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Residues in contact with PRO 256 (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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254B ARG* 3.5 29.6 - - - +
255B ASN* 1.4 88.3 - - - +
257B GLN* 1.3 62.3 + - + +
259B ASN* 3.2 15.7 + - + +
260B LYS* 3.2 38.4 + - - +
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B MET* 3.5 29.8 - - + +
255B ASN* 3.2 17.2 + - - +
256B PRO* 1.3 80.0 - - + +
258B ALA* 1.3 62.0 + - - +
260B LYS* 3.5 21.3 + - + +
261B GLY 3.5 8.8 + - - -
265B ILE* 3.7 19.2 - - + +
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Residues in contact with ALA 258 (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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151B ARG* 3.8 14.8 + - - +
249B MET* 4.4 2.7 - - - -
250B HIS 3.8 11.4 - - - +
251B PRO 4.0 2.0 - - - +
252B SER 3.5 14.8 - - - +
255B ASN* 2.8 31.7 + - - +
257B GLN* 1.3 78.5 - - - +
259B ASN* 1.3 58.3 + - - +
261B GLY 3.5 0.3 + - - -
262B TRP* 3.1 41.7 + - + +
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 2.7 40.4 + - - +
253B PRO* 2.8 35.6 + - - +
255B ASN 3.2 6.4 + - - -
256B PRO* 3.2 14.3 + - + +
258B ALA* 1.3 77.4 - - - +
260B LYS* 1.3 60.5 + - + +
292E G 3.2 33.5 + - - +
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PRO* 3.2 31.5 + - - +
257B GLN* 3.5 12.9 + - - +
258B ALA 3.2 0.6 - - - -
259B ASN* 1.3 81.7 - - + +
261B GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLN 3.5 7.5 + - - -
258B ALA 3.5 1.2 + - - -
260B LYS* 1.3 81.4 - - - +
262B TRP* 1.3 61.5 + - - +
263B GLU* 3.3 2.7 - - - -
264B GLY* 3.3 6.2 + - - -
265B ILE* 2.9 32.7 + - - +
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Residues in contact with TRP 262 (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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151B ARG* 3.4 44.9 - - + -
152B PHE* 3.9 25.8 - + - -
155B LEU* 3.9 21.5 - - + -
248B ILE* 4.3 7.6 - - + -
249B MET* 2.7 37.4 + - - -
250B HIS 3.6 6.5 - - - -
251B PRO* 3.4 36.2 - - + -
258B ALA* 3.1 30.7 + - + +
261B GLY* 1.3 72.6 - - - +
263B GLU* 1.3 83.4 + - + +
265B ILE* 3.1 6.8 + - - +
266B VAL* 2.8 53.1 + - + +
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Residues in contact with GLU 263 (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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151B ARG 4.6 2.6 - - - +
154B SER* 3.9 8.0 + - - +
155B LEU* 3.2 44.7 + - + +
158B SER* 4.2 9.4 + - - -
261B GLY 3.3 0.8 - - - -
262B TRP* 1.3 92.9 - - + +
264B GLY* 1.4 52.3 + - - +
266B VAL* 3.8 1.8 - - - +
267B ARG* 2.8 61.5 + - - +
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Residues in contact with GLY 264 (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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261B GLY* 3.3 7.5 + - - -
262B TRP 3.2 0.2 - - - -
263B GLU* 1.4 79.1 - - - +
265B ILE* 1.3 64.0 + - - +
267B ARG* 3.6 10.4 + - - +
268B GLY* 3.4 14.2 + - - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B MET* 3.9 35.4 - - + -
257B GLN* 3.7 29.2 - - + +
261B GLY 2.9 19.9 + - - +
262B TRP* 3.6 5.2 - - - +
264B GLY* 1.3 76.0 - - - +
266B VAL* 1.3 58.2 + - - +
268B GLY* 3.2 4.3 + - - -
269B GLN* 2.9 51.8 + - + +
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.3 9.9 - - + -
248B ILE* 3.6 32.3 - - + -
249B MET* 3.9 9.9 - - + +
262B TRP* 2.8 62.6 + - + +
263B GLU 4.1 2.0 - - - +
265B ILE* 1.3 70.6 - - + +
267B ARG* 1.3 62.1 + - - +
269B GLN* 3.1 16.7 + - - +
270B LEU* 2.8 42.3 + - + +
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Residues in contact with ARG 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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155B LEU* 4.1 13.6 + - + +
158B SER* 3.7 22.8 + - - -
159B LEU* 3.7 34.4 - - + +
263B GLU* 2.8 49.7 + - - +
264B GLY* 3.8 9.2 - - - +
266B VAL* 1.3 76.2 - - - +
268B GLY* 1.3 57.0 + - - +
270B LEU* 3.4 9.0 + - - +
271B LEU* 2.9 27.5 + - - +
276B LEU* 4.1 11.9 - - + +
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Residues in contact with GLY 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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264B GLY 3.4 6.2 + - - -
265B ILE 3.2 7.8 + - - -
267B ARG* 1.3 77.7 - - - +
269B GLN* 1.3 63.2 + - - +
271B LEU* 3.4 12.1 - - - +
272B GLU* 3.1 26.3 + - - +
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Residues in contact with GLN 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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226B ARG* 5.9 3.4 - - - +
247B GLY 4.8 5.1 - - - +
248B ILE* 3.1 21.1 - - + +
249B MET* 2.9 37.7 + - - +
265B ILE* 2.9 37.2 + - + +
266B VAL* 3.1 11.4 + - - +
268B GLY* 1.3 73.4 - - - +
270B LEU* 1.3 60.4 + - - +
272B GLU* 3.4 9.2 + - - +
273B LEU* 3.2 29.9 + - - +
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Residues in contact with LEU 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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92B PHE* 4.0 25.8 - - + -
155B LEU* 3.9 27.4 - - + -
156B PHE* 4.0 8.3 - - + -
159B LEU* 4.0 17.5 - - + -
222B ILE* 4.2 4.0 - - + -
248B ILE* 4.0 13.5 - - + -
266B VAL* 2.8 30.1 + - + +
267B ARG* 3.8 5.2 - - - +
269B GLN* 1.3 70.8 - - - +
271B LEU* 1.3 68.3 + - - +
273B LEU* 3.3 9.6 + - + +
275B VAL* 3.3 45.5 + - + +
276B LEU* 3.9 11.2 + - + -
279B LEU* 4.6 2.7 - - + -
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Residues in contact with LEU 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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267B ARG 2.9 14.2 + - - +
268B GLY* 3.4 13.7 - - - +
270B LEU* 1.3 72.2 - - - +
272B GLU* 1.3 56.0 + - - +
274B GLY* 2.8 29.1 + - - -
276B LEU* 3.8 26.9 - - + +
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Residues in contact with GLU 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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268B GLY 3.1 11.9 + - - +
269B GLN* 3.4 13.0 + - - +
271B LEU* 1.3 78.9 - - + +
273B LEU* 1.3 61.8 + - + +
274B GLY 3.3 0.4 + - - -
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Residues in contact with LEU 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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220B LEU* 5.0 8.0 - - + +
222B ILE* 4.1 24.7 - - + -
246B LYS* 3.5 44.4 - - + -
247B GLY 4.1 19.5 - - - +
248B ILE* 4.5 6.1 - - + -
269B GLN* 3.2 20.3 + - + +
270B LEU* 3.7 8.3 - - - +
271B LEU 2.8 4.0 + - - -
272B GLU* 1.3 77.3 - - + +
274B GLY* 1.3 61.1 + - - +
275B VAL* 3.5 13.7 + - + +
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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