Contacts of the helix formed by residues 256 - 270 (chain B) in PDB entry 4OG2
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 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B VAL* 4.5 11.9 - - + -
70B LEU* 4.1 15.0 - - + -
131B LEU* 3.9 43.5 - - + -
202B ASP* 4.1 12.3 - - - +
204B PHE* 4.1 21.5 - - + -
231B THR* 4.2 20.2 - - + -
255B GLY* 1.3 80.7 - - - +
257B ALA* 1.3 58.5 + - - +
259B ASP* 2.9 23.3 + - - +
260B GLY* 2.9 24.6 + - - -
281B GLY* 3.2 11.1 - - - +
282B LEU* 3.8 3.1 - - - +
501B LEU* 4.5 1.1 - - + -
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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
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66B ASN 5.5 1.7 + - - +
69B LEU* 4.2 20.6 - - + -
70B LEU* 4.2 7.7 - - + +
256B LEU* 1.3 75.6 - - - +
258B ALA* 1.3 62.4 + - - +
261B GLY* 2.8 28.6 + - - -
281B GLY 3.1 16.2 + - - +
282B LEU* 4.6 4.3 - - - +
284B THR* 3.9 23.3 - - + -
286B ASN 5.8 0.4 - - - -
287B VAL* 3.7 12.1 - - + +
290B VAL* 4.5 2.6 - - + +
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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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66B ASN* 3.8 31.9 + - + +
69B LEU* 3.9 21.5 - - + +
231B THR 6.0 0.9 - - - +
257B ALA* 1.3 78.8 - - - +
259B ASP* 1.3 63.5 + - - +
262B ASN* 2.8 37.6 + - - +
290B VAL* 3.8 8.4 - - + +
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Residues in contact with ASP 259 (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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229B PHE* 3.3 26.8 - - + -
231B THR* 3.5 41.9 + - - +
233B ASP 4.7 3.1 - - - +
236B PHE* 3.8 17.6 - - + -
255B GLY* 3.5 1.9 - - - -
256B LEU* 2.9 43.1 + - - +
257B ALA 3.5 0.3 + - - -
258B ALA* 1.3 73.6 + - - +
260B GLY* 1.3 67.0 + - - -
262B ASN* 3.2 3.1 + - - -
263B LEU* 2.9 24.1 + - - +
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Residues in contact with GLY 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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229B PHE* 5.3 1.1 - - - -
253B ILE* 4.3 12.5 - - - +
255B GLY* 5.2 0.7 - - - -
256B LEU 2.9 21.9 + - - -
259B ASP* 1.3 79.2 - - - +
261B GLY* 1.3 63.2 + - - +
263B LEU* 3.3 4.1 + - - +
264B VAL* 3.0 26.9 + - - +
282B LEU* 3.7 20.5 - - - +
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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 ALA 2.8 18.1 + - - -
260B GLY* 1.3 75.8 - - - +
262B ASN* 1.3 57.7 + - - +
264B VAL* 3.4 3.1 + - - +
265B ARG* 3.0 22.7 + - - +
282B LEU* 4.2 0.2 - - - +
287B VAL* 3.6 22.4 - - - +
290B VAL* 3.5 11.9 - - - -
291B CYS* 3.5 18.5 - - - +
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Residues in contact with ASN 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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233B ASP 6.0 0.2 - - - +
234B THR* 5.2 4.8 - - - +
236B PHE* 4.0 15.0 - - + -
258B ALA* 2.8 31.7 + - - +
259B ASP* 3.2 4.0 + - - +
261B GLY* 1.3 73.0 - - - +
263B LEU* 1.3 60.7 + - - +
265B ARG* 2.9 40.9 + - - +
266B GLN* 2.9 34.2 + - - +
290B VAL* 3.4 16.9 - - - +
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Residues in contact with LEU 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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197B PHE* 3.7 40.4 - - + -
229B PHE* 3.7 26.9 - - + -
236B PHE* 3.6 37.4 - - + -
240B ALA* 4.8 3.8 - - + -
253B ILE* 3.9 20.4 - - + -
259B ASP 2.9 16.9 + - - +
260B GLY* 3.6 4.9 - - - +
262B ASN* 1.3 74.5 - - - +
264B VAL* 1.3 65.8 + - - +
266B GLN* 3.2 1.2 + - - +
267B LEU* 2.9 38.3 + - + +
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Residues in contact with VAL 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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253B ILE* 3.6 21.3 - - + -
260B GLY 3.0 19.9 + - - +
261B GLY* 3.5 8.7 - - - +
263B LEU* 1.3 76.3 - - - +
265B ARG* 1.3 62.8 + - - +
267B LEU* 3.4 5.9 + - - +
268B ARG* 3.1 23.8 + - + +
276B ILE* 4.1 24.2 - - + -
282B LEU* 3.9 15.0 - - + -
291B CYS* 4.1 12.8 - - + -
294B LEU 3.4 23.6 - - - +
298B VAL* 4.1 14.6 - - + -
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Residues in contact with ARG 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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234B THR 4.8 1.2 + - - -
261B GLY 3.0 13.8 + - - +
262B ASN* 2.9 34.4 + - - +
264B VAL* 1.3 78.3 - - - +
266B GLN* 1.3 86.2 + - - +
268B ARG* 3.3 2.4 + - - +
269B GLU* 2.8 80.8 + - - +
290B VAL 3.8 16.3 + - - -
291B CYS* 4.1 14.1 - - + +
292B LYS* 6.0 1.3 - - - -
294B LEU* 3.8 17.6 - - + +
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Residues in contact with GLN 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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234B THR 2.9 26.3 + - - -
235B ASP* 3.9 1.7 - - - +
236B PHE* 2.9 42.7 + - + -
237B GLN* 3.0 23.3 + - - +
240B ALA* 4.8 1.8 - - + -
262B ASN* 2.9 16.4 + - - +
263B LEU* 4.0 4.3 - - - +
265B ARG* 1.3 99.0 - - - +
267B LEU* 1.3 65.8 + - - +
269B GLU* 3.4 18.9 + - - +
270B LEU* 3.0 32.3 + - + +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 4.1 13.2 - - + -
240B ALA* 3.7 33.4 - - + +
243B ALA* 5.0 1.6 - - + -
244B ILE* 3.8 13.0 - - + +
251B VAL* 3.9 29.4 - - + -
253B ILE* 4.0 13.0 - - + -
263B LEU* 2.9 37.5 + - + +
264B VAL* 3.6 5.2 - - - +
266B GLN* 1.3 76.1 - - - +
268B ARG* 1.3 61.7 + - - +
270B LEU* 3.2 9.9 + - - +
271B GLY 3.3 0.3 + - - -
272B TYR* 3.1 38.6 + - + +
276B ILE* 4.9 6.5 - - + -
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Residues in contact with ARG 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 VAL* 3.1 22.1 + - + +
265B ARG 3.7 3.8 - - - +
267B LEU* 1.3 76.2 - - - +
269B GLU* 1.3 58.7 + - - +
271B GLY* 2.9 21.0 + - - -
272B TYR* 2.9 32.9 + - - +
273B GLN* 3.4 10.5 + - - +
274B GLY 2.8 29.6 + - - -
275B ALA* 4.8 0.6 - - - +
276B ILE* 3.5 29.6 - - + +
294B LEU* 3.7 46.5 + - + +
296B ASP 4.2 15.6 + - - -
297B GLY* 5.4 4.4 - - - -
298B VAL* 5.5 1.0 - - - +
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Residues in contact with GLU 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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237B GLN* 4.9 4.0 + - - -
265B ARG* 2.8 62.9 + - - +
266B GLN* 3.7 17.3 - - - +
267B LEU 3.3 0.2 - - - -
268B ARG* 1.3 76.7 - - - +
270B LEU* 1.3 61.5 + - + +
271B GLY* 3.2 1.8 + - - -
294B LEU* 4.0 13.3 - - + +
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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
----------------------------------------------------------
237B GLN* 3.6 35.7 - - - +
240B ALA* 3.7 25.8 - - + -
241B THR* 3.9 20.6 - - - +
244B ILE* 3.6 25.8 - - + +
266B GLN 3.0 20.1 + - - +
268B ARG 3.1 0.6 - - - -
269B GLU* 1.3 77.5 - - + +
271B GLY* 1.3 58.1 + - - +
272B TYR 3.6 2.4 + - - -
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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