Contacts of the helix formed by residues 254 - 270 (chain B) in PDB entry 4OGB
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 LYS 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B THR* 1.3 70.8 - - - +
255B LYS* 1.3 65.3 + - + +
256B GLN 3.0 1.6 - - - -
257B ARG* 2.5 51.2 + - + +
258B GLN* 2.6 38.0 - - - +
244C GLU* 2.8 36.1 + - - +
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Residues in contact with LYS 255 (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 THR* 3.6 3.1 + - - +
254B LYS* 1.3 85.1 - - + +
256B GLN* 1.3 61.1 + - - +
257B ARG 3.3 0.5 + - - -
258B GLN* 3.0 14.0 - - + +
259B SER* 3.5 21.5 + - - -
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Residues in contact with GLN 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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135B PHE* 3.7 27.8 - - - -
188B LEU* 3.6 27.3 - - + +
252B LEU* 3.8 13.7 - - + +
253B THR* 2.8 54.9 + - - +
254B LYS 3.0 0.6 + - - -
255B LYS* 1.3 79.2 - - - +
257B ARG* 1.3 55.8 + - - +
260B LEU* 2.8 33.7 + - - +
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Residues in contact with ARG 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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247B ASP* 5.6 0.6 + - - -
249B PHE* 3.1 20.1 + - + +
250B GLN* 2.7 32.7 + - - +
252B LEU* 3.1 27.5 + - + -
253B THR 3.6 9.4 - - - +
254B LYS* 2.5 46.0 + - + +
256B GLN* 1.3 65.0 - - - +
258B GLN* 1.3 57.8 + - - +
259B SER 3.1 1.3 - - - -
260B LEU* 4.6 6.7 - - + +
261B ARG* 2.7 39.4 + - + +
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Residues in contact with GLN 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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254B LYS* 2.6 61.9 - - - +
255B LYS* 3.0 16.3 - - - +
257B ARG* 1.3 75.0 - - - +
259B SER* 1.3 58.1 + - - +
261B ARG* 4.1 6.0 - - - +
262B LYS* 3.1 28.1 + - - +
244C GLU* 5.0 4.2 + - - -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.4 10.8 - - - -
255B LYS 3.5 14.0 + - - -
256B GLN 4.3 1.6 - - - -
257B ARG 3.1 0.6 - - - -
258B GLN* 1.3 77.6 - - - +
260B LEU* 1.3 59.1 + - - +
261B ARG 3.1 1.3 - - - -
262B LYS* 3.9 3.3 - - - +
263B MET* 2.9 48.2 + - - +
303B TYR* 5.0 7.3 - - - -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.3 11.4 - - + +
191B LEU* 3.7 17.5 - - + -
192B ALA* 3.6 36.3 - - + +
195B PHE* 5.2 1.1 - - + -
238B PHE* 6.5 0.7 - - + -
249B PHE* 3.7 45.8 - - + -
252B LEU* 4.2 8.3 - - + -
256B GLN 2.8 25.7 + - - +
257B ARG* 4.1 5.4 - - + +
259B SER* 1.3 72.9 - - - +
261B ARG* 1.3 59.9 + - + +
263B MET* 4.0 9.7 - - - +
264B VAL* 3.1 42.1 + - + +
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Residues in contact with ARG 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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216A ASN* 5.7 0.7 - - - -
220A ALA 3.6 9.3 + - - -
221A LEU* 3.3 39.8 + - - +
224A ASN* 4.0 4.2 - - - +
225A ASP* 2.5 44.0 + - - +
238B PHE* 3.7 33.5 - - + -
257B ARG* 2.7 24.1 + - + +
258B GLN* 4.1 6.1 - - - +
260B LEU* 1.3 74.2 - - + +
262B LYS* 1.3 65.3 + - - +
264B VAL* 3.4 2.3 + - - +
265B ILE* 3.1 45.1 + - + +
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Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 5.8 3.4 - - - +
258B GLN 3.1 21.5 + - - +
259B SER* 4.0 4.7 - - - +
261B ARG* 1.3 78.6 - - - +
263B MET* 1.3 57.2 + - - +
265B ILE* 3.5 8.9 + - + +
266B ASP* 3.0 45.3 + - - +
303B TYR* 3.6 28.5 - - + +
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.1 15.3 - - + -
189B GLU* 3.5 40.8 - - + +
192B ALA* 3.9 25.1 - - + -
259B SER* 2.9 39.2 + - - +
260B LEU* 4.0 4.3 - - - +
262B LYS* 1.3 77.7 - - + +
264B VAL* 1.3 57.2 + - - +
266B ASP* 3.3 1.6 + - - +
267B ILE* 2.9 37.3 + - + +
303B TYR* 3.6 32.5 - - + +
307B ILE* 4.0 9.0 - - + -
310B LEU* 4.4 9.4 - - - -
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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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192B ALA* 3.8 24.2 - - - +
195B PHE* 3.4 32.1 - - + -
196B ALA* 4.3 7.4 - - - -
199B ILE* 3.9 14.4 - - + -
234B LEU* 3.9 2.9 - - + -
238B PHE* 3.6 28.3 - - + -
260B LEU* 3.1 24.4 + - + +
261B ARG 3.4 3.6 + - - +
263B MET* 1.3 75.8 - - - +
265B ILE* 1.3 58.0 + - - +
267B ILE* 3.4 0.3 + - - +
268B VAL* 3.0 39.1 + - + +
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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
----------------------------------------------------------
224A ASN* 3.8 41.7 - - + +
225A ASP* 4.6 4.0 - - + +
226A SER* 5.0 1.6 - - - +
234B LEU* 3.9 8.9 - - + +
238B PHE* 3.9 15.7 - - + -
261B ARG* 3.1 58.8 + - + +
262B LYS* 3.7 7.4 - - + +
264B VAL* 1.3 77.2 - - - +
266B ASP* 1.3 69.4 + - - +
269B LEU* 3.1 40.2 + - + +
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Residues in contact with ASP 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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262B LYS* 3.0 28.9 + - - +
263B MET 3.7 1.1 - - - +
265B ILE* 1.3 83.0 - - - +
267B ILE* 1.3 65.3 + - - +
269B LEU* 4.3 3.7 - - - +
270B ALA 3.5 7.8 + - - -
303B TYR* 2.6 34.8 + - - -
307B ILE* 3.5 21.7 - - + +
311B GLN* 2.8 28.8 + - - +
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Residues in contact with ILE 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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192B ALA* 4.1 9.0 - - + +
193B ALA* 3.7 31.4 - - + +
196B ALA* 3.6 15.7 - - + -
263B MET 2.9 23.9 + - - +
264B VAL 3.8 2.9 - - - +
266B ASP* 1.3 73.1 - - - +
268B VAL* 1.3 59.1 + - - +
270B ALA* 2.7 31.5 + - - +
271B THR* 3.5 5.2 + - - +
307B ILE* 4.0 13.5 - - + -
310B LEU* 4.0 31.0 - - + +
311B GLN* 4.0 8.4 - - - +
314B VAL* 3.6 33.4 - - + -
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Residues in contact with VAL 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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196B ALA* 3.8 31.9 - - + +
199B ILE* 4.3 5.4 - - + -
200B HIS* 4.0 25.6 - - + +
230B GLU* 3.9 17.3 - - - +
233B HIS* 4.4 3.6 - - + -
234B LEU* 3.6 32.3 - - + -
264B VAL* 3.0 19.7 + - + +
267B ILE* 1.3 75.0 - - - +
269B LEU* 1.3 58.3 + - - +
271B THR* 2.4 37.8 + - - +
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Residues in contact with LEU 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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224A ASN* 4.7 3.8 - - + -
226A SER* 4.9 8.5 - - - +
227B SER* 4.3 10.5 - - - +
230B GLU* 3.8 21.8 - - + -
231B ASN* 3.9 28.7 - - - +
234B LEU* 3.7 14.4 - - + -
265B ILE* 3.1 39.6 + - + +
266B ASP* 4.4 4.0 - - - +
268B VAL* 1.3 77.7 - - - +
270B ALA* 1.3 59.2 + - - +
271B THR 3.1 1.4 + - - -
272B ASP* 3.4 20.5 + - - +
275B LYS* 3.9 16.8 + - - +
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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
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266B ASP 3.5 12.5 + - - +
267B ILE 2.7 13.4 + - - +
269B LEU* 1.3 75.2 - - - +
271B THR* 1.3 62.2 + - - +
272B ASP 3.2 7.9 + - - +
275B LYS* 4.7 7.7 - - + +
279B LEU* 3.4 36.3 - - + +
311B GLN* 3.7 26.0 - - + +
315B HIS* 4.1 10.1 + - - -
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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