Contacts of the helix formed by residues 253 - 270 (chain D) 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 THR 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251D ASN 3.9 2.0 + - - +
252D LEU* 1.3 75.4 - - - +
254D LYS* 1.3 65.2 + - - +
255D LYS* 3.5 8.9 + - - +
256D GLN* 2.9 37.9 + - - +
257D ARG* 2.9 21.6 + - - +
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Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU* 2.9 36.5 + - + +
213C ILE 4.5 0.2 + - - -
214C ASN* 2.8 31.8 + - - +
216C ASN* 3.0 17.2 + - - +
253D THR* 1.3 74.4 - - - +
255D LYS* 1.3 61.2 + - + +
257D ARG* 3.3 22.5 + - + +
258D GLN* 2.9 59.8 + - + +
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Residues in contact with LYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D THR* 3.3 8.3 + - - +
254D LYS* 1.3 80.7 - - + +
256D GLN* 1.3 61.0 + - + +
258D GLN* 3.4 9.3 + - - +
259D SER* 3.1 26.3 + - - -
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Residues in contact with GLN 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 4.0 24.1 - - - -
188D LEU* 3.6 20.8 - - + +
251D ASN 4.6 0.9 - - - +
252D LEU* 3.3 24.9 - - + +
253D THR* 2.9 43.0 + - + +
255D LYS* 1.3 75.4 - - + +
257D ARG* 1.3 58.0 + - - +
259D SER* 4.7 0.2 - - - -
260D LEU* 2.9 33.8 + - - +
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Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU* 2.9 41.4 + - - -
216C ASN* 4.1 7.7 - - - +
247D ASP* 6.1 0.7 - - - -
249D PHE* 3.6 27.8 - - + +
250D GLN* 5.3 2.9 + - - +
252D LEU* 3.1 32.0 + - + -
253D THR 2.9 14.0 + - - +
254D LYS* 3.5 29.8 - - + +
256D GLN* 1.3 75.8 - - - +
258D GLN* 1.3 56.5 + - + +
260D LEU* 3.8 6.9 - - + +
261D ARG* 2.9 31.8 + - - +
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Residues in contact with GLN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C GLN* 4.5 5.3 - - - +
213C ILE* 4.6 7.7 + - - +
214C ASN* 2.9 41.4 + - - +
254D LYS* 2.9 48.8 + - + +
255D LYS* 4.0 8.5 - - - +
257D ARG* 1.3 76.2 - - - +
259D SER* 1.3 63.5 + - - +
261D ARG* 3.7 5.9 - - - +
262D LYS* 3.0 24.8 + - - +
507D PEG 3.9 5.0 + - - +
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Residues in contact with SER 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 3.6 10.9 - - - +
255D LYS 3.1 17.8 + - - -
256D GLN 3.8 2.5 - - - -
258D GLN* 1.3 77.0 - - - +
260D LEU* 1.3 62.8 + - - +
262D LYS* 3.3 6.5 + - - +
263D MET* 3.0 48.3 + - - +
303D TYR* 6.0 0.3 - - - -
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.1 13.1 - - + +
191D LEU* 4.1 12.6 - - + +
192D ALA* 3.5 38.6 - - + +
195D PHE* 5.3 0.7 - - + -
238D PHE* 5.9 2.9 - - + -
249D PHE* 3.5 48.5 - - + -
252D LEU* 3.8 12.6 - - + -
256D GLN 2.9 17.3 + - - +
257D ARG* 3.8 5.6 - - + +
259D SER* 1.3 76.4 + - - +
261D ARG* 1.3 65.7 + - - +
263D MET* 3.2 9.6 + - - +
264D VAL* 2.9 34.6 + - + +
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE* 6.0 0.6 + - - -
216C ASN* 5.7 4.9 - - - -
220C ALA 3.1 17.0 + - - -
221C LEU* 3.7 17.9 + - - +
224C ASN* 3.7 12.7 + - - +
225C ASP* 2.9 40.8 + - - +
238D PHE* 3.3 61.0 - - + +
257D ARG 2.9 20.1 + - - +
258D GLN* 3.7 6.5 - - - +
260D LEU* 1.3 77.9 - - - +
262D LYS* 1.3 62.8 + - - +
264D VAL* 3.3 1.2 + - - +
265D ILE* 3.0 38.5 + - + +
507D PEG 4.1 1.3 - - - +
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Residues in contact with LYS 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D GLN 3.0 15.1 + - - +
259D SER* 3.7 5.8 - - - +
261D ARG* 1.3 76.2 - - - +
263D MET* 1.3 52.8 + - + +
265D ILE* 3.2 2.8 + - - +
266D ASP* 2.8 48.0 + - - +
303D TYR* 3.7 21.5 - - + +
506D EDO 4.0 12.2 + - - -
507D PEG 2.6 63.7 + - - +
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Residues in contact with MET 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.1 15.0 - - + +
189D GLU* 3.6 49.4 - - + +
192D ALA* 3.9 12.1 - - + -
259D SER* 3.0 39.5 + - - +
260D LEU 3.7 2.9 - - - +
262D LYS* 1.3 74.3 - - + +
264D VAL* 1.3 54.2 + - - +
266D ASP* 3.0 2.6 + - - +
267D ILE* 2.7 43.0 + - + +
303D TYR* 3.8 34.5 - - + +
307D ILE* 3.8 13.0 - - + -
310D LEU* 4.7 4.5 - - - -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ALA* 3.7 28.7 - - - +
195D PHE* 3.8 17.9 - - + -
196D ALA* 4.1 14.6 - - + -
199D ILE* 3.8 24.2 - - + -
234D LEU* 3.8 3.1 - - + -
238D PHE* 3.5 24.2 - - + -
260D LEU* 2.9 29.6 + - + +
261D ARG 3.7 3.6 - - - +
263D MET* 1.3 74.6 - - - +
265D ILE* 1.3 63.3 + - - +
267D ILE* 3.2 1.4 + - - +
268D VAL* 2.9 24.8 + - - +
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C ASN* 3.8 31.0 - - + +
234D LEU* 3.6 23.1 - - + +
238D PHE* 4.0 6.1 - - + -
261D ARG* 3.0 54.4 + - + +
262D LYS 3.6 3.4 - - - +
264D VAL* 1.3 76.4 - - - +
266D ASP* 1.3 64.5 + - - +
269D LEU* 3.1 47.7 + - + +
507D PEG 3.8 28.7 - - - -
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Residues in contact with ASP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D LYS* 2.8 21.1 + - - +
263D MET 3.5 4.9 - - - +
265D ILE* 1.3 73.4 - - - +
267D ILE* 1.3 63.2 + - - +
269D LEU* 5.0 1.9 - - - +
270D ALA 3.5 9.9 + - - -
303D TYR* 2.6 23.6 + - - -
307D ILE* 3.7 16.4 - - + -
311D GLN* 3.0 24.8 + - - +
506D EDO 2.9 32.6 + - - -
507D PEG 2.9 28.2 + - - -
509D EDO 3.5 7.4 + - - -
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Residues in contact with ILE 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ALA* 4.3 4.7 - - + +
193D ALA* 4.0 28.5 - - + +
196D ALA* 3.7 14.1 - - + -
263D MET* 2.7 31.0 + - + +
264D VAL 3.8 2.9 - - - +
266D ASP* 1.3 73.9 - - - +
268D VAL* 1.3 64.9 + - + +
270D ALA* 3.1 18.2 + - - +
271D THR* 3.6 6.9 + - - +
307D ILE* 4.0 15.3 - - + -
310D LEU* 4.0 28.3 - - + +
311D GLN* 4.0 11.2 - - + +
314D VAL* 3.6 36.3 - - + -
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ALA* 3.6 34.3 - - + +
199D ILE* 4.3 4.3 - - + -
200D HIS* 3.9 29.6 - - + +
230D GLU* 3.9 16.9 - - + +
233D HIS* 4.5 2.9 - - + -
234D LEU* 3.7 29.8 - - + -
264D VAL* 2.9 19.8 + - + +
267D ILE* 1.3 78.5 - - + +
269D LEU* 1.3 61.2 + - - +
271D THR* 2.7 32.2 + - - +
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C ASN* 5.6 1.3 - - + -
226C SER* 4.8 9.9 - - - +
227D SER* 4.7 8.2 + - - +
230D GLU* 4.5 5.8 - - + -
231D ASN* 3.9 35.2 - - - +
234D LEU* 3.6 20.6 - - + -
265D ILE* 3.1 37.2 + - + +
266D ASP* 5.3 2.5 - - - +
268D VAL* 1.3 76.6 - - - +
270D ALA* 1.3 60.6 + - - +
271D THR 3.2 1.2 + - - -
272D ASP* 3.3 21.7 + - - +
275D LYS* 3.8 8.1 - - + +
507D PEG 5.5 2.0 - - - -
509D EDO 3.7 21.5 - - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D ASP 3.5 12.3 + - - +
267D ILE 3.1 13.0 + - - +
269D LEU* 1.3 78.4 - - - +
271D THR* 1.3 60.5 + - - +
272D ASP 3.2 7.2 + - - +
275D LYS* 4.7 4.6 - - - +
279D LEU* 3.4 26.7 - - + +
311D GLN* 3.7 33.2 - - + +
315D HIS* 4.2 7.2 + - - -
509D EDO 3.9 12.2 - - - +
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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
------------------------------------------------------------
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