Contacts of the helix formed by residues 253 - 270 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ASN 3.7 2.6 + - - +
252C LEU* 1.3 75.9 - - - +
254C LYS* 1.3 66.2 + - - +
255C LYS* 3.5 8.3 + - - +
256C GLN* 3.1 34.0 + - + +
257C ARG* 2.9 20.9 + - - +
504C EDO 5.0 3.1 - - - +
505C EDO 5.2 0.2 - - - -
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLU* 3.1 41.6 + - - -
245B ASN* 5.4 2.2 - - - +
252C LEU 3.9 0.4 + - - -
253C THR* 1.3 72.3 - - - +
255C LYS* 1.3 58.9 + - - +
257C ARG* 3.2 42.0 + - - +
258C GLN* 2.9 32.0 + - + +
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C THR* 3.2 8.0 + - - +
254C LYS* 1.3 82.3 - - - +
256C GLN* 1.3 62.3 + - - +
258C GLN* 3.7 6.7 + - + +
259C SER* 3.2 22.7 + - - -
505C EDO 3.4 34.7 + - - +
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Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.6 24.7 - - - -
188C LEU* 3.9 16.5 - - + +
252C LEU* 3.5 19.8 - - + +
253C THR* 3.1 30.0 + - - +
255C LYS* 1.3 74.3 - - - +
257C ARG* 1.3 67.3 + - - +
259C SER* 3.1 3.3 + - - -
260C LEU* 2.8 25.6 + - - +
504C EDO 2.5 30.0 + - - -
505C EDO 3.8 20.8 - - - -
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ASP* 5.9 1.8 - - - -
249C PHE* 4.1 21.8 - - + +
250C GLN* 6.0 0.4 - - - +
252C LEU* 3.9 20.7 + - + +
253C THR 2.9 13.3 + - - +
254C LYS* 3.4 53.2 + - - +
256C GLN* 1.3 76.7 - - - +
258C GLN* 1.3 65.6 + - - +
260C LEU* 3.2 9.3 + - - +
261C ARG* 3.0 22.8 + - - +
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Residues in contact with GLN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS* 2.9 23.2 + - + +
255C LYS* 4.1 6.3 - - + +
257C ARG* 1.3 75.1 - - - +
259C SER* 1.3 65.6 + - - +
261C ARG* 3.2 9.6 + - - +
262C LYS* 3.2 26.6 + - + +
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Residues in contact with SER 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.6 12.4 - - - +
255C LYS* 3.2 14.8 + - - -
256C GLN 3.1 4.7 + - - -
258C GLN* 1.3 83.3 - - - +
260C LEU* 1.3 62.4 + - - +
262C LYS* 3.5 5.4 + - - +
263C MET* 3.2 42.7 + - - +
303C TYR* 6.1 0.3 - - - -
505C EDO 3.9 13.1 + - - -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 4.2 14.8 - - + +
191C LEU* 4.1 15.7 - - + +
192C ALA* 3.6 37.5 - - + +
195C PHE* 5.1 1.1 - - + -
238C PHE* 6.2 1.6 - - + -
249C PHE* 3.5 51.1 - - + -
252C LEU* 5.1 2.9 - - + -
256C GLN 2.8 16.8 + - - +
257C ARG* 3.5 8.7 - - - +
259C SER* 1.3 77.0 - - - +
261C ARG* 1.3 63.5 + - - +
263C MET* 3.2 10.5 + - - +
264C VAL* 3.0 35.4 + - + +
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Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C PHE* 4.1 31.9 - - + -
257C ARG 3.0 12.9 + - - +
258C GLN* 3.2 12.9 + - - +
260C LEU* 1.3 76.0 - - - +
262C LYS* 1.3 64.2 + - - +
264C VAL* 3.9 1.2 - - - +
265C ILE* 3.0 57.2 + - + +
507C EDO 4.3 1.4 + - - -
216D ASN* 5.5 2.6 + - - -
220D ALA 3.9 2.8 + - - -
221D LEU* 3.8 38.6 + - - +
224D ASN* 3.8 8.3 + - - +
225D ASP* 2.9 42.8 + - - +
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Residues in contact with LYS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C GLN* 3.2 17.7 + - + +
259C SER* 4.0 5.8 - - - +
261C ARG* 1.3 79.2 - - - +
263C MET* 1.3 58.0 + - - +
265C ILE* 3.6 4.9 + - - +
266C ASP* 2.9 43.9 + - - +
303C TYR* 3.5 27.5 - - + +
507C EDO 2.9 51.7 + - - +
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Residues in contact with MET 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.9 33.0 - - + +
189C GLU* 3.6 33.0 - - + +
192C ALA* 3.9 10.1 - - + -
259C SER* 3.2 37.6 + - - +
260C LEU* 3.2 7.4 + - - +
262C LYS* 1.3 75.0 - - + +
264C VAL* 1.3 60.8 + - - +
266C ASP* 3.1 2.3 + - - +
267C ILE* 2.8 36.5 + - + +
303C TYR* 3.9 32.3 - - + +
307C ILE* 3.9 12.3 - - + -
310C LEU* 4.9 3.6 - - - -
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ALA* 3.5 32.1 - - - +
195C PHE* 3.9 16.8 - - + -
196C ALA* 3.9 16.6 - - + -
199C ILE* 3.8 29.2 - - + -
234C LEU* 4.1 2.2 - - + -
238C PHE* 3.9 15.7 - - + -
260C LEU* 3.0 26.7 + - + +
261C ARG 3.9 3.1 - - - +
263C MET* 1.3 71.9 - - - +
265C ILE* 1.3 62.0 + - - +
267C ILE* 3.7 0.6 - - - -
268C VAL* 2.8 30.9 + - + +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C LEU* 3.8 11.4 - - + +
238C PHE* 3.9 15.0 - - + -
261C ARG* 3.0 65.0 + - + +
262C LYS* 3.6 4.0 - - - +
264C VAL* 1.3 76.5 - - - +
266C ASP* 1.3 64.8 + - - +
268C VAL* 4.0 0.3 - - - -
269C LEU* 3.1 40.8 + - + +
507C EDO 4.0 20.6 - - - +
224D ASN* 3.6 35.9 - - + +
226D SER* 5.9 0.2 - - - +
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Residues in contact with ASP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LYS* 2.9 33.2 + - - +
263C MET 3.6 3.8 - - - +
265C ILE* 1.3 78.3 - - - +
267C ILE* 1.3 63.0 + - - +
269C LEU* 5.5 0.5 - - - +
270C ALA 3.4 5.0 + - - -
303C TYR* 2.6 28.6 + - - -
307C ILE* 3.8 18.0 - - + +
311C GLN* 2.9 26.7 + - - +
507C EDO 3.0 22.0 + - - -
508C EDO 3.2 19.8 + - - -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ALA* 4.1 9.4 - - + +
193C ALA* 3.7 31.0 - - + +
196C ALA* 3.7 13.2 - - + -
263C MET 2.8 22.8 + - - +
264C VAL 3.8 2.9 - - - +
266C ASP* 1.3 75.8 - - - +
268C VAL* 1.3 67.9 + - - +
270C ALA* 3.1 16.8 + - - +
271C THR* 3.5 7.3 + - - +
307C ILE* 4.0 14.6 - - + -
310C LEU* 4.0 28.5 - - + +
311C GLN* 4.0 7.8 - - - +
314C VAL* 3.6 35.6 - - + +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ALA* 3.7 33.0 - - + +
199C ILE* 4.2 6.5 - - + -
200C HIS* 4.2 23.8 - - + +
230C GLU* 3.8 17.4 - - + +
233C HIS* 4.5 3.8 - - + -
234C LEU* 3.6 32.5 - - + -
264C VAL* 2.8 26.9 + - + +
267C ILE* 1.3 72.8 - - + +
269C LEU* 1.3 58.1 + - - +
271C THR* 2.6 35.5 + - - +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C SER* 4.4 7.0 - - - -
230C GLU* 4.0 8.7 - - + -
231C ASN* 3.8 33.4 - - - +
234C LEU* 3.7 19.5 - - + -
265C ILE* 3.1 37.7 + - + +
266C ASP* 5.3 0.9 - - - +
268C VAL* 1.3 76.0 - - - +
270C ALA* 1.3 61.0 + - - +
271C THR 3.1 1.3 + - - -
272C ASP* 3.3 13.5 + - - +
275C LYS* 3.3 21.1 - - - +
508C EDO 3.7 25.1 - - - +
224D ASN* 4.2 10.5 - - + +
226D SER* 5.6 4.5 - - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C ASP 3.4 13.8 + - - +
267C ILE 3.1 12.3 + - - +
269C LEU* 1.3 79.6 - - - +
271C THR* 1.3 58.6 + - - +
272C ASP 3.2 8.6 + - - +
275C LYS* 4.5 4.6 - - - +
279C LEU* 3.7 28.7 - - + +
311C GLN* 3.8 32.3 - - + +
315C HIS* 4.3 7.3 + - - -
508C EDO 4.1 9.6 + - - +
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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
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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