Contacts of the helix formed by residues 274 - 287 (chain L) in PDB entry 1RBO
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 PHE 274 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L VAL* 3.6 25.6 - - + -
114L THR* 3.4 24.2 - - - +
117L PHE* 3.5 37.0 - + + -
269L TYR* 3.5 32.5 - + - -
270L LEU* 3.9 26.2 - - + -
273L GLY* 1.3 68.8 - - - -
275L THR* 1.3 64.9 + - - +
277L ASN* 3.7 3.9 - - + +
278L THR* 2.8 33.4 + - - +
314L LEU* 4.8 2.0 - - + -
317L ALA* 4.0 11.4 - - + -
321L SER* 4.5 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L THR* 3.1 23.9 + - - +
247L CYS* 5.5 9.0 - - - -
273L GLY* 3.4 0.6 - - - -
274L PHE* 1.3 78.4 - - - +
276L ALA* 1.3 63.8 + - - +
278L THR* 3.4 5.0 + - - -
279L THR* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246L THR 6.3 0.2 - - - -
247L CYS* 4.8 16.4 - - - +
250L MET* 3.4 33.6 - - + +
267L HIS* 4.3 6.1 - - + +
272L GLY* 4.0 14.6 - - - +
273L GLY 3.5 7.9 + - - +
274L PHE 3.3 0.4 - - - -
275L THR* 1.3 78.9 - - - +
277L ASN* 1.3 63.5 + - - +
279L THR* 3.3 4.8 + - - -
280L LEU* 3.1 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267L HIS* 2.9 35.1 + - + +
269L TYR* 3.5 16.9 - - + +
273L GLY 2.9 20.1 + - - +
274L PHE* 3.3 6.9 + - + +
276L ALA* 1.3 77.2 - - - +
278L THR* 1.3 56.8 + - - +
280L LEU* 3.2 3.9 + - - +
281L SER* 2.8 26.5 + - - -
291L LEU* 4.6 3.0 - - - +
293L ILE* 3.3 24.0 - - - +
318L LEU* 3.8 4.7 - - - +
321L SER* 3.0 22.3 + - - +
322L GLY 3.2 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 278 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L GLY 4.5 15.8 + - - +
113L VAL* 5.5 4.3 + - - +
148L PHE* 6.2 1.6 - - + -
274L PHE* 2.8 19.7 + - - +
275L THR* 3.9 4.7 - - - -
277L ASN* 1.3 72.7 - - - +
279L THR* 1.3 64.9 + - - +
281L SER* 3.3 4.2 + - - -
282L HIS* 3.1 50.1 + - + +
321L SER* 2.8 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247L CYS* 5.5 9.1 - - + -
250L MET* 3.8 17.3 - - + -
251L MET* 3.9 17.7 - - + -
275L THR* 3.3 12.8 + - - +
276L ALA* 3.3 10.4 + - - -
277L ASN 3.3 0.4 - - - -
278L THR* 1.3 79.5 - - - +
280L LEU* 1.3 62.1 + - - +
282L HIS* 3.3 8.0 + - - +
283L TYR* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L ALA* 4.2 15.9 - - + -
250L MET* 4.0 17.7 - - + -
251L MET* 4.8 4.0 - - - -
254L ALA* 3.8 28.7 - - + -
265L VAL* 5.1 2.5 - - + -
266L MET 4.6 0.2 - - - +
267L HIS* 3.5 39.7 - - + +
276L ALA 3.1 14.0 + - - +
277L ASN* 3.6 7.9 - - - +
279L THR* 1.3 76.5 - - - +
281L SER* 1.3 59.0 + - - +
283L TYR* 3.1 9.4 + - + +
284L CYS* 2.8 43.6 + - - -
291L LEU* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLN* 3.1 25.0 + - - -
150L GLY 3.6 0.3 + - - -
152L PRO* 3.6 8.0 - - - +
277L ASN 2.8 17.5 + - - -
278L THR 3.3 3.8 + - - -
280L LEU* 1.3 76.0 - - - +
282L HIS* 1.3 62.7 + - - +
284L CYS 3.3 0.9 + - - -
285L ARG 3.1 17.5 + - - -
291L LEU* 3.9 12.3 - - - +
321L SER 3.1 24.5 + - - -
322L GLY* 3.3 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 282 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLN* 3.2 44.8 + - + +
278L THR* 3.1 37.1 + - + +
279L THR* 3.7 9.0 - - - +
281L SER* 1.3 75.8 - - - +
283L TYR* 1.3 62.6 + - - +
285L ARG* 3.3 3.6 + - - +
286L ASP* 3.1 32.1 + - - +
321L SER 4.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251L MET* 3.2 31.9 - - + -
254L ALA* 3.8 28.3 - - + -
255L VAL* 3.6 31.7 - - + +
258L ARG* 3.7 15.8 - - - +
279L THR* 3.0 14.0 + - + +
280L LEU* 3.5 12.6 - - + +
282L HIS* 1.3 76.7 - - - +
284L CYS* 1.3 61.4 + - - +
286L ASP* 3.2 5.3 + - - -
287L ASN* 2.9 59.7 + - - +
289L LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 284 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L PRO* 3.9 12.8 - - + -
153L HIS* 3.6 1.0 + - - -
265L VAL* 3.8 29.8 - - - -
280L LEU* 2.8 31.5 + - - +
281L SER 3.7 4.7 - - - +
283L TYR* 1.3 77.6 - - - +
285L ARG* 1.3 56.9 + - - +
287L ASN 4.5 0.2 - - - +
288L GLY* 2.9 26.7 + - - -
289L LEU* 3.0 41.9 + - - +
291L LEU* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG* 3.8 48.5 - - - +
215B ARG* 3.6 18.7 - - - +
216B ASP* 6.0 1.3 - - - -
149L GLN* 3.4 54.0 + - - +
151L PRO 2.9 23.8 + - - -
152L PRO* 2.7 30.4 + - + +
153L HIS* 4.6 5.6 - - - -
281L SER 3.1 9.6 + - - +
282L HIS 3.6 3.4 - - - +
283L TYR 3.3 0.2 - - - -
284L CYS* 1.3 77.1 - - - +
286L ASP* 1.3 69.5 + - - +
287L ASN 3.3 0.9 + - - -
288L GLY* 3.6 3.3 + - - -
372L PRO* 4.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 5.6 7.0 - - - -
215B ARG* 3.0 19.4 + - - +
252B LYS* 4.1 31.2 + - - +
258L ARG* 5.3 0.5 + - - -
282L HIS* 3.1 20.1 + - - +
283L TYR* 3.6 9.7 - - + +
285L ARG* 1.3 83.9 - - - +
287L ASN* 1.3 70.0 + - - +
288L GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ARG* 3.5 17.4 + - - +
258L ARG* 3.1 36.2 + - + +
283L TYR* 2.9 64.9 + - + +
284L CYS 4.6 0.2 - - - +
286L ASP* 1.3 89.1 - - - +
288L GLY* 1.3 64.4 + - - +
289L LEU* 3.3 5.6 + - + +
59S PRO* 3.8 17.7 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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