Contacts of the helix formed by residues 274 - 287 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E VAL* 3.6 25.6 - - + -
114E THR* 3.5 23.3 - - - +
117E PHE* 3.5 37.9 - + + -
269E TYR* 3.5 31.6 - + - -
270E LEU* 3.9 26.0 - - + -
273E GLY* 1.3 69.4 - - - -
275E THR* 1.3 64.8 + - - +
277E ASN* 3.7 3.5 - - + +
278E THR* 2.8 33.2 + - - +
314E LEU* 4.8 2.5 - - + -
317E ALA* 4.0 11.9 - - + -
321E SER* 4.5 10.8 - - - -
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Residues in contact with THR 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E THR* 3.1 24.5 + - - +
247E CYS* 5.5 8.7 - - - -
273E GLY 3.4 0.4 - - - -
274E PHE* 1.3 78.1 - - - +
276E ALA* 1.3 63.1 + - - +
278E THR* 3.4 4.8 + - - -
279E THR* 3.3 23.3 + - - +
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Residues in contact with ALA 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E THR 6.3 0.2 - - - -
247E CYS* 4.8 15.9 - - - +
250E MET* 3.4 33.3 - - + +
267E HIS* 4.3 5.8 - - + +
272E GLY* 4.0 15.3 - - - +
273E GLY* 3.5 7.8 + - - +
274E PHE 3.3 0.2 - - - -
275E THR* 1.3 79.7 - - - +
277E ASN* 1.3 62.6 + - - +
279E THR* 3.3 4.8 + - - -
280E LEU* 3.1 17.7 + - - +
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Residues in contact with ASN 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E HIS* 2.9 33.9 + - + +
269E TYR* 3.5 16.9 - - + +
273E GLY 2.9 18.9 + - - +
274E PHE* 3.3 7.2 + - + +
276E ALA* 1.3 77.1 - - - +
278E THR* 1.3 56.1 + - - +
280E LEU* 3.2 4.2 + - - +
281E SER* 2.8 26.7 + - - -
291E LEU* 4.6 3.0 - - - +
293E ILE* 3.3 24.2 - - - +
318E LEU* 3.8 4.7 - - - +
321E SER* 3.0 22.7 + - - +
322E GLY 3.2 17.7 + - - +
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Residues in contact with THR 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E GLY 4.5 16.2 + - - +
113E VAL* 5.5 4.3 + - - +
148E PHE* 6.2 1.3 - - + -
274E PHE* 2.8 19.8 + - - +
275E THR* 3.9 4.7 - - - -
277E ASN* 1.3 73.2 - - - +
279E THR* 1.3 66.6 + - - +
281E SER* 3.3 4.4 + - - -
282E HIS* 3.1 50.1 + - + +
321E SER* 2.8 27.9 + - - +
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Residues in contact with THR 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E CYS* 5.5 8.2 - - + -
250E MET* 3.8 18.6 - - + -
251E MET* 3.9 17.7 - - + -
275E THR* 3.3 13.8 + - - +
276E ALA* 3.3 10.0 + - - -
277E ASN 3.3 0.2 - - - -
278E THR* 1.3 80.0 - - - +
280E LEU* 1.3 62.4 + - - +
282E HIS* 3.3 8.4 + - - +
283E TYR* 3.0 20.7 + - + +
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Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E ALA* 4.2 15.9 - - + -
250E MET* 4.0 17.3 - - + -
251E MET* 4.8 4.0 - - - -
254E ALA* 3.8 28.3 - - + -
265E VAL* 5.1 2.5 - - + -
266E MET 4.6 0.7 - - - +
267E HIS* 3.5 39.9 - - + +
276E ALA 3.1 13.1 + - - +
277E ASN* 3.2 8.7 + - - +
279E THR* 1.3 75.4 - - - +
281E SER* 1.3 59.3 + - - +
283E TYR* 3.1 9.9 + - + +
284E CYS* 2.8 44.8 + - - -
291E LEU* 3.9 12.8 - - + -
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Residues in contact with SER 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E GLN* 3.1 24.8 + - - -
150E GLY 3.6 0.3 + - - -
152E PRO* 3.6 8.0 - - - +
277E ASN 2.8 16.4 + - - -
278E THR 3.3 4.7 + - - -
280E LEU* 1.3 74.7 - - - +
282E HIS* 1.3 63.8 + - - +
284E CYS 3.3 0.9 + - - -
285E ARG 3.1 17.7 + - - -
291E LEU* 3.9 12.9 - - - +
321E SER 3.1 24.5 + - - -
322E GLY* 3.3 21.9 - - - -
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Residues in contact with HIS 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E GLN* 3.2 43.0 + - + +
278E THR* 3.1 37.3 + - + +
279E THR* 3.7 9.6 - - - +
281E SER* 1.3 76.9 - - - +
283E TYR* 1.3 63.3 + - - +
285E ARG* 3.3 3.6 + - - +
286E ASP* 3.1 31.9 + - - +
321E SER 4.8 4.0 - - - -
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Residues in contact with TYR 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E MET* 3.2 29.4 - - + -
254E ALA* 3.8 27.4 - - + -
255E VAL* 3.6 31.9 - - + +
258E ARG* 3.7 15.8 - - - +
279E THR 3.0 13.4 + - - +
280E LEU* 3.5 12.8 - - + +
282E HIS* 1.3 76.8 - - - +
284E CYS* 1.3 60.0 + - - +
286E ASP* 3.2 6.0 + - + -
287E ASN* 2.9 59.7 + - - +
289E LEU* 3.9 19.3 - - + -
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Residues in contact with CYS 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PRO* 3.9 12.3 - - + -
153E HIS* 3.6 0.9 + - - -
265E VAL* 3.8 29.6 - - - -
280E LEU* 2.8 31.1 + - - +
281E SER 3.7 5.2 - - - +
282E HIS 3.3 0.4 - - - -
283E TYR* 1.3 77.8 - - - +
285E ARG* 1.3 58.6 + - - +
288E GLY* 2.9 26.2 + - - -
289E LEU* 3.0 41.9 + - - +
291E LEU* 4.1 12.6 - - + -
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Residues in contact with ARG 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E GLN* 3.4 52.5 + - - +
151E PRO 2.9 24.2 + - - -
152E PRO* 2.7 29.2 + - + +
153E HIS* 4.6 6.0 - - - -
281E SER 3.1 9.8 + - - +
282E HIS 3.6 3.8 - - - +
284E CYS* 1.3 76.5 - - - +
286E ASP* 1.3 69.8 + - - +
287E ASN 3.3 1.0 + - - -
288E GLY* 3.6 3.1 + - - -
372E PRO* 4.9 8.5 - - - +
213H ARG* 3.8 48.5 - - - +
215H ARG* 3.6 19.1 - - - +
216H ASP* 6.0 0.9 - - - -
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Residues in contact with ASP 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG* 5.3 0.2 + - - -
282E HIS* 3.1 19.7 + - - +
283E TYR* 3.2 9.7 + - + +
285E ARG* 1.3 84.1 - - - +
287E ASN* 1.3 69.4 + - - +
214H TRP* 5.6 6.2 - - - -
215H ARG* 3.0 19.7 + - - +
252H LYS* 4.1 30.1 + - - +
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Residues in contact with ASN 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG* 3.1 35.8 + - + +
283E TYR* 2.9 64.7 + - + +
284E CYS 4.6 0.2 - - - +
285E ARG 3.2 0.2 - - - -
286E ASP* 1.3 89.2 - - - +
288E GLY* 1.3 63.8 + - - +
289E LEU* 3.3 5.6 + - + +
59F PRO* 3.8 18.2 - - - +
215H ARG* 3.5 18.3 + - - +
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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