Contacts of the helix formed by residues 274 - 287 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H VAL* 3.6 26.0 - - + -
114H THR* 3.4 25.4 - - - +
117H PHE* 3.5 37.9 - + - -
269H TYR* 3.5 31.4 - + - -
270H LEU* 3.9 26.7 - - + -
273H GLY* 1.3 70.2 - - - -
275H THR* 1.3 64.9 + - - +
277H ASN* 3.7 3.5 - - + +
278H THR* 2.8 32.7 + - - +
314H LEU* 4.8 2.7 - - + -
317H ALA* 4.0 12.1 - - + -
321H SER* 4.5 11.2 - - - -
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Residues in contact with THR 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 3.1 24.0 + - - +
247H CYS* 5.5 8.7 - - - -
273H GLY 3.4 0.8 - - - -
274H PHE* 1.3 78.1 - - - +
276H ALA* 1.3 63.8 + - - +
278H THR* 3.4 4.6 + - - -
279H THR* 3.3 22.9 + - - +
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Residues in contact with ALA 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H THR 6.3 0.7 - - - -
247H CYS* 4.8 16.6 - - - +
250H MET* 3.4 33.8 - - + +
267H HIS* 4.3 6.3 - - + +
272H GLY* 4.0 15.0 - - - +
273H GLY* 3.5 7.6 + - - +
275H THR* 1.3 77.8 - - - +
277H ASN* 1.3 63.7 + - - +
279H THR* 3.3 4.8 + - - -
280H LEU 3.1 17.7 + - - -
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Residues in contact with ASN 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H HIS* 2.9 34.3 + - + +
269H TYR* 3.5 16.5 - - + +
273H GLY 2.9 18.7 + - - +
274H PHE* 3.3 7.4 + - + +
276H ALA* 1.3 76.3 - - - +
278H THR* 1.3 56.6 + - - +
280H LEU* 3.2 3.9 + - - +
281H SER* 2.8 26.5 + - - -
291H LEU* 4.6 2.8 - - - +
293H ILE* 3.3 24.5 - - - +
318H LEU* 3.8 5.0 - - - +
321H SER* 3.0 21.5 + - - +
322H GLY 3.2 17.8 + - - +
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Residues in contact with THR 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLY 4.5 16.7 + - - +
113H VAL* 5.5 4.3 + - - +
148H PHE* 6.2 0.9 - - + -
274H PHE* 2.8 19.2 + - - +
275H THR* 3.9 5.6 - - - -
277H ASN* 1.3 73.3 - - - +
279H THR* 1.3 64.8 + - - +
281H SER* 3.3 4.6 + - - -
282H HIS* 3.1 50.1 + - + +
321H SER* 2.8 27.7 + - - +
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Residues in contact with THR 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H CYS* 5.5 8.4 - - + -
250H MET* 3.8 18.2 - - + -
251H MET* 3.9 18.4 - - + -
275H THR* 3.3 13.7 + - - +
276H ALA* 3.3 10.4 + - - -
277H ASN 3.3 0.2 - - - -
278H THR* 1.3 79.9 - - - +
280H LEU* 1.3 61.3 + - - +
282H HIS* 3.3 8.2 + - - +
283H TYR* 3.0 20.3 + - - +
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Residues in contact with LEU 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA* 4.2 15.7 - - + -
250H MET* 4.0 16.6 - - + -
251H MET* 4.8 3.8 - - - -
254H ALA* 3.8 28.0 - - + -
265H VAL* 5.1 2.5 - - + -
266H MET 4.6 0.7 - - - +
267H HIS* 3.5 39.7 - - + +
276H ALA 3.1 13.0 + - - +
277H ASN* 3.2 8.3 + - - +
279H THR* 1.3 76.9 - - - +
281H SER* 1.3 59.7 + - - +
283H TYR* 3.1 9.8 + - + +
284H CYS* 2.8 44.9 + - - -
291H LEU* 3.9 12.8 - - + -
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Residues in contact with SER 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H GLN* 3.1 24.5 + - - -
150H GLY 3.6 0.2 + - - -
152H PRO* 3.6 7.8 - - - +
277H ASN 2.8 17.0 + - - -
278H THR 3.3 4.2 + - - -
280H LEU* 1.3 75.1 - - - +
282H HIS* 1.3 63.4 + - - +
284H CYS 3.3 1.0 + - - -
285H ARG 3.1 17.5 + - - -
291H LEU* 3.9 12.5 - - - +
321H SER 3.1 24.4 + - - -
322H GLY* 3.3 22.0 - - - -
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Residues in contact with HIS 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H GLN* 3.2 42.4 + - + +
278H THR* 3.1 35.7 + - + +
279H THR* 3.7 9.6 - - - +
280H LEU 3.2 0.2 - - - -
281H SER* 1.3 77.1 - - - +
283H TYR* 1.3 63.4 + - - +
285H ARG* 3.3 3.3 + - - +
286H ASP* 3.1 31.9 + - - +
321H SER 4.8 4.5 - - - -
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Residues in contact with TYR 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H MET* 3.2 31.2 - - + -
254H ALA* 3.8 26.7 - - + -
255H VAL* 3.6 32.2 - - + +
258H ARG* 3.7 16.5 - - - +
279H THR 3.0 13.8 + - - +
280H LEU* 3.1 13.9 + - + +
282H HIS* 1.3 77.5 - - - +
284H CYS* 1.3 60.9 + - - +
286H ASP* 3.2 5.6 + - + -
287H ASN* 2.9 60.4 + - - +
289H LEU* 3.9 20.2 - - + -
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Residues in contact with CYS 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO* 3.9 12.1 - - + -
153H HIS* 3.6 1.0 + - - -
265H VAL* 3.8 28.7 - - - -
280H LEU* 2.8 31.3 + - - +
281H SER 3.7 4.7 - - - +
282H HIS 3.3 0.4 - - - -
283H TYR* 1.3 76.7 - - - +
285H ARG* 1.3 57.5 + - - +
287H ASN 4.5 0.2 - - - +
288H GLY* 2.9 26.5 + - - -
289H LEU* 3.0 42.6 + - - +
291H LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H GLN* 3.4 54.1 + - - +
151H PRO 2.9 24.4 + - - -
152H PRO* 2.7 29.1 + - + +
153H HIS* 4.6 6.6 - - - +
281H SER 3.1 8.8 + - - +
282H HIS 3.6 3.1 - - - +
284H CYS* 1.3 77.8 - - - +
286H ASP* 1.3 70.4 + - - +
287H ASN 3.3 0.5 + - - -
288H GLY* 3.6 2.8 + - - -
372H PRO* 4.9 8.5 - - - +
213L ARG* 3.8 48.3 - - - +
215L ARG* 3.6 20.2 - - - +
216L ASP* 6.1 0.7 - - - -
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Residues in contact with ASP 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ARG* 5.3 0.3 + - - -
282H HIS* 3.1 19.7 + - - +
283H TYR* 3.6 10.7 - - + +
285H ARG* 1.3 84.3 - - - +
287H ASN* 1.3 70.7 + - - +
288H GLY 3.7 0.2 - - - -
214L TRP* 5.6 6.3 - - - -
215L ARG* 3.0 19.5 + - - +
252L LYS* 4.0 29.5 + - - +
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Residues in contact with ASN 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ARG* 3.1 35.5 + - + +
283H TYR* 2.9 64.1 + - + +
284H CYS 4.6 0.2 - - - +
286H ASP* 1.3 89.5 - - - +
288H GLY* 1.3 64.2 + - - +
289H LEU* 3.3 5.8 + - + +
59I PRO* 3.8 18.0 - - - +
215L ARG* 3.5 17.4 + - - +
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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