Contacts of the helix formed by residues 214 - 232 (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 TRP 214 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ASP* 5.6 6.5 + - - -
207H ASN 3.5 18.6 - - - +
208H SER* 3.1 28.8 + - - -
212H MET 3.9 0.6 + - - -
213H ARG* 1.3 73.1 - - + +
215H ARG* 1.3 94.5 + - + +
217H ARG* 3.2 17.9 + - - +
218H PHE* 3.0 44.8 + + + -
241H ASN 5.5 0.2 - - - +
252H LYS* 3.7 38.2 - - + +
253H ARG* 3.6 53.3 - - + +
256H PHE* 3.7 34.3 - + + -
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Residues in contact with ARG 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E HIS* 6.4 0.2 - - - -
161E LYS* 5.6 1.2 - - - +
258E ARG* 3.4 23.2 - - - +
285E ARG* 3.6 21.8 - - - +
286E ASP* 3.0 24.9 + - - +
287E ASN* 3.5 17.7 + - - +
288E GLY* 3.6 17.3 - - - +
58F SER* 4.8 7.5 + - - -
59F PRO* 4.6 3.0 + - - +
213H ARG* 3.4 3.1 - - + +
214H TRP* 1.3 105.2 - - + +
216H ASP* 1.3 65.2 + - - +
218H PHE* 3.4 2.9 + - - +
219H LEU* 3.1 40.1 + - - +
256H PHE* 3.4 49.7 - - + -
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Residues in contact with ASP 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PRO 5.1 3.1 - - - +
153E HIS* 3.7 13.0 + - - -
157E VAL* 3.5 31.1 - - + +
161E LYS* 2.9 34.8 + - - +
285E ARG* 6.0 1.0 - - - -
182H ALA* 3.6 18.6 - - + -
213H ARG* 3.3 24.6 + - - +
215H ARG* 1.3 78.6 - - - +
217H ARG* 1.3 62.8 + - - +
219H LEU* 3.4 2.7 + - - +
220H PHE* 3.1 30.0 + - + -
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Residues in contact with ARG 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H ALA* 3.8 10.0 - - - +
185H TYR* 3.8 13.5 - - + -
202H ASP* 2.9 40.6 + - - +
206H VAL* 3.4 26.0 + - - +
207H ASN* 3.0 30.5 + - - +
212H MET* 3.5 37.8 + - - +
213H ARG 3.2 3.6 + - - +
214H TRP* 3.2 16.6 + - - +
216H ASP* 1.3 79.8 - - - +
218H PHE* 1.3 75.7 + - + +
220H PHE* 3.4 0.9 + - - -
221H CYS* 2.9 48.5 + - - +
240H LEU* 5.0 0.6 - - + +
241H ASN 4.2 5.1 + - - -
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Residues in contact with PHE 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 3.0 53.5 + + + +
215H ARG 3.7 4.9 - - - +
216H ASP 3.4 0.2 - - - -
217H ARG* 1.3 97.6 - - - +
219H LEU* 1.3 58.5 + - - +
221H CYS* 3.9 1.2 - - - +
222H ALA* 3.0 30.5 + - - +
240H LEU* 3.7 52.0 - - + +
241H ASN 3.6 20.4 - - - -
242H ALA* 5.8 0.2 - - + -
253H ARG* 3.3 31.6 - - + -
256H PHE* 3.8 18.6 - + + -
257H ALA* 4.4 7.4 - - + -
260H LEU* 3.8 7.6 - - + +
265H VAL* 5.8 0.4 - - + -
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Residues in contact with LEU 219 (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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161E LYS* 4.0 20.6 - - + +
58F SER* 4.2 12.1 - - - +
59F PRO 3.9 7.9 - - - +
60F GLY 3.6 31.6 - - - +
61F TYR* 3.9 26.9 - - + -
65F ARG* 5.0 3.8 + - - +
215H ARG* 3.1 23.9 + - - +
216H ASP 3.6 4.9 - - - +
218H PHE* 1.3 79.2 - - - +
220H PHE* 1.3 63.9 + - + +
222H ALA* 3.3 6.8 + - - +
223H GLU* 3.2 17.7 + - - +
256H PHE* 3.5 28.9 - - + -
260H LEU* 4.2 5.4 - - + -
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Residues in contact with PHE 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E VAL* 5.2 3.1 - - + -
160E ASP* 3.7 42.6 - - + -
161E LYS* 3.8 27.6 - - + -
65F ARG* 3.9 28.5 - - + -
66F TYR* 3.4 33.4 - + - +
182H ALA* 3.7 28.0 - - + +
183H LYS* 3.8 20.6 - - + -
186H GLY* 4.4 2.5 - - - -
216H ASP* 3.1 25.8 + - + +
217H ARG 4.1 1.1 - - - +
219H LEU* 1.3 74.3 - - + +
221H CYS* 1.3 61.4 + - - +
223H GLU* 3.3 6.2 + - - +
224H ALA* 3.0 28.6 + - - +
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Residues in contact with CYS 221 (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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185H TYR* 3.9 13.0 - - - -
186H GLY* 4.5 7.0 - - - -
189H VAL* 4.2 10.8 - - + +
217H ARG* 2.9 35.5 + - - +
218H PHE 3.9 2.9 - - - +
220H PHE* 1.3 74.6 - - - +
222H ALA* 1.3 60.3 + - - +
224H ALA* 3.4 6.9 + - - +
225H LEU* 2.9 33.8 + - - +
238H HIS* 3.7 40.8 - - + +
240H LEU* 4.2 7.0 - - + -
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Residues in contact with ALA 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F TYR* 4.3 4.7 - - + -
218H PHE 3.0 18.4 + - - +
219H LEU 3.6 4.9 - - - +
221H CYS* 1.3 75.7 - - - +
223H GLU* 1.3 63.6 + - - +
225H LEU* 3.4 11.6 + - - +
226H TYR* 3.0 47.0 + - + -
240H LEU* 6.0 0.2 - - - +
260H LEU* 4.2 24.9 - - + -
262H VAL* 4.3 8.3 - - + -
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Residues in contact with GLU 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F TYR* 3.4 23.0 - - + +
62F TYR 3.1 16.6 - - - +
63F ASP* 4.2 8.5 - - - +
64F GLY 3.5 5.2 + - - +
65F ARG* 2.9 59.7 + - - +
66F TYR* 3.2 27.7 + - + +
219H LEU 3.2 10.4 + - - +
220H PHE* 3.6 11.0 - - - +
221H CYS 3.3 0.2 - - - -
222H ALA* 1.3 79.8 - - - +
224H ALA* 1.3 62.7 + - - +
226H TYR* 3.9 2.4 - - - +
227H LYS* 3.1 23.9 + - + +
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Residues in contact with ALA 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F TYR* 4.0 9.4 - - + -
186H GLY* 3.1 30.7 - - - +
189H VAL* 4.0 6.1 - - + -
190H TYR* 3.8 22.8 - - + +
220H PHE 3.0 16.8 + - - +
221H CYS 3.7 3.8 - - - +
223H GLU* 1.3 77.6 - - - +
225H LEU* 1.3 62.0 + - - +
227H LYS* 3.3 5.5 + - - +
228H ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL* 4.9 0.2 - - + -
193H LEU* 3.8 25.3 - - + +
221H CYS* 2.9 21.3 + - + +
222H ALA* 3.8 9.4 - - - +
224H ALA* 1.3 73.2 - - - +
226H TYR* 1.3 82.5 + - + +
228H ALA* 3.4 2.4 + - - +
229H GLN* 3.0 35.5 + - - +
236H LYS* 3.8 23.6 - - + +
237H GLY* 4.3 1.6 - - - -
238H HIS* 3.9 32.1 - - + +
240H LEU* 6.1 1.1 - - + -
262H VAL* 3.9 26.0 - - + -
263H PRO* 4.8 4.9 - - + -
62I TYR* 6.1 0.2 - - - +
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Residues in contact with TYR 226 (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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55F HIS* 3.6 62.9 + + + +
56F HIS* 6.1 0.9 - - + -
61F TYR* 3.9 5.8 - + - +
63F ASP* 4.9 0.4 - - - +
222H ALA* 3.0 39.2 + - + +
223H GLU 3.9 3.1 - - - +
225H LEU* 1.3 90.0 - - + +
227H LYS* 1.3 62.4 + - - +
229H GLN* 3.5 16.8 + - - +
230H ALA* 3.1 24.9 + - - +
260H LEU* 2.9 27.4 + - + -
261H GLY 3.4 8.8 + - - -
262H VAL* 3.8 8.4 + - + +
263H PRO* 6.3 0.4 - - + -
53I ARG* 3.1 30.1 + - - -
62I TYR* 5.8 3.1 - + - -
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Residues in contact with LYS 227 (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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45F GLU* 2.9 33.6 + - - -
48F HIS* 5.8 3.6 + - - +
52F TYR* 6.1 0.7 - - - +
55F HIS* 5.8 1.3 - - - -
64F GLY* 5.6 4.6 - - - +
66F TYR* 3.0 34.8 + - + +
67F TRP 4.4 2.2 - - - -
68F THR* 4.7 0.9 - - - -
190H TYR* 3.4 44.9 - - + -
223H GLU* 3.1 19.5 + - + +
224H ALA* 3.6 5.4 - - - +
225H LEU 3.3 0.2 - - - -
226H TYR* 1.3 77.6 - - - +
228H ALA* 1.3 61.2 + - - +
230H ALA* 3.4 5.2 + - - +
231H GLU* 3.0 25.3 + - + +
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Residues in contact with ALA 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H TYR* 3.8 15.9 - - + +
193H LEU* 3.4 33.9 - - + -
194H ARG* 3.8 12.8 - - - +
224H ALA 3.1 16.3 + - - +
225H LEU 3.8 3.6 - - - +
227H LYS* 1.3 75.6 - - - +
229H GLN* 1.3 61.3 + - - +
231H GLU* 3.3 2.7 + - - +
232H THR* 3.0 32.9 + - - +
236H LYS* 4.3 2.7 - - + -
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Residues in contact with GLN 229 (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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225H LEU* 3.0 22.8 + - - +
226H TYR* 3.8 16.9 - - - +
228H ALA* 1.3 74.7 - - - +
230H ALA* 1.3 60.6 + - - +
233H GLY* 2.9 29.8 + - - -
234H GLU 3.3 23.6 - - - +
235H ILE* 3.5 14.7 - - + +
236H LYS* 3.0 38.5 + - + +
51I VAL* 4.2 10.7 - - + +
53I ARG* 5.6 2.1 - - - +
62I TYR* 3.8 25.1 + - - -
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Residues in contact with ALA 230 (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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55F HIS* 5.6 7.6 - - + +
226H TYR 3.1 17.2 + - - +
227H LYS* 3.8 6.1 - - - +
229H GLN* 1.3 77.8 - - - +
231H GLU* 1.3 62.8 + - - +
233H GLY* 4.0 0.5 + - - -
10I LYS* 3.2 22.2 + - - -
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Residues in contact with GLU 231 (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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190H TYR* 2.6 29.2 + - - -
194H ARG* 2.9 43.6 + - - +
227H LYS* 3.0 19.4 + - + +
228H ALA* 3.6 4.9 - - - +
230H ALA* 1.3 77.6 - - - +
232H THR* 1.3 62.2 + - + +
4I TRP* 5.2 0.3 - - - -
5I PRO 4.0 4.7 - - - +
6I ILE* 3.6 30.7 - - - +
9I LEU* 4.2 13.5 + - + +
10I LYS* 3.3 20.3 + - - +
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Residues in contact with THR 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H LEU 4.3 4.5 - - - +
194H ARG* 3.5 34.8 - - + +
228H ALA 3.0 18.6 + - - +
231H GLU* 1.3 83.6 - - + +
233H GLY* 1.3 63.9 + - - +
234H GLU* 3.3 16.6 + - - -
236H LYS* 3.3 17.7 - - - +
9I LEU 4.4 9.0 - - - +
10I LYS* 3.5 3.9 - - - -
11I LYS* 2.8 31.8 + - + +
17I TYR* 4.7 9.9 - - - +
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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