Contacts of the helix formed by residues 182 - 195 (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 ALA 182 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156E GLN* 5.1 1.8 - - - +
157E VAL* 5.8 5.2 - - + -
181H SER* 1.3 72.5 - - - +
183H LYS* 1.3 63.9 + - - +
185H TYR* 3.3 4.9 + - - +
186H GLY 3.2 17.0 + - - -
211H PHE 4.6 0.8 + - - -
212H MET* 3.7 22.8 - - + +
216H ASP* 3.6 37.5 - - + -
217H ARG* 3.8 5.6 - - - +
220H PHE* 3.7 22.2 - - + +
221H CYS* 5.4 0.2 - - - -
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Residues in contact with LYS 183 (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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160E ASP* 3.4 42.5 + - + +
163E ASN* 3.2 23.0 - - - +
165E TYR* 2.9 29.7 + - - +
65F ARG* 4.9 9.3 + - + +
66F TYR* 2.7 44.5 + - + +
100F ARG* 5.7 1.6 - - - +
111F GLN* 3.9 6.5 + - - +
181H SER* 3.3 3.5 + - - +
182H ALA* 1.3 79.9 - - - +
184H ASN* 1.3 61.9 + - - +
187H ARG* 3.1 35.2 + - - +
220H PHE* 3.8 15.5 - - + -
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Residues in contact with ASN 184 (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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104F PHE* 4.0 14.3 - - - -
109F GLU* 2.9 37.6 - - - +
180H LEU* 4.2 16.4 - - + +
181H SER* 3.2 15.1 + - - +
183H LYS* 1.3 74.7 - - - +
185H TYR* 1.3 64.5 + - - +
187H ARG* 3.0 40.6 + - - +
188H ALA* 3.0 23.7 + - - +
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Residues in contact with TYR 185 (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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174H ILE* 3.6 36.0 + - + +
176H PRO 5.1 2.2 - - - -
177H LYS 4.8 4.4 + - - -
180H LEU* 4.1 21.0 - - + +
181H SER 2.9 10.5 + - - +
182H ALA 3.3 11.0 - - - +
183H LYS 3.2 0.2 - - - -
184H ASN* 1.3 76.1 - - - +
186H GLY* 1.3 57.0 + - - +
188H ALA* 3.3 5.7 + - - +
189H VAL* 2.9 32.7 + - + +
202H ASP* 3.3 40.5 - - - -
203H ASP* 3.3 9.5 + - - +
206H VAL* 3.8 10.9 - - + +
212H MET* 3.6 30.7 - - + -
217H ARG* 3.8 14.6 - - + -
221H CYS* 3.9 16.2 - - - -
238H HIS* 3.9 11.7 - - - -
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Residues in contact with GLY 186 (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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66F TYR* 3.2 19.7 - - - -
182H ALA 3.2 9.0 + - - -
183H LYS 3.4 0.2 + - - -
184H ASN 3.3 0.2 - - - -
185H TYR* 1.3 75.7 - - - +
187H ARG* 1.3 59.3 + - - +
189H VAL* 3.2 5.1 + - - -
190H TYR* 2.9 26.5 + - - +
220H PHE 4.1 10.3 - - - -
221H CYS* 4.5 3.3 - - - -
224H ALA* 3.1 19.2 - - - +
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Residues in contact with ARG 187 (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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43F GLU* 2.8 31.1 + - - -
66F TYR* 3.4 19.8 + - + -
69F MET* 3.7 30.5 - - + -
102F ILE* 4.1 4.8 - - - +
104F PHE* 3.5 14.6 - - - -
111F GLN* 2.8 30.1 + - - +
183H LYS* 3.1 36.7 + - - +
184H ASN* 3.0 34.8 - - - +
185H TYR 3.3 0.4 - - - -
186H GLY* 1.3 75.1 - - - +
188H ALA* 1.3 64.6 + - - +
190H TYR* 3.4 4.3 + - - +
191H GLU* 3.3 31.5 + - + +
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Residues in contact with ALA 188 (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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174H ILE* 4.1 24.2 - - + -
180H LEU* 5.2 3.4 - - + -
184H ASN 3.0 13.4 + - - +
185H TYR* 3.3 8.7 + - - +
187H ARG* 1.3 78.9 - - - +
189H VAL* 1.3 63.2 + - - +
191H GLU* 3.4 1.2 + - - -
192H CYS* 3.1 22.9 + - - -
407H LEU* 4.7 5.8 - - + -
413H ASN* 3.2 27.2 + - - +
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Residues in contact with VAL 189 (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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174H ILE* 4.0 13.0 - - + -
185H TYR* 2.9 21.0 + - + +
186H GLY* 3.5 9.9 - - - +
187H ARG 3.2 0.2 - - - -
188H ALA* 1.3 72.7 - - - +
190H TYR* 1.3 65.7 + - - +
192H CYS* 3.3 2.1 + - - +
193H LEU* 3.0 38.6 + - + +
200H THR* 3.3 22.0 - - - +
221H CYS* 4.2 13.2 - - - +
224H ALA* 4.0 12.1 - - + -
238H HIS* 3.4 36.1 - - + +
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Residues in contact with TYR 190 (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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66F TYR* 5.0 7.0 - + + -
67F TRP 3.8 13.0 - - - -
68F THR* 3.2 31.7 - - - +
186H GLY 2.9 15.7 + - - +
187H ARG* 3.9 4.9 - - - +
188H ALA 3.4 0.2 - - - -
189H VAL* 1.3 75.3 - - - +
191H GLU* 1.3 82.0 + - + +
193H LEU* 3.9 0.5 - - - +
194H ARG* 3.0 47.2 + - + +
224H ALA* 3.8 20.6 - - + +
227H LYS* 3.4 35.1 - - + -
228H ALA* 3.8 21.1 - - + -
231H GLU* 2.6 29.7 + - - -
6I ILE* 3.8 0.2 - - - +
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Residues in contact with GLU 191 (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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67F TRP 4.3 0.9 - - - +
68F THR* 3.7 0.9 - - - -
69F MET* 3.0 47.5 + - + +
187H ARG* 3.3 23.2 + - + +
188H ALA* 3.8 1.8 - - - +
189H VAL 3.3 0.4 - - - -
190H TYR* 1.3 93.6 - - + +
192H CYS* 1.3 61.1 + - - +
194H ARG* 3.0 36.5 + - - +
195H GLY 3.6 0.2 + - - -
413H ASN* 3.6 22.9 - - + +
414H ALA* 3.1 32.0 + - - +
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Residues in contact with CYS 192 (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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172H CYS* 3.8 24.7 - - - -
174H ILE* 4.2 9.6 - - - -
188H ALA 3.1 20.5 + - - +
191H GLU* 1.3 74.1 - - - +
193H LEU* 1.3 66.6 + - - +
195H GLY* 3.2 2.1 + - - -
197H LEU* 3.8 14.2 + - + +
200H THR* 3.5 19.7 - - + -
406H THR* 4.0 7.0 - - - -
407H LEU* 4.3 1.6 - - - -
413H ASN* 3.5 29.6 - - - -
417H ALA* 3.2 24.9 - - - +
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Residues in contact with LEU 193 (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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189H VAL* 3.0 38.3 + - + +
192H CYS* 1.3 78.2 - - - +
194H ARG* 1.3 61.2 + - - +
195H GLY 3.1 1.2 + - - -
196H GLY 3.2 4.5 + - - -
197H LEU* 3.6 15.6 - - + +
198H ASP 3.8 9.6 - - - +
199H PHE* 3.8 29.2 - - - +
200H THR* 3.8 11.2 - - + +
224H ALA 4.8 0.2 - - - +
225H LEU* 3.8 29.4 - - + -
228H ALA* 3.4 17.0 - - + -
236H LYS* 2.9 38.5 + - + -
237H GLY 3.9 4.5 - - - +
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Residues in contact with ARG 194 (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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68F THR* 3.8 7.4 + - - -
69F MET 4.9 2.4 + - - -
190H TYR* 3.0 46.9 + - + +
191H GLU* 3.0 34.3 + - - +
193H LEU* 1.3 77.0 - - - +
195H GLY* 1.3 61.8 + - - +
196H GLY 3.3 0.4 - - - -
228H ALA* 3.8 4.6 - - + +
231H GLU* 2.9 33.9 + - - +
232H THR* 3.5 23.3 - - + +
414H ALA* 3.8 10.4 - - + +
3I VAL* 4.5 6.5 - - - +
4I TRP* 2.8 54.9 + - - +
5I PRO 3.3 7.1 + - - -
6I ILE* 2.9 21.8 - - - +
17I TYR* 4.3 2.1 + - - -
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Residues in contact with GLY 195 (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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191H GLU 3.6 1.6 + - - -
192H CYS 3.2 4.2 + - - -
193H LEU 3.1 1.4 - - - -
194H ARG* 1.3 81.3 - - - +
196H GLY* 1.3 57.5 + - - +
414H ALA* 3.6 15.0 - - - -
417H ALA* 3.4 19.1 - - - -
418H VAL* 3.2 36.3 + - - +
421H ARG* 4.4 0.2 - - - +
4I TRP* 4.4 4.5 - - - -
17I TYR* 3.7 8.8 - - - -
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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