Contacts of the helix formed by residues 182 - 195 (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 ALA 182 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156H GLN* 5.0 2.0 - - - +
157H VAL* 5.8 4.7 - - + -
181L SER* 1.3 74.4 - - - +
183L LYS* 1.3 62.6 + - - +
185L TYR* 3.3 4.5 + - - +
186L GLY 3.2 17.7 + - - -
211L PHE 4.6 0.4 + - - -
212L MET* 3.7 23.1 - - + +
216L ASP* 3.6 38.6 - - + -
217L ARG* 3.8 6.0 - - - +
220L PHE* 3.7 21.5 - - + +
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Residues in contact with LYS 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H ASP* 3.4 41.1 + - + +
163H ASN* 3.2 22.8 - - - +
165H TYR* 2.8 31.4 + - - +
65I ARG* 4.9 8.9 + - + +
66I TYR* 2.8 43.8 + - + +
100I ARG* 5.7 1.8 - - - +
111I GLN* 3.8 15.8 + - - +
181L SER* 3.3 3.5 + - - +
182L ALA* 1.3 79.7 - - - +
184L ASN* 1.3 61.0 + - - +
187L ARG* 3.1 26.0 + - - +
220L PHE* 3.8 15.5 - - + -
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Residues in contact with ASN 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I PHE* 4.0 13.7 - - - -
109I GLU* 2.8 37.4 - - - +
180L LEU* 4.2 17.1 - - + +
181L SER* 3.2 14.7 + - - +
183L LYS* 1.3 74.0 - - - +
185L TYR* 1.3 65.5 + - - +
187L ARG* 3.0 40.8 + - + +
188L ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L ILE* 3.6 36.8 + - + +
176L PRO 5.1 2.0 - - - -
177L LYS 4.8 4.0 + - - -
180L LEU* 4.1 19.9 - - + +
181L SER 2.9 10.7 + - - +
182L ALA 3.3 10.8 - - - +
184L ASN* 1.3 76.4 - - - +
186L GLY* 1.3 57.0 + - - +
188L ALA* 3.3 6.6 + - - +
189L VAL* 2.9 32.9 + - + +
202L ASP* 3.3 40.5 - - - -
203L ASP 3.3 9.5 + - - -
206L VAL* 3.8 11.2 - - + +
212L MET* 3.6 30.1 - - + -
217L ARG* 3.8 15.7 - - + -
221L CYS* 3.9 16.6 - - - -
238L HIS* 3.9 11.4 - - - -
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Residues in contact with GLY 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I TYR* 3.2 21.0 - - - -
182L ALA 3.2 8.8 + - - -
183L LYS 3.4 0.4 + - - -
185L TYR* 1.3 75.9 - - - +
187L ARG* 1.3 60.1 + - - +
189L VAL* 3.2 5.1 + - - -
190L TYR* 2.9 25.5 + - - +
220L PHE 4.1 9.6 - - - -
221L CYS* 4.5 3.3 - - - -
224L ALA* 3.1 19.0 - - - +
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Residues in contact with ARG 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLU* 2.8 31.3 + - - -
66I TYR* 3.4 19.6 + - + -
69I MET* 3.7 31.0 - - + -
102I ILE* 4.0 5.3 - - - +
104I PHE* 3.5 15.4 - - - -
111I GLN* 2.8 28.9 + - - +
183L LYS* 3.1 37.1 + - - +
184L ASN* 3.0 35.2 - - + +
185L TYR 3.3 0.2 - - - -
186L GLY* 1.3 76.2 - - - +
188L ALA* 1.3 65.6 + - - +
190L TYR* 3.4 4.7 + - - +
191L GLU* 3.3 31.0 + - + +
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Residues in contact with ALA 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L ILE* 4.1 23.6 - - + -
180L LEU* 5.2 3.6 - - + -
184L ASN 3.0 12.1 + - - +
185L TYR* 3.6 8.1 - - - +
187L ARG* 1.3 80.7 - - + +
189L VAL* 1.3 62.6 + - - +
191L GLU* 3.4 1.0 + - - -
192L CYS* 3.1 23.4 + - - -
407L LEU* 4.7 5.6 - - + -
413L ASN* 3.2 27.0 + - - +
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Residues in contact with VAL 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L ILE* 4.0 12.6 - - + -
185L TYR* 2.9 21.9 + - + +
186L GLY* 3.5 10.5 - - - +
187L ARG 3.2 0.2 - - - -
188L ALA* 1.3 73.6 - - - +
190L TYR* 1.3 66.4 + - - +
192L CYS* 3.3 2.6 + - - +
193L LEU* 3.0 37.9 + - + +
200L THR* 3.3 22.9 - - - +
221L CYS* 4.2 14.1 - - - +
224L ALA* 4.0 12.1 - - + -
238L HIS* 3.4 35.0 - - + +
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Residues in contact with TYR 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I TYR* 5.0 6.5 - + + -
67I TRP 3.8 12.8 - - - -
68I THR* 3.2 30.7 - - - +
186L GLY 2.9 16.2 + - - +
187L ARG* 3.9 5.2 - - - +
188L ALA 3.4 0.2 - - - -
189L VAL* 1.3 75.3 - - - +
191L GLU* 1.3 83.8 + - + +
193L LEU* 3.9 0.5 - - - +
194L ARG* 3.0 46.8 + - + +
224L ALA* 3.8 20.6 - - + -
227L LYS* 3.4 35.6 - - + -
228L ALA* 3.8 21.5 - - + -
231L GLU* 2.6 29.5 + - - -
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Residues in contact with GLU 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I TRP 4.3 0.9 - - - +
68I THR* 3.7 1.0 - - - -
69I MET* 2.9 49.0 + - + +
187L ARG* 3.3 23.3 + - + +
188L ALA* 3.8 1.8 - - - +
190L TYR* 1.3 91.4 - - + +
192L CYS* 1.3 62.2 + - - +
194L ARG* 3.0 36.5 + - - +
413L ASN* 3.6 22.9 - - + +
414L ALA* 3.1 32.1 + - - +
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Residues in contact with CYS 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L CYS* 3.8 24.2 - - - -
174L ILE* 4.2 9.6 - - - -
188L ALA 3.1 20.2 + - - +
189L VAL 3.3 0.4 + - - +
191L GLU* 1.3 75.0 - - - +
193L LEU* 1.3 65.4 + - - +
195L GLY 3.2 1.9 + - - -
197L LEU* 3.8 14.6 + - + +
200L THR* 3.5 19.1 - - + -
406L THR* 4.0 6.3 - - - -
407L LEU* 4.3 2.2 - - - -
413L ASN* 3.5 29.6 - - - -
417L ALA* 3.2 24.2 - - - +
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Residues in contact with LEU 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 3.0 38.2 + - + +
192L CYS* 1.3 77.8 - - - +
194L ARG* 1.3 62.6 + - - +
195L GLY 3.1 1.0 + - - -
196L GLY 3.2 4.9 + - - -
197L LEU* 3.6 16.1 - - + +
198L ASP 3.8 9.4 - - - +
199L PHE* 3.8 29.2 - - - +
200L THR* 3.8 10.8 - - + +
225L LEU* 3.8 29.6 - - + -
228L ALA* 3.4 16.6 - - + -
236L LYS* 2.9 38.6 + - + -
237L GLY 3.9 4.7 - - - +
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Residues in contact with ARG 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I THR* 3.8 8.2 + - - -
69I MET 4.9 2.2 + - - -
190L TYR* 3.0 48.2 + - + +
191L GLU* 3.0 34.0 + - - +
193L LEU* 1.3 75.6 - - - +
195L GLY* 1.3 61.5 + - - +
196L GLY 3.3 1.3 + - - -
228L ALA* 3.8 5.3 - - + +
231L GLU* 2.9 34.9 + - - +
232L THR* 3.5 22.3 - - + +
414L ALA* 3.8 9.8 - - + +
3S VAL* 4.5 6.1 - - - +
4S TRP* 2.8 56.0 + - + +
5S PRO 3.3 7.1 + - - -
6S ILE* 2.9 21.4 - - - +
17S TYR* 4.3 2.3 + - - -
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Residues in contact with GLY 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L GLU 3.6 0.8 + - - -
192L CYS 3.2 4.2 + - - -
193L LEU 3.1 1.8 - - - -
194L ARG* 1.3 81.8 - - - +
196L GLY* 1.3 56.2 + - - +
414L ALA* 3.6 15.3 - - - -
417L ALA* 3.4 18.6 - - - +
418L VAL* 3.2 35.9 + - - +
421L ARG* 4.4 0.2 - - - +
4S TRP* 4.4 4.5 - - - -
17S TYR* 3.7 9.0 - - - -
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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