Contacts of the helix formed by residues 164 - 179 (chain G) in PDB entry 1RFU
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 SER 164 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162G ILE* 3.2 7.1 - - - +
163G HIS* 1.3 84.8 - - - +
165G GLN* 1.3 65.7 + - - +
166G GLU* 3.4 10.9 + - - +
167G GLU* 2.6 39.3 + - - +
168G ALA* 3.0 17.0 + - - +
190G LEU* 3.8 11.3 - - - +
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Residues in contact with GLN 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G SER* 1.3 72.1 - - - +
166G GLU* 1.3 67.6 + - - +
168G ALA* 2.7 20.4 + - - +
169G LEU* 2.8 16.1 + - + +
190G LEU* 3.3 21.0 - - + +
200G MET* 4.2 4.3 - - - +
202G LEU* 4.2 16.8 - - + -
220G ARG* 2.5 39.5 + - - +
312G LEU* 3.4 34.3 - - - +
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Residues in contact with GLU 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G SER* 3.4 10.3 + - - +
165G GLN* 1.3 77.2 - - - +
167G GLU* 1.3 62.3 + - - +
168G ALA 2.5 13.3 + - - -
169G LEU* 2.5 27.9 + - + +
170G GLU* 2.8 30.9 + - + +
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Residues in contact with GLU 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G ARG* 2.9 32.1 + - - -
161G LYS 3.8 2.6 - - - +
162G ILE* 3.5 15.2 - - + +
163G HIS* 2.5 48.6 + - + +
164G SER* 2.6 38.5 + - - +
166G GLU* 1.3 76.3 + - - +
168G ALA* 1.3 63.4 + - - +
170G GLU* 3.6 15.5 - - - +
171G VAL* 3.2 24.4 + - - +
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Residues in contact with ALA 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G ILE* 3.2 19.2 - - + +
164G SER 3.0 10.7 + - - +
165G GLN 2.7 15.1 + - - +
166G GLU 2.5 3.6 + - - -
167G GLU* 1.3 69.2 - - - +
169G LEU* 1.3 65.3 + - - +
170G GLU 2.9 1.6 - - - -
171G VAL* 2.7 19.3 + - - +
172G MET* 3.2 14.6 + - + +
185G ILE* 5.7 5.9 - - + +
188G SER* 6.4 0.9 - - - -
190G LEU* 4.0 5.2 - - + -
202G LEU* 3.5 23.6 - - + -
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Residues in contact with LEU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G GLN* 2.8 22.8 + - + +
166G GLU* 2.5 21.7 + - + +
168G ALA* 1.3 70.9 - - - +
170G GLU* 1.3 61.5 + - + +
172G MET* 3.3 22.7 + - + +
173G ASP* 3.1 28.5 + - - +
202G LEU* 5.1 2.9 - - + -
218G ARG* 3.3 51.9 + - - +
312G LEU* 4.1 27.1 - - + -
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Residues in contact with GLU 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G ARG* 2.8 33.6 + - - +
166G GLU* 2.8 35.5 + - + +
167G GLU* 3.6 18.2 - - - +
168G ALA 2.7 4.0 + - - -
169G LEU* 1.3 73.8 - - + +
171G VAL* 1.3 51.2 + - - +
173G ASP* 2.6 36.6 + - - +
174G MET* 2.7 22.0 + - + +
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Residues in contact with VAL 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ALA* 3.8 15.5 - - + +
158G THR* 3.0 35.0 - - + +
160G ARG* 4.8 13.0 - - + +
162G ILE* 3.3 22.4 - - + -
167G GLU 3.2 16.2 - - - +
168G ALA 2.7 12.5 + - - +
170G GLU* 1.3 72.7 - - + +
172G MET* 1.3 50.5 + - + +
174G MET* 3.3 12.6 - - - +
175G LEU* 2.6 53.6 + - + +
185G ILE* 5.4 2.7 - - + -
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Residues in contact with MET 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ALA* 3.2 7.9 + - + +
169G LEU* 3.5 38.1 - - + +
170G GLU 3.0 0.8 - - - -
171G VAL* 1.3 73.1 - - - +
173G ASP* 1.3 57.2 + - - +
175G LEU* 3.4 7.5 - - - +
176G HIS* 2.8 41.9 + - - -
183G VAL* 3.3 21.5 - - + +
185G ILE* 4.2 16.2 - - + -
202G LEU* 3.3 53.6 - - + +
203G GLY 4.2 0.4 - - - -
204G SER* 3.6 36.1 - - - -
218G ARG* 5.4 0.2 - - - +
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Residues in contact with ASP 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G LEU* 3.1 13.9 + - - +
170G GLU* 2.6 24.0 + - - +
172G MET* 1.3 73.1 - - - +
174G MET* 1.3 54.8 + - + +
176G HIS* 3.1 10.4 + - - +
177G SER* 2.9 28.7 + - - -
204G SER* 4.7 3.1 + - - -
206G ARG* 5.6 6.2 + - - +
218G ARG* 2.8 34.7 + - - -
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Residues in contact with MET 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G THR* 3.3 43.1 - - + +
160G ARG* 3.6 33.7 - - - -
170G GLU* 2.7 22.0 + - + +
171G VAL* 3.3 10.8 - - - +
173G ASP* 1.3 75.7 - - + +
175G LEU* 1.3 61.8 + - - +
177G SER* 3.0 23.3 + - - -
178G MET* 3.2 16.1 + - - +
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Residues in contact with LEU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G VAL* 5.1 2.9 - - + -
147G ILE* 3.7 25.4 - - + -
149G PRO* 4.4 3.4 - - + -
154G ALA* 4.6 2.5 - - + +
157G LEU* 4.1 26.2 - - + -
158G THR* 3.4 18.4 - - + -
171G VAL* 2.6 43.9 + - + +
172G MET* 3.4 4.9 - - - +
174G MET* 1.3 69.9 - - - +
176G HIS* 1.3 69.2 + - - +
178G MET* 2.7 29.8 + - - +
179G GLY 3.3 2.9 + - - -
180G PRO* 3.4 8.5 - - - +
183G VAL* 3.6 23.1 - - + -
185G ILE* 4.3 13.5 - - + -
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Residues in contact with HIS 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G MET 2.8 30.9 + - - -
173G ASP* 3.2 13.7 - - - +
175G LEU* 1.3 70.3 - - - +
177G SER* 1.3 54.6 + - - +
178G MET 2.8 0.5 + - - -
179G GLY* 2.5 34.8 + - - +
180G PRO* 2.8 29.3 + - - +
181G ASP* 2.6 34.6 + - - -
182G THR 3.7 0.9 - - - -
183G VAL* 3.7 8.7 - - + +
204G SER* 2.7 43.8 + - - -
205G GLN 4.0 1.2 + - - -
206G ARG* 4.0 31.5 - - + +
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Residues in contact with SER 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G ASP 2.9 11.6 + - - -
174G MET* 3.0 18.7 + - - -
176G HIS* 1.3 74.8 - - - +
178G MET* 1.3 61.8 + - - +
179G GLY 3.6 0.2 + - - -
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Residues in contact with MET 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ARG* 3.2 44.6 - - + +
141G VAL* 3.8 22.0 - - + -
142G PRO* 3.0 28.2 - - + +
157G LEU* 4.5 10.8 - - - +
158G THR* 4.6 7.6 - - - -
174G MET* 3.2 16.2 - - - +
175G LEU* 2.7 30.0 + - - +
177G SER* 1.3 77.7 - - - +
179G GLY* 1.3 57.9 + - - +
180G PRO* 3.9 1.6 - - - -
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Residues in contact with GLY 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G PRO 3.5 15.3 - - - -
144G ALA 3.6 5.9 - - - +
176G HIS 2.5 18.9 + - - +
177G SER 3.2 0.8 - - - -
178G MET* 1.3 74.4 - - - +
180G PRO* 1.3 71.2 - - - +
181G ASP* 3.5 14.2 + - - +
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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