Contacts of the helix formed by residues 164 - 179 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162E ILE* 3.1 8.3 - - - +
163E HIS* 1.3 84.0 - - - +
165E GLN* 1.3 65.3 + - - +
166E GLU* 3.5 10.8 + - - +
167E GLU* 2.7 35.6 + - - +
168E ALA* 3.0 16.3 + - - +
190E LEU* 3.7 12.0 - - - +
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Residues in contact with GLN 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E SER* 1.3 72.6 - - - +
166E GLU* 1.3 56.3 + - - +
168E ALA* 2.7 30.3 + - - +
169E LEU* 2.8 17.5 + - + +
190E LEU* 3.3 21.0 - - + +
200E MET* 4.1 3.7 - - + +
202E LEU* 4.2 15.7 - - + -
220E ARG* 2.5 39.0 + - - +
312E LEU* 3.5 34.3 - - - +
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Residues in contact with GLU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E SER* 3.5 10.7 + - - +
165E GLN* 1.3 76.2 - - - +
167E GLU* 1.3 61.1 + - - +
168E ALA 2.4 13.5 + - - -
169E LEU* 2.5 29.6 + - + +
170E GLU* 2.8 31.5 + - + +
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Residues in contact with GLU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E ARG* 2.9 31.0 + - - -
161E LYS 3.6 4.0 - - - +
162E ILE* 3.5 15.6 - - + +
163E HIS* 2.4 48.4 + - + +
164E SER* 2.7 32.7 + - - +
166E GLU* 1.3 80.1 + - + +
168E ALA* 1.3 63.5 + - - +
170E GLU* 3.5 14.8 + - - +
171E VAL* 3.3 24.1 + - - +
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Residues in contact with ALA 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ILE* 3.3 18.8 - - + +
164E SER 3.0 9.7 + - - +
165E GLN 2.7 18.8 + - - +
166E GLU 2.4 5.8 + - - -
167E GLU* 1.3 67.7 - - - +
169E LEU* 1.3 62.8 + - - +
170E GLU 2.7 3.3 + - - -
171E VAL* 2.7 17.1 + - - +
172E MET* 3.2 14.0 + - + +
185E ILE* 5.7 5.7 - - + +
190E LEU* 4.0 5.6 - - + -
202E LEU* 3.5 24.5 - - + -
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Residues in contact with LEU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLN* 2.8 27.0 + - + +
166E GLU* 2.5 22.8 + - + +
168E ALA* 1.3 71.8 - - - +
170E GLU* 1.3 61.3 + - + +
172E MET* 3.4 21.0 + - + +
173E ASP* 3.2 27.5 + - - +
202E LEU* 5.0 2.7 - - + -
218E ARG* 3.3 51.6 + - - +
219E ILE 6.1 0.2 - - - +
312E LEU* 4.2 21.3 - - + -
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E ARG* 2.8 35.0 + - - +
166E GLU* 2.8 34.8 + - + +
167E GLU* 3.5 17.4 - - - +
168E ALA 2.7 4.4 + - - -
169E LEU* 1.3 73.2 - - + +
171E VAL* 1.3 53.6 + - - +
173E ASP* 2.6 36.7 + - - +
174E MET* 2.7 21.7 + - + +
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Residues in contact with VAL 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ALA* 3.9 14.8 - - + +
158E THR* 3.1 36.1 - - + +
160E ARG* 4.8 13.2 - - + +
162E ILE* 3.3 23.1 - - + -
167E GLU 3.3 15.0 - - - +
168E ALA* 2.7 12.6 + - - +
170E GLU* 1.3 73.8 - - + +
172E MET* 1.3 51.6 + - + +
174E MET* 3.3 12.1 - - - +
175E LEU* 2.6 52.9 + - + +
185E ILE* 5.5 2.2 - - + -
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Residues in contact with MET 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ALA 3.2 7.0 + - - +
169E LEU* 3.6 36.8 - - + +
170E GLU 3.0 1.0 - - - -
171E VAL* 1.3 74.9 - - - +
173E ASP* 1.3 62.1 + - - +
175E LEU* 3.2 8.5 + - + +
176E HIS* 2.8 37.2 + - - -
183E VAL* 3.4 21.0 - - + +
185E ILE* 4.3 15.5 - - + -
202E LEU* 3.3 53.4 - - + +
203E GLY 4.2 0.7 - - - -
204E SER* 3.6 34.5 - - - -
218E ARG* 5.3 0.4 - - - +
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Residues in contact with ASP 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LEU 3.2 12.5 - - - +
170E GLU* 2.6 22.8 + - - +
172E MET* 1.3 73.5 - - - +
174E MET* 1.3 54.4 + - + +
176E HIS* 3.2 14.1 + - - +
177E SER* 2.8 28.3 + - - -
204E SER* 4.6 0.2 + - - -
206E ARG* 5.6 6.0 + - - +
218E ARG* 2.8 35.5 + - - -
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Residues in contact with MET 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E THR* 3.3 41.3 - - + +
160E ARG* 3.6 33.9 - - + -
170E GLU* 2.7 21.2 + - + +
171E VAL* 3.3 11.4 - - - +
173E ASP* 1.3 75.4 - - + +
175E LEU* 1.3 58.0 + - - +
177E SER* 2.9 30.3 + - - -
178E MET* 3.1 13.4 + - + +
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Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E VAL* 5.2 2.2 - - + -
147E ILE* 3.8 25.8 - - + -
149E PRO* 4.5 2.9 - - + -
154E ALA* 4.6 3.1 - - + +
157E LEU* 4.1 25.1 - - + -
158E THR* 3.4 18.4 - - + -
171E VAL* 2.6 44.4 + - + +
172E MET* 3.3 5.2 - - - +
174E MET* 1.3 70.2 - - - +
176E HIS* 1.3 70.1 + - - +
178E MET* 2.7 29.8 + - - +
179E GLY 3.3 3.1 + - - -
180E PRO* 3.4 7.8 - - - +
183E VAL* 3.6 24.2 - - + -
185E ILE* 4.3 12.6 - - + -
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Residues in contact with HIS 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E MET 2.8 31.8 + - - -
173E ASP* 3.3 12.6 - - - +
175E LEU* 1.3 69.7 - - - +
177E SER* 1.3 56.7 + - - +
179E GLY* 2.5 34.5 + - - +
180E PRO* 2.9 30.2 + - - +
181E ASP* 2.7 33.9 + - - -
182E THR 3.8 1.1 - - - -
183E VAL* 3.8 8.1 - - + +
204E SER* 2.7 43.8 + - - -
205E GLN 4.0 1.0 + - - -
206E ARG* 4.0 30.6 - - + +
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Residues in contact with SER 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ASP 2.8 14.2 + - - -
174E MET* 2.9 19.0 + - - -
176E HIS* 1.3 75.8 - - - +
178E MET* 1.3 63.7 + - - +
179E GLY 3.4 0.3 + - - -
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Residues in contact with MET 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 3.3 44.4 - - + +
141E VAL* 3.8 21.8 - - + -
142E PRO* 3.0 28.9 - - + +
157E LEU* 4.5 7.9 - - + +
158E THR* 4.6 9.2 - - - -
174E MET* 3.2 18.6 - - - +
175E LEU* 2.7 33.4 + - - +
177E SER* 1.3 78.1 - - - +
179E GLY* 1.3 54.9 + - - -
180E PRO* 3.9 1.3 - - - -
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Residues in contact with GLY 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E PRO 3.5 14.8 - - - -
144E ALA 3.6 5.3 - - - +
176E HIS 2.5 19.1 + - - +
177E SER 3.2 1.7 - - - -
178E MET* 1.3 75.3 - - - +
180E PRO* 1.4 71.5 - - - +
181E ASP* 3.5 14.7 + - - +
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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