Contacts of the helix formed by residues 164 - 179 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H ILE* 3.1 7.8 - - - +
163H HIS* 1.3 84.2 - - - +
165H GLN* 1.3 65.9 + - - +
166H GLU* 3.6 10.4 + - - +
167H GLU* 2.6 35.7 + - - +
168H ALA 3.0 16.3 + - - -
190H LEU* 3.7 12.0 - - - +
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Residues in contact with GLN 165 (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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164H SER* 1.3 72.6 - - - +
166H GLU* 1.3 55.3 + - - +
168H ALA* 2.6 30.3 + - - +
169H LEU* 2.8 20.1 + - + +
190H LEU* 3.1 21.2 - - + +
200H MET* 4.2 3.8 - - - +
202H LEU* 4.3 15.5 - - + -
220H ARG* 2.5 40.7 + - - +
312H LEU* 3.6 30.6 - - - +
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H SER* 3.6 10.6 + - - +
165H GLN* 1.3 74.4 - - - +
167H GLU* 1.3 70.8 + - - +
168H ALA 2.5 5.7 + - - -
169H LEU* 2.6 26.9 + - + +
170H GLU* 2.8 33.0 + - + +
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Residues in contact with GLU 167 (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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160H ARG* 3.0 32.3 + - - -
161H LYS 3.7 3.3 - - - +
162H ILE* 3.4 15.4 - - + +
163H HIS* 2.6 48.1 + - + +
164H SER* 2.6 33.8 + - - +
166H GLU* 1.3 80.3 - - + +
168H ALA* 1.3 64.5 + - - +
170H GLU* 3.6 14.5 + - - +
171H VAL* 3.3 24.1 + - - +
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Residues in contact with ALA 168 (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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162H ILE* 3.2 18.6 - - + +
164H SER 3.0 8.4 + - - +
165H GLN 2.6 17.8 + - - +
166H GLU 2.5 3.8 + - - -
167H GLU* 1.3 68.6 - - - +
169H LEU* 1.3 65.9 + - - +
170H GLU 2.7 3.4 + - - -
171H VAL* 2.8 16.7 + - - +
172H MET* 3.2 16.0 + - + +
185H ILE* 5.8 5.3 - - + +
188H SER* 6.4 0.4 - - - -
190H LEU* 4.0 5.6 - - + -
202H LEU* 3.4 24.2 - - + -
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Residues in contact with LEU 169 (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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165H GLN* 2.8 30.2 + - + +
166H GLU* 2.6 22.2 + - + +
168H ALA* 1.3 71.2 - - - +
170H GLU* 1.3 62.5 + - + +
172H MET* 3.4 21.0 + - + +
173H ASP* 3.0 28.0 + - - +
202H LEU* 5.1 2.5 - - + -
218H ARG* 3.4 51.3 + - - +
312H LEU* 4.2 20.2 - - + -
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Residues in contact with GLU 170 (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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160H ARG* 2.8 35.5 + - - +
166H GLU* 2.8 39.2 + - + +
167H GLU* 3.7 18.4 - - - +
168H ALA 2.7 4.4 + - - -
169H LEU* 1.3 69.5 - - + +
171H VAL* 1.3 51.9 + - - +
173H ASP* 2.5 38.4 + - - +
174H MET* 2.7 21.3 + - + +
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Residues in contact with VAL 171 (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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154H ALA* 3.9 15.5 - - + +
158H THR* 3.0 35.4 - - + +
160H ARG* 4.7 11.9 - - + +
162H ILE* 3.3 32.1 - - + -
167H GLU* 3.3 6.1 - - - +
168H ALA* 2.8 12.0 + - - +
170H GLU* 1.3 73.2 - - - +
172H MET* 1.3 50.9 + - - +
174H MET* 3.3 14.3 - - - +
175H LEU* 2.6 53.8 + - + +
185H ILE* 5.4 2.0 - - + -
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Residues in contact with MET 172 (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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168H ALA 3.2 7.2 + - - +
169H LEU* 3.6 33.0 - - + +
170H GLU 2.9 1.0 + - - -
171H VAL* 1.3 74.4 - - - +
173H ASP* 1.3 58.8 + - - +
175H LEU* 3.4 8.4 - - + +
176H HIS* 2.7 40.8 + - - -
183H VAL* 3.3 22.3 - - + +
185H ILE* 4.1 15.7 - - + -
202H LEU* 3.2 58.8 - - + +
203H GLY 4.1 0.9 - - - -
204H SER* 3.8 33.4 - - - +
218H ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 173 (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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169H LEU 3.0 14.9 + - - +
170H GLU* 2.5 24.4 + - - +
172H MET* 1.3 73.1 - - - +
174H MET* 1.3 54.8 - - + +
176H HIS* 3.4 14.1 - - - +
177H SER* 2.9 27.9 + - - -
206H ARG* 5.9 4.0 + - - +
218H ARG* 2.8 34.8 + - - -
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Residues in contact with MET 174 (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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158H THR* 3.5 39.7 - - + +
160H ARG* 3.5 35.9 - - + -
170H GLU* 2.7 20.0 + - + +
171H VAL* 3.3 11.9 - - - +
173H ASP* 1.3 72.2 - - + +
175H LEU* 1.3 65.8 + - - +
177H SER* 3.0 22.8 + - - -
178H MET* 3.1 16.2 + - - +
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Residues in contact with LEU 175 (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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141H VAL* 5.1 2.7 - - + -
147H ILE* 3.7 25.1 - - + -
149H PRO* 4.6 2.0 - - + -
154H ALA* 4.6 1.8 - - + +
157H LEU* 4.1 25.8 - - + -
158H THR* 3.5 17.7 - - + -
171H VAL* 2.6 47.5 + - + +
172H MET* 3.4 11.4 - - - +
174H MET* 1.3 68.9 - - - +
176H HIS* 1.3 69.2 + - - +
178H MET* 2.6 30.2 + - - +
179H GLY 3.3 2.4 + - - -
180H PRO* 3.5 7.3 - - - +
183H VAL* 3.6 16.8 - - + -
185H ILE* 4.3 13.2 - - + -
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Residues in contact with HIS 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H MET 2.7 30.5 + - - -
173H ASP* 3.4 13.9 - - - +
175H LEU* 1.3 69.8 - - - +
177H SER* 1.3 54.4 + - - +
178H MET 2.8 0.5 + - - -
179H GLY* 2.4 35.7 + - - +
180H PRO* 2.9 29.8 + - - +
181H ASP* 2.7 35.3 + - - -
182H THR 3.7 1.1 - - - -
183H VAL* 3.8 7.6 - - + +
204H SER* 2.7 41.1 + - - -
205H GLN* 3.9 1.6 + - - -
206H ARG* 3.9 33.0 - - + +
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Residues in contact with SER 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ASP 2.9 10.9 + - - -
174H MET* 3.0 18.1 + - - -
176H HIS* 1.3 79.2 - - - +
178H MET* 1.3 60.5 + - - +
179H GLY* 3.2 0.7 + - - -
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Residues in contact with MET 178 (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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137H ARG* 3.3 44.4 - - + +
141H VAL* 3.8 19.1 - - + -
142H PRO* 3.0 29.0 - - + +
157H LEU* 4.4 8.5 - - + +
158H THR* 4.5 16.4 - - - -
174H MET* 3.1 16.6 - - - +
175H LEU* 2.6 29.9 + - - +
177H SER* 1.3 76.5 - - - +
179H GLY* 1.3 53.5 + - - -
180H PRO* 3.9 1.8 - - - -
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Residues in contact with GLY 179 (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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142H PRO 3.4 14.4 - - - -
144H ALA 3.6 5.5 - - - +
176H HIS 2.4 18.3 + - - +
177H SER 3.2 1.9 - - - -
178H MET* 1.3 74.3 - - - +
180H PRO* 1.3 71.3 - - - +
181H 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