Contacts of the helix formed by residues 159 - 183 (chain H) in PDB entry 2R9R
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 159 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLN* 5.7 2.1 + - - -
152H LEU* 4.8 5.2 - - - +
156H PRO 3.4 5.2 - - - +
157H GLU* 3.0 4.6 - - - -
158H SER* 1.3 91.5 + - - +
160H GLY* 1.3 66.0 + - - +
161H PRO* 3.4 17.5 - - - +
162H ALA* 3.2 23.2 + - - +
163H ARG* 3.3 9.1 + - - +
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Residues in contact with GLY 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H SER* 1.3 72.0 - - - +
161H PRO* 1.3 70.7 - - - +
163H ARG* 3.1 24.0 + - - +
164H ILE* 3.2 18.0 + - - +
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Residues in contact with PRO 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 4.8 12.3 - - + -
159H SER* 3.4 15.7 - - - +
160H GLY* 1.3 87.2 - - - +
162H ALA* 1.3 63.4 + - - +
164H ILE* 3.2 13.9 + - + +
165H ILE* 3.1 30.3 + - + +
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Residues in contact with ALA 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 3.7 24.6 - - - +
155H TYR 3.6 7.9 - - - +
156H PRO* 3.4 16.5 - - + +
158H SER* 3.2 27.6 - - - +
159H SER* 3.2 14.7 + - - +
160H GLY 3.2 0.2 - - - -
161H PRO* 1.3 80.7 - - - +
163H ARG* 1.3 62.6 + - - +
165H ILE* 3.4 4.7 + - - +
166H ALA* 3.2 19.8 + - - +
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Residues in contact with ARG 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H PRO* 3.1 20.6 - - + +
157H GLU* 3.0 36.8 + - - +
159H SER 3.3 8.0 + - - +
160H GLY* 3.1 15.0 + - - +
162H ALA* 1.3 77.8 - - - +
164H ILE* 1.3 57.7 + - + +
166H ALA* 2.9 9.4 + - - +
167H ILE* 2.8 44.2 + - + +
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Residues in contact with ILE 164 (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 GLY 3.2 17.3 - - - +
161H PRO* 3.3 15.3 - - + +
163H ARG* 1.3 78.3 - - + +
165H ILE* 1.3 59.0 + - + +
167H ILE* 3.2 9.0 + - + +
168H VAL* 2.9 46.0 + - + +
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Residues in contact with ILE 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 3.1 51.8 - - + +
153H PHE* 3.7 36.1 - - + -
161H PRO* 3.1 15.6 + - + +
162H ALA 3.6 5.8 - - - +
163H ARG 3.2 0.2 - - - -
164H ILE* 1.3 77.5 - - + +
166H ALA* 1.3 53.3 + - - +
168H VAL* 3.6 7.4 + - - +
169H SER* 2.8 39.1 + - - +
232H TRP* 3.9 15.4 - - + -
236H GLU* 5.3 0.4 - - - +
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Residues in contact with ALA 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H PRO* 4.0 27.1 - - + -
162H ALA 3.2 9.7 + - - +
163H ARG* 2.9 10.0 + - - +
165H ILE* 1.3 78.0 - - - +
167H ILE* 1.3 67.9 + - + +
169H SER* 3.2 4.7 + - - -
170H VAL* 3.1 28.4 + - - +
306H HIS* 4.0 20.8 - - + +
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Residues in contact with ILE 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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163H ARG* 2.8 30.4 + - + +
164H ILE* 3.7 9.2 - - + +
166H ALA* 1.3 74.3 - - + +
168H VAL* 1.3 64.2 + - + +
170H VAL* 3.3 10.1 + - + +
171H MET* 3.0 42.3 + - + +
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Residues in contact with VAL 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H ILE* 2.9 34.7 + - + +
165H ILE* 3.8 6.1 - - - +
167H ILE* 1.3 77.6 - - + +
169H SER* 1.3 58.4 - - - +
171H MET* 3.2 9.0 + - + +
172H VAL* 2.9 45.6 + - + +
232H TRP* 3.7 29.2 - - + -
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Residues in contact with SER 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H ILE* 2.8 21.2 + - - +
166H ALA* 3.2 10.6 + - - -
168H VAL* 1.3 77.6 - - - +
170H VAL* 1.3 58.7 + - - +
172H VAL* 3.5 2.4 + - - +
173H ILE* 2.9 35.1 + - - +
232H TRP* 3.5 19.6 + - - +
233H PHE* 5.0 0.7 - - - -
236H GLU* 2.7 29.8 + - - -
306H HIS* 3.8 17.0 - - - -
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Residues in contact with VAL 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H ALA 3.1 16.4 + - - +
167H ILE* 3.6 11.7 - - + +
168H VAL 3.2 0.2 - - - -
169H SER* 1.3 73.2 - - - +
171H MET* 1.3 76.0 + - + +
173H ILE* 3.3 8.3 + - - +
174H LEU* 2.9 38.0 + - + +
303H LEU* 4.3 14.6 - - + -
306H HIS* 3.8 30.7 - - + +
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Residues in contact with MET 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ILE* 3.0 29.6 + - + +
168H VAL* 3.5 9.9 - - + +
170H VAL* 1.3 94.7 - - + +
172H VAL* 1.3 58.0 + - + +
174H LEU* 3.4 18.1 + - + +
175H ILE* 2.9 44.2 + - + +
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Residues in contact with VAL 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H VAL* 2.9 36.2 + - + +
169H SER 3.8 4.5 - - - +
171H MET* 1.3 73.6 - - + +
173H ILE* 1.3 60.8 + - - +
175H ILE* 3.4 9.7 + - + +
176H SER* 2.9 27.7 + - - -
229H CYS* 3.9 27.2 - - - -
232H TRP* 4.1 24.5 - - + -
233H PHE* 3.6 20.2 - - + -
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Residues in contact with ILE 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H SER* 2.9 28.1 + - - +
170H VAL 3.6 4.0 - - - +
171H MET 3.3 0.2 - - - -
172H VAL* 1.3 77.5 - - - +
174H LEU* 1.3 63.8 + - - +
176H SER* 2.6 25.0 + - - +
177H ILE* 3.1 20.0 + - + +
233H PHE* 3.9 18.8 - - + -
236H GLU* 5.8 1.1 - - - +
299H ARG 3.7 20.6 - - - +
302H LYS* 3.5 39.0 - - + +
303H LEU* 3.7 30.5 - - + -
306H HIS* 4.4 9.6 - - + +
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Residues in contact with LEU 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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170H VAL* 2.9 29.0 + - + +
171H MET* 3.7 24.7 - - + +
173H ILE* 1.3 76.5 - - - +
175H ILE* 1.3 63.4 + - + +
177H ILE* 3.3 11.8 + - + +
178H VAL* 3.1 32.1 + - + +
303H LEU* 4.2 26.0 - - + -
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Residues in contact with ILE 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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171H MET* 2.9 30.7 + - + +
172H VAL* 3.7 8.5 - - + +
174H LEU* 1.3 76.9 - - + +
176H SER* 1.3 60.2 + - - +
178H VAL* 3.9 5.6 - - + +
179H SER* 2.9 29.1 + - - -
225H VAL* 4.0 22.4 - - + -
229H CYS* 4.1 7.4 - - - -
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Residues in contact with SER 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H VAL 2.9 15.6 + - - -
173H ILE* 2.6 23.4 + - - -
175H ILE* 1.3 77.7 - - - +
177H ILE* 1.3 55.9 + - - +
179H SER* 4.1 4.1 - - - -
180H PHE* 3.2 18.0 + - - +
226H GLU* 5.4 0.4 - - - -
229H CYS* 3.8 23.8 - - - -
233H PHE* 3.6 7.6 - - - -
299H ARG* 2.8 51.8 + - - +
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Residues in contact with ILE 177 (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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173H ILE* 3.1 32.2 + - + +
174H LEU* 3.6 19.3 - - + +
175H ILE 3.1 0.2 - - - -
176H SER* 1.3 79.8 - - - +
178H VAL* 1.3 69.0 + - + +
180H PHE* 3.1 7.2 + - - +
181H CYS* 2.9 35.0 + - - -
297H ILE* 4.9 10.3 - - + -
299H ARG* 4.3 14.8 - - + +
300H ILE* 3.3 37.9 - - + -
303H LEU* 4.6 2.5 - - + -
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Residues in contact with VAL 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H LEU* 3.1 19.1 + - + +
175H ILE* 3.9 6.3 - - - +
177H ILE* 1.3 79.3 - - + +
179H SER* 1.3 58.7 + - - +
181H CYS* 3.3 6.4 + - - +
182H LEU* 3.0 54.1 + - + +
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Residues in contact with SER 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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175H ILE* 2.9 18.6 + - - -
176H SER* 4.2 4.5 - - - -
178H VAL* 1.3 76.9 - - - +
180H PHE* 1.3 64.6 + - - +
182H LEU* 3.3 9.8 + - - +
183H GLU* 3.2 28.9 + - - +
222H PHE* 3.8 19.2 + - - -
225H VAL* 3.6 32.2 - - - +
226H GLU* 4.9 4.1 + - - +
296H ARG* 6.2 0.2 - - - -
299H ARG* 5.9 0.4 - - - -
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Residues in contact with PHE 180 (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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176H SER 3.2 18.8 + - - +
177H ILE* 3.1 7.5 + - - +
179H SER* 1.3 78.1 - - - +
181H CYS* 1.3 69.3 + - - +
183H GLU* 3.4 24.8 - - - +
184H THR* 4.3 7.3 - - - +
293H ARG* 3.4 37.9 + - + -
294H ILE* 4.8 3.8 - - - -
296H ARG* 3.4 41.2 - - + +
297H ILE* 3.7 44.4 - - + -
299H ARG* 4.1 8.5 - - - +
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Residues in contact with CYS 181 (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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177H ILE* 2.9 32.3 + - - +
178H VAL* 3.7 6.7 - - - +
180H PHE* 1.3 84.4 - - - +
182H LEU* 1.3 63.9 + - + +
183H GLU 3.0 4.9 - - - -
184H THR* 2.7 29.8 + - - -
185H LEU* 4.0 4.4 + - - +
297H ILE* 5.4 3.8 - - - -
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Residues in contact with LEU 182 (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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178H VAL* 3.0 40.0 + - + +
179H SER* 3.3 7.8 + - - +
181H CYS* 1.3 77.6 - - + +
183H GLU* 1.3 61.2 + - - +
184H THR 3.0 2.1 + - - -
185H LEU* 3.1 37.5 + - + -
188H PHE* 3.2 30.3 - - + -
222H PHE* 4.1 14.1 - - + -
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Residues in contact with GLU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H SER* 3.2 24.6 + - - +
180H PHE* 3.4 13.3 - - - +
181H CYS 3.0 0.4 - - - -
182H LEU* 1.3 76.4 - - - +
184H THR* 1.3 59.6 + - - +
185H LEU 4.9 0.4 - - - -
188H PHE* 5.3 1.2 - - - +
189H ARG* 4.0 18.0 + - - +
211H GLY* 3.2 36.6 - - - +
212H TYR* 3.9 7.9 - - - -
222H PHE* 3.6 29.7 - - + +
226H GLU* 5.0 0.7 - - - +
293H ARG* 3.8 15.3 + - - +
296H ARG* 2.9 43.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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