Contacts of the helix formed by residues 164 - 181 (chain U) in PDB entry 5IYB
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 ASP 164 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163U ALA* 1.3 72.0 - - - +
165U GLU* 1.3 64.2 + - - +
166U GLU* 3.9 17.2 + - - +
167U GLU* 3.1 36.5 + - + +
168U LEU* 3.1 27.2 + - - +
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Residues in contact with GLU 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149U ALA* 4.0 22.5 - - - +
152U LEU* 3.4 30.5 - - + +
153U ARG* 3.2 28.9 + - + +
158U TYR* 3.8 26.8 - - + -
163U ALA* 3.4 11.4 + - - +
164U ASP* 1.3 77.5 - - - +
166U GLU* 1.3 78.3 + - - +
168U LEU* 4.4 4.9 - - - -
169U GLY* 2.9 24.1 + - - -
211U LEU* 4.3 15.7 - - + -
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Residues in contact with GLU 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145U ARG* 5.6 1.4 - - - +
149U ALA* 3.8 23.8 - - + +
153U ARG* 2.3 35.2 + - - +
164U ASP* 3.3 12.1 + - - +
165U GLU* 1.3 90.5 - - - +
167U GLU* 1.3 58.8 + - - +
169U GLY* 3.6 0.9 + - - -
170U SER* 2.8 32.3 + - - -
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Residues in contact with GLU 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132U ARG* 2.4 37.5 + - - -
133U ALA* 4.5 10.5 - - + +
164U ASP* 3.1 33.2 + - + +
166U GLU* 1.3 74.9 - - - +
168U LEU* 1.3 60.6 + - - +
170U SER* 3.2 8.3 + - - -
171U GLN* 2.9 42.4 + - - +
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Residues in contact with LEU 168 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U LEU* 4.8 9.9 - - + -
164U ASP 3.1 17.0 + - - +
165U GLU* 3.9 4.9 - - - +
167U GLU* 1.3 76.2 - - - +
169U GLY* 1.3 53.1 + - - +
171U GLN* 3.1 15.3 + - + +
172U ILE* 2.8 45.0 + - + +
210U VAL* 3.8 36.3 - - + +
211U LEU* 4.7 13.2 - - + +
213U GLY* 6.2 1.3 - - - -
215U ILE 5.3 3.4 - - - +
217U PRO* 4.1 31.9 - - + -
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Residues in contact with GLY 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145U ARG* 5.2 5.4 - - - -
148U LEU* 3.8 17.7 - - - +
149U ALA 5.1 2.5 - - - -
152U LEU* 4.2 6.0 - - - +
165U GLU 2.9 18.8 + - - -
166U GLU* 3.8 1.8 - - - -
168U LEU* 1.3 73.6 - - - +
170U SER* 1.3 57.1 + - - +
172U ILE* 3.3 14.4 + - - +
173U GLU* 2.9 29.6 + - - +
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Residues in contact with SER 170 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133U ALA* 4.2 14.5 - - - +
145U ARG* 3.6 42.9 + - - +
166U GLU 2.8 20.3 + - - -
167U GLU* 3.4 10.8 - - - -
169U GLY* 1.3 75.2 - - - +
171U GLN* 1.3 57.8 + - - +
173U GLU* 3.6 3.6 + - - +
174U GLU* 3.0 28.8 + - - +
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Residues in contact with GLN 171 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132U ARG 5.3 5.1 - - - +
133U ALA* 3.8 17.9 - - + +
167U GLU* 2.9 38.8 + - - +
168U LEU* 3.1 16.3 + - - +
170U SER* 1.3 75.4 - - - +
172U ILE* 1.3 57.9 + - - +
174U GLU* 3.8 5.6 - - - +
175U ALA* 2.9 31.0 + - - +
217U PRO* 3.8 27.2 - - + +
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Residues in contact with ILE 172 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U LEU* 4.3 13.9 - - + -
152U LEU* 4.5 11.2 - - + -
168U LEU* 2.8 37.1 + - + +
169U GLY* 3.4 15.5 - - - +
171U GLN* 1.3 71.7 - - - +
173U GLU* 1.3 57.4 + - - +
175U ALA* 3.2 4.9 + - - +
176U ILE* 2.9 50.0 + - + +
198U LEU* 5.2 3.8 - - + -
210U VAL* 5.1 6.3 - - + -
217U PRO* 3.8 21.0 - - + +
220U PHE* 3.5 44.4 - - + -
221U ALA 5.6 0.4 - - - +
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Residues in contact with GLU 173 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141U ARG* 2.7 51.2 + - - +
144U CYS* 5.0 2.2 - - + -
145U ARG* 3.2 41.9 + - + +
148U LEU* 4.0 15.7 - - + -
169U GLY 2.9 17.5 + - - +
170U SER 3.8 2.5 - - - +
172U ILE* 1.3 76.3 - - - +
174U GLU* 1.3 64.3 + - - +
176U ILE* 3.3 10.3 + - - +
177U TYR* 2.9 24.9 + - - +
187U TYR* 2.7 27.1 + - - +
191U VAL* 5.6 1.1 - - + -
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Residues in contact with GLU 174 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134U PRO* 4.6 31.1 - - + +
136U THR* 5.0 1.6 - - - +
141U ARG* 3.2 20.5 + - - -
145U ARG* 4.1 9.6 + - - +
170U SER 3.0 19.2 + - - +
171U GLN* 3.8 7.2 - - - +
173U GLU* 1.3 79.9 + - - +
175U ALA* 1.3 53.1 + - - +
177U TYR* 3.1 13.0 + - - +
178U GLN* 2.8 56.4 + - - +
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Residues in contact with ALA 175 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171U GLN 2.9 19.4 + - - +
172U ILE 3.5 4.7 - - - +
174U GLU* 1.3 73.1 - - - +
176U ILE* 1.3 64.9 + - - +
178U GLN* 3.4 27.4 + - - +
179U GLU* 3.6 6.1 + - - +
217U PRO* 4.0 20.0 - - + +
218U ASP* 4.1 21.6 - - + +
221U ALA* 4.3 10.3 - - + +
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Residues in contact with ILE 176 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U LEU* 5.1 1.6 - - + -
172U ILE* 2.9 37.9 + - + +
173U GLU* 3.5 8.3 - - - +
175U ALA* 1.3 73.9 - - - +
177U TYR* 1.3 58.8 + - - +
179U GLU* 2.9 23.0 + - + +
180U ILE* 3.0 18.6 + - + +
187U TYR* 3.5 29.6 - - + +
190U ARG* 4.9 13.7 - - + -
191U VAL* 3.6 33.2 - - + +
194U ARG* 4.5 12.1 - - + -
221U ALA* 4.6 20.0 - - - +
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Residues in contact with TYR 177 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141U ARG* 3.1 58.0 + - - +
173U GLU* 2.9 13.0 + - - +
174U GLU* 3.3 17.0 - - - +
176U ILE* 1.3 76.1 - - - +
178U GLN* 1.3 63.0 + - + +
181U ARG* 2.8 66.9 + - + +
182U ASN* 4.5 7.6 - - - -
183U THR* 5.9 2.9 - - + -
187U TYR* 4.1 13.4 - + + -
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Residues in contact with GLN 178 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174U GLU* 2.8 44.7 + - - +
175U ALA* 3.5 18.1 - - - +
176U ILE 3.2 0.4 - - - -
177U TYR* 1.3 75.3 - - + +
179U GLU* 1.3 59.8 + - - +
181U ARG* 3.2 25.1 + - - +
218U ASP* 5.1 7.8 - - - +
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Residues in contact with GLU 179 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175U ALA 3.6 6.7 + - - +
176U ILE* 2.9 12.3 + - + +
178U GLN* 1.3 82.8 - - - +
180U ILE* 1.3 73.9 + - + +
181U ARG* 3.9 14.5 + - - +
190U ARG* 5.1 12.6 - - - +
221U ALA* 6.2 1.8 - - + -
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Residues in contact with ILE 180 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176U ILE* 3.0 16.1 + - + +
179U GLU* 1.3 89.2 - - + +
181U ARG* 1.3 72.6 + - - +
182U ASN* 3.0 20.5 + - + +
184U ASP* 4.7 5.6 - - + -
186U LYS* 5.0 13.2 - - + +
187U TYR* 3.5 52.7 - - + +
190U ARG* 4.8 20.6 - - - +
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Residues in contact with ARG 181 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PRO* 5.9 5.3 - - - +
50E GLU* 5.9 0.8 + - - -
177U TYR* 2.8 58.5 + - + +
178U GLN* 3.2 25.2 + - - +
179U GLU* 3.9 12.7 + - - +
180U ILE* 1.3 75.5 + - - +
182U ASN* 1.3 58.8 + - - +
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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
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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