Contacts of the helix formed by residues 180 - 195 (chain E) in PDB entry 4OA5
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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140E SER* 5.1 1.7 - - - -
178E LYS 4.3 0.2 + - - -
179E VAL* 1.3 73.7 - - - +
181E SER* 1.3 58.5 + - - +
182E ASN* 3.3 11.3 + - - +
183E ALA* 3.0 31.6 + - - +
184E HIS* 2.9 27.5 + - - +
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Residues in contact with SER 181 (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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175E PRO* 3.9 22.3 - - - +
176E THR 5.3 0.9 + - - -
179E VAL 3.4 4.9 + - - -
180E SER* 1.3 70.2 + - - +
182E ASN* 1.3 64.0 + - - +
184E HIS* 3.7 6.9 + - - +
185E ALA* 2.9 31.7 + - - +
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Residues in contact with ASN 182 (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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89C LYS* 6.0 4.0 - - - +
116C GLU* 3.7 38.5 + - + +
140E SER* 3.9 17.6 + - - +
180E SER* 3.2 8.0 + - - +
181E SER* 1.3 82.7 - - - +
183E ALA* 1.3 61.8 + - - +
185E ALA* 3.9 4.5 - - - +
186E SER* 3.0 24.9 + - - -
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Residues in contact with ALA 183 (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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139E LYS* 4.1 22.4 - - + +
140E SER* 4.0 15.8 - - - +
166E LEU* 3.6 16.6 - - + -
180E SER* 3.0 28.5 + - - +
182E ASN* 1.3 74.8 - - - +
184E HIS* 1.3 57.7 + - - +
186E SER* 3.3 2.9 + - - -
187E MET* 2.9 31.2 + - - +
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Residues in contact with HIS 184 (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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166E LEU* 3.4 13.6 - - + +
169E SER* 3.0 34.5 + - - -
170E VAL* 4.2 3.8 - - - -
172E ASP 2.9 28.4 + - - -
173E GLU 3.3 18.8 - - - -
175E PRO* 3.6 39.2 - - + +
179E VAL* 4.1 2.2 - - + -
180E SER 2.9 16.4 + - - +
181E SER 3.7 3.6 + - - +
183E ALA* 1.3 73.8 - - - +
185E ALA* 1.3 68.6 + - - +
187E MET* 3.3 1.0 + - - +
188E ARG* 2.9 45.1 + - + +
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Residues in contact with ALA 185 (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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116C GLU* 6.3 1.6 - - + -
119C ALA* 4.5 17.6 - - + +
120C GLN* 6.4 0.2 - - - +
181E SER 2.9 20.6 + - - +
182E ASN* 3.9 5.8 - - - +
184E HIS* 1.3 79.0 + - - +
186E SER* 1.3 62.8 + - - +
188E ARG* 3.7 5.4 + - - +
189E ALA* 3.2 23.6 + - - +
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Residues in contact with SER 186 (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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119C ALA* 4.9 3.5 - - - +
139E LYS 3.2 18.3 + - - -
140E SER 3.5 19.9 + - - -
142E TYR* 3.6 10.9 + - - +
143E LEU* 3.7 22.4 + - - +
182E ASN 3.0 19.5 + - - -
183E ALA 3.6 4.5 - - - -
185E ALA* 1.3 76.9 - - - +
187E MET* 1.3 59.6 + - - +
189E ALA* 3.4 2.4 + - - +
190E PHE* 2.9 29.0 + - - +
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Residues in contact with MET 187 (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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139E LYS* 3.8 31.0 - - + +
142E TYR* 3.5 39.7 - - + -
163E ASN 3.5 17.3 - - - +
164E THR* 3.6 39.9 - - - +
166E LEU* 4.3 13.2 - - + -
170E VAL* 3.9 11.0 - - + -
183E ALA 2.9 15.0 + - - +
184E HIS 3.3 2.9 + - - +
186E SER* 1.3 73.2 - - - +
188E ARG* 1.3 67.1 + - - +
190E PHE* 3.6 5.8 - - - +
191E ASN* 2.9 29.8 + - - +
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Residues in contact with ARG 188 (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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170E VAL* 2.9 38.7 + - + +
171E PHE* 3.7 15.4 + - - +
172E ASP 3.8 12.7 + - - -
173E GLU* 3.6 30.7 + - - +
184E HIS* 2.9 36.1 + - + +
185E ALA* 3.9 6.1 - - - +
187E MET* 1.3 76.8 - - - +
189E ALA* 1.3 56.9 + - - +
191E ASN* 3.6 3.6 + - - +
192E ASP* 3.0 29.3 + - - +
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Residues in contact with ALA 189 (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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119C ALA* 5.3 4.3 - - + +
122C ASN* 3.6 21.9 - - + +
123C THR* 6.5 0.7 - - + -
143E LEU* 3.9 17.4 - - + +
185E ALA 3.2 16.5 + - - +
186E SER 3.9 2.7 - - - +
188E ARG* 1.3 76.4 - - - +
190E PHE* 1.3 61.7 + - - +
192E ASP* 3.7 5.7 - - - +
193E GLU* 2.8 31.9 + - - +
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Residues in contact with PHE 190 (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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135E ILE* 4.1 15.0 - - + -
142E TYR* 3.6 44.9 - + + -
143E LEU* 3.7 10.9 - - + +
146E LEU* 3.9 25.2 - - + +
159E ILE* 4.6 3.8 - - + -
161E ALA* 3.7 22.0 - - + -
164E THR* 3.9 20.0 - - + -
186E SER 2.9 18.8 + - - +
187E MET* 3.6 9.6 - - - +
189E ALA* 1.3 76.4 - - - +
191E ASN* 1.3 75.6 + - - +
193E GLU* 3.4 2.6 + - - +
194E LEU* 3.2 49.9 + - + +
212E MET* 4.2 3.1 - - + -
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Residues in contact with ASN 191 (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 THR* 2.9 34.1 + - - -
170E VAL* 3.7 20.2 - - + +
187E MET* 2.9 15.8 + - - +
188E ARG* 4.0 3.6 - - - +
190E PHE* 1.3 89.0 - - - +
192E ASP* 1.3 58.3 + - - +
194E LEU* 3.2 3.8 + - - +
195E ALA* 3.0 28.2 + - - +
204E ILE* 3.8 19.0 - - + +
212E MET* 3.4 18.9 - - + +
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Residues in contact with ASP 192 (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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188E ARG 3.0 19.7 + - - +
189E ALA* 3.7 7.0 - - - +
190E PHE 3.3 0.2 - - - -
191E ASN* 1.3 78.0 - - - +
193E GLU* 1.3 63.2 + - - +
195E ALA* 3.2 21.2 + - - +
196E ASN* 3.7 4.3 + - - +
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Residues in contact with GLU 193 (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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122C ASN* 4.9 11.0 + - - +
125C LYS* 3.1 30.0 + - - -
126C GLU* 5.1 0.2 - - - +
143E LEU* 5.5 0.2 - - + -
146E LEU* 3.5 26.5 - - + -
150E LYS* 3.5 19.3 + - - +
189E ALA 2.8 20.0 + - - +
190E PHE 3.7 4.5 - - - +
192E ASP* 1.3 73.2 + - - +
194E LEU* 1.3 57.2 + - - +
196E ASN* 3.1 30.9 + - - +
199E LYS* 4.0 12.2 - - - +
200E TYR* 2.8 38.4 + - + +
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Residues in contact with LEU 194 (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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146E LEU* 3.8 18.4 - - + -
159E ILE* 4.2 10.3 - - + -
190E PHE* 3.2 52.8 + - + +
191E ASN 3.2 5.1 + - - +
193E GLU* 1.3 75.6 - - - +
195E ALA* 1.3 57.3 + - - +
196E ASN 3.2 2.2 + - - +
200E TYR* 3.6 44.0 - - + +
202E SER* 2.7 31.8 + - - +
212E MET* 3.7 27.8 - - + -
214E SER* 3.7 11.0 - - - +
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Residues in contact with ALA 195 (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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191E ASN 3.0 12.5 + - - +
192E ASP* 3.5 18.8 - - - +
193E GLU 3.1 1.0 - - - -
194E LEU* 1.3 74.7 - - - +
196E ASN* 1.3 58.7 + - - +
197E LYS* 3.1 22.2 + - - +
200E TYR 5.4 0.2 - - - -
202E SER* 5.3 1.8 - - - -
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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