Contacts of the helix formed by residues 181 - 195 (chain E) in PDB entry 3J8B
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 ASN 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176E GLU* 3.1 22.9 + - + +
177E ILE* 5.7 0.7 - - - -
179E MET* 3.4 6.6 - - + +
180E GLN* 1.3 77.1 - - - +
182E TRP* 1.3 61.8 + - - +
183E ASP* 3.4 4.7 - - + +
184E ALA* 3.5 15.8 + - + +
185E ALA* 3.4 14.0 + - - +
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Residues in contact with TRP 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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177E ILE* 6.2 1.1 - - - +
180E GLN 3.9 3.2 + - - -
181E ASN* 1.3 70.7 - - - +
183E ASP* 1.3 67.7 + - - +
185E ALA* 3.2 9.7 + - + +
186E MET* 2.9 21.0 + - - +
215E ILE* 3.6 37.3 - - + +
218E SER* 4.5 13.5 - - - -
219E LEU* 5.4 3.4 - - + +
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Residues in contact with ASP 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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181E ASN* 4.9 4.3 - - + -
182E TRP* 1.3 75.6 - - - +
184E ALA* 1.3 65.0 + - - +
186E MET* 2.9 18.6 + - - +
187E GLU* 2.9 12.2 + - - +
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Residues in contact with ALA 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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172E LYS 6.5 0.2 - - - -
176E GLU* 4.1 14.1 - - + -
181E ASN* 3.5 19.0 + - + +
182E TRP 3.3 0.4 - - - -
183E ASP* 1.3 79.7 - - - +
185E ALA* 1.3 56.8 + - - +
187E GLU* 3.2 11.2 + - - +
188E ASP* 2.9 31.2 + - - +
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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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173E LEU* 5.2 16.1 - - + +
176E GLU* 4.3 10.2 - - + +
177E ILE* 5.2 7.0 - - + +
181E ASN 3.4 6.3 + - - +
182E TRP* 3.2 20.6 + - + +
183E ASP 3.1 0.2 - - - -
184E ALA* 1.3 79.2 - - - +
186E MET* 1.3 57.7 + - - +
188E ASP* 3.5 2.2 + - - +
189E LEU* 2.9 28.5 + - - +
211E ARG* 5.0 12.8 - - + +
215E ILE* 4.3 10.5 - - + -
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Residues in contact with MET 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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182E TRP 2.9 10.8 + - - +
183E ASP* 2.9 10.5 + - - +
185E ALA* 1.3 74.9 - - - +
187E GLU* 1.3 65.6 + - - +
189E LEU* 2.9 10.8 + - - +
190E THR* 2.9 23.7 + - - -
212E THR* 5.9 2.9 - - - +
215E ILE* 4.5 10.2 - - + +
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Residues in contact with GLU 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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183E ASP 2.9 12.2 + - - +
184E ALA* 3.2 15.7 + - - +
186E MET* 1.3 74.8 - - - +
188E ASP* 1.3 56.8 + - - +
190E THR* 3.0 9.0 + - - -
191E ARG* 2.9 26.7 + - - +
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Residues in contact with ASP 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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169E LEU* 3.9 28.9 - - + +
172E LYS* 4.5 15.7 - - + -
173E LEU* 5.1 5.8 - - + +
184E ALA 2.9 17.0 + - - +
185E ALA* 3.8 3.4 - - - +
187E GLU* 1.3 73.0 - - - +
189E LEU* 1.3 56.5 + - - +
191E ARG* 3.8 8.7 - - + -
192E LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 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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185E ALA 2.9 15.8 + - - +
186E MET* 2.9 16.4 + - - +
188E ASP* 1.3 77.0 - - - +
190E THR* 1.3 56.1 + - - +
192E LEU* 3.9 4.0 - - - +
193E LYS* 2.9 33.3 + - - +
208E LEU* 5.0 14.4 - - + +
211E ARG* 5.6 4.3 - - + -
212E THR* 4.9 19.3 - - - +
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Residues in contact with THR 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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186E MET 2.9 11.2 + - - -
187E GLU* 3.6 9.0 - - - -
189E LEU* 1.3 73.3 - - - +
191E ARG* 1.3 55.3 + - - +
193E LYS* 5.1 1.3 - - - -
194E GLU* 2.3 46.0 + - - +
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Residues in contact with ARG 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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169E LEU* 5.7 2.0 - - + -
187E GLU 2.9 15.9 + - - +
188E ASP* 3.9 11.2 - - + +
190E THR* 1.3 77.2 - - - +
192E LEU* 1.3 62.0 + - - +
194E GLU* 4.1 2.3 - - - +
195E THR* 3.1 22.2 + - - -
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Residues in contact with LEU 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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166E LEU* 5.1 15.0 - - + +
169E LEU* 3.8 19.9 - - + +
188E ASP 3.0 20.6 + - - +
189E LEU* 3.9 4.7 - - - +
191E ARG* 1.3 78.0 - - - +
193E LYS* 1.3 58.9 + - + +
195E THR* 3.2 25.1 + - - +
197E ASP 5.5 1.2 - - - +
208E LEU* 5.7 7.2 - - + -
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Residues in contact with LYS 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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189E LEU 2.9 20.5 + - - +
190E THR* 5.1 1.3 - - - -
192E LEU* 1.3 71.2 - - + +
194E GLU* 1.3 63.5 + - - +
195E THR 3.3 5.2 - - - +
208E LEU* 5.4 10.5 - - + -
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Residues in contact with GLU 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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190E THR* 2.3 32.7 + - - +
191E ARG* 4.1 3.4 - - - +
193E LYS* 1.3 77.8 - - - +
195E THR* 1.3 65.6 + - - +
196E ILE* 3.4 3.8 + - - -
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Residues in contact with THR 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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161E THR* 5.2 18.2 - - - -
162E ASP* 6.0 2.7 - - - -
165E ALA* 6.4 0.2 - - - -
166E LEU* 6.1 3.1 - - - -
191E ARG 3.1 16.1 + - - -
192E LEU* 3.2 20.3 + - - +
193E LYS 4.0 5.5 - - - +
194E GLU* 1.3 78.9 - - - +
196E ILE* 1.3 66.0 + - - +
197E ASP 3.3 11.3 + - - +
198E ASN* 4.8 4.5 + - - +
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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