Contacts of the helix formed by residues 165 - 180 (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 ALA 165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E ARG* 6.5 0.7 - - - +
158E VAL* 4.6 9.6 - - + -
160E ALA 4.1 0.4 - - - +
161E THR* 2.5 39.4 + - - +
164E ASN* 1.3 78.1 - - - +
166E LEU* 1.3 58.4 + - - +
167E SER 3.3 1.3 - - - -
168E SER* 3.2 8.4 + - - -
169E LEU* 2.9 25.1 + - - +
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Residues in contact with LEU 166 (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 2.8 10.1 + - - +
162E ASP* 2.8 27.9 + - - +
165E ALA* 1.3 74.2 - - - +
167E SER* 1.3 55.9 + - - +
169E LEU* 3.0 11.2 - - + +
170E TRP* 2.9 25.3 + - - +
192E LEU* 5.1 15.2 - - + +
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Residues in contact with SER 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E ARG 3.1 21.4 + - - -
164E ASN* 4.5 1.3 - - - -
165E ALA 3.3 0.4 - - - -
166E LEU* 1.3 74.9 - - - +
168E SER* 1.3 65.0 + - - +
169E LEU 3.1 0.2 - - - -
170E TRP* 3.3 9.2 + - - +
171E GLY* 3.0 19.6 + - - -
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Residues in contact with SER 168 (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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151E LEU* 4.6 20.1 - - - +
152E TYR* 5.5 4.7 - - - -
154E PHE* 5.2 11.0 - - - -
155E ARG* 5.6 2.9 - - - -
164E ASN 3.5 16.1 + - - -
165E ALA* 3.2 13.1 + - - -
167E SER* 1.3 78.0 - - - +
169E LEU* 1.3 58.3 + - - +
171E GLY* 3.3 2.4 + - - -
172E LYS* 2.9 29.3 + - - +
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Residues in contact with LEU 169 (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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165E ALA 2.9 12.7 + - - +
166E LEU* 3.0 14.1 + - - +
168E SER* 1.3 73.3 - - - +
170E TRP* 1.3 62.5 + - - +
172E LYS* 3.1 4.9 + - - +
173E LEU* 2.8 26.2 + - - +
188E ASP* 3.9 21.8 - - + +
191E ARG* 5.7 2.0 - - + -
192E LEU* 3.8 28.0 - - + +
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Residues in contact with TRP 170 (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 2.9 15.2 + - - +
167E SER* 3.6 11.4 - - - +
169E LEU* 1.3 71.8 - - - +
171E GLY* 1.3 57.6 + - - +
173E LEU* 3.3 9.4 + - - +
174E ALA* 2.9 27.2 + - - +
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Residues in contact with GLY 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 5.4 7.9 - - - -
167E SER 3.0 14.8 + - - -
168E SER* 3.7 3.4 - - - -
170E TRP* 1.3 71.5 - - - +
172E LYS* 1.3 62.4 + - - +
173E LEU 2.9 4.7 - - - -
174E ALA* 3.0 8.3 + - - +
175E SER* 2.9 25.3 + - - -
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Residues in contact with LYS 172 (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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148E ALA* 6.0 3.8 - - + +
151E LEU* 5.2 7.6 - - + +
152E TYR* 5.6 11.0 - - + +
168E SER 2.9 19.3 + - - +
169E LEU* 3.8 4.0 - - - +
171E GLY* 1.3 71.9 - - - +
173E LEU* 1.3 56.4 + - - +
175E SER* 4.3 5.3 - - - -
176E GLU* 2.9 34.0 + - - +
184E ALA 6.5 0.2 - - - -
188E ASP* 4.5 15.7 - - + -
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Residues in contact with LEU 173 (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 2.8 17.5 + - - +
170E TRP* 3.3 9.9 - - - +
172E LYS* 1.3 76.5 - - - +
174E ALA* 1.3 59.8 - - - +
176E GLU* 3.9 2.9 - - - +
177E ILE* 2.9 32.4 + - - +
185E ALA* 5.2 16.6 - - + +
188E ASP* 5.1 6.9 - - + +
211E ARG* 5.0 16.6 - - + -
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Residues in contact with ALA 174 (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 TRP 2.9 13.0 + - - +
171E GLY* 3.0 10.3 + - - +
173E LEU* 1.3 77.0 - - - +
175E SER* 1.3 63.0 + - - +
177E ILE* 3.5 6.0 + - - +
178E LEU* 3.0 24.1 + - - +
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Residues in contact with SER 175 (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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144E TYR* 5.0 11.4 - - - +
147E ALA* 5.2 7.0 - - - -
148E ALA* 4.6 28.0 - - - -
171E GLY 2.9 15.6 + - - -
172E LYS* 4.3 3.4 - - - -
174E ALA* 1.3 77.1 - - - +
176E GLU* 1.3 58.0 + - - +
178E LEU* 3.4 6.9 + - - +
179E MET* 2.9 29.9 + - - +
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Residues in contact with GLU 176 (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 2.9 21.8 + - - +
173E LEU* 3.9 2.9 - - - +
175E SER* 1.3 74.3 - - - +
177E ILE* 1.3 66.2 + - - +
179E MET* 3.1 4.9 + - - -
180E GLN 2.8 19.6 + - - -
181E ASN* 3.1 31.1 + - + +
184E ALA* 4.1 17.9 - - + -
185E ALA* 4.3 7.2 - - - +
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Residues in contact with ILE 177 (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 2.9 18.4 + - - +
174E ALA* 3.6 6.1 - - - +
176E GLU* 1.3 74.7 - - - +
178E LEU* 1.3 58.6 + - - +
180E GLN* 3.1 19.6 + - - +
181E ASN 4.7 2.0 + - - +
182E TRP* 6.2 0.7 - - - +
185E ALA* 5.2 6.9 - - + +
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Residues in contact with LEU 178 (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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17E HIS* 4.8 19.7 - - + -
144E TYR* 6.0 5.4 - - + -
174E ALA 3.0 17.6 + - - +
175E SER* 3.8 7.0 - - - +
176E GLU 3.2 0.4 - - - -
177E ILE* 1.3 77.6 - - - +
179E MET* 1.3 58.7 + - - +
180E GLN* 3.2 1.8 - - - +
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Residues in contact with MET 179 (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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144E TYR* 5.1 13.7 - - + -
175E SER 2.9 16.7 + - - +
176E GLU* 3.1 6.0 + - - +
178E LEU* 1.3 76.7 - - - +
180E GLN* 1.3 71.8 + - - +
181E ASN* 3.5 4.8 + - + +
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Residues in contact with GLN 180 (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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176E GLU 2.8 6.3 + - - -
177E ILE* 3.1 14.1 + - - +
178E LEU 3.2 1.9 - - - +
179E MET* 1.3 83.5 - - - +
181E ASN* 1.3 57.6 + - - +
182E TRP* 3.9 3.0 + - - -
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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