Contacts of the helix formed by residues 181 - 196 (chain E) in PDB entry 2BWJ
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 THR 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E GLY* 1.3 73.3 - - - -
182E PRO* 1.3 63.9 - - - +
183E GLU* 3.5 15.9 + - + +
184E ASP* 3.0 28.3 + - + +
185E VAL* 2.7 36.2 + - - +
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Residues in contact with PRO 182 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E THR* 6.4 1.8 - - - -
27E GLN* 2.9 26.2 + - - +
30E LYS* 3.9 15.5 + - - +
180E GLY 4.4 2.0 - - - +
181E THR* 1.3 84.2 - - + +
183E GLU* 1.3 72.9 + - - +
185E VAL* 4.3 1.8 - - + -
186E PHE* 2.9 26.9 + - - +
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Residues in contact with GLU 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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30E LYS* 4.3 14.6 + - - +
181E THR* 3.6 14.6 - - - +
182E PRO* 1.3 100.8 - - - +
184E ASP* 1.3 56.5 + - - +
186E PHE* 3.4 4.2 + - - +
187E LEU* 3.1 38.0 + - + +
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Residues in contact with ASP 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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180E GLY* 4.6 8.9 - - - -
181E THR* 3.0 24.8 + - + +
183E GLU* 1.3 73.0 - - - +
185E VAL* 1.3 66.5 + - - +
187E LEU* 3.4 14.6 + - - +
188E GLN* 3.1 42.2 + - - +
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Residues in contact with VAL 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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22E SER 5.8 1.1 - - - +
27E GLN* 3.7 25.8 - - + +
121E MET* 3.7 30.3 - - + -
176E ILE* 3.9 2.9 - - + +
177E ASN 3.5 22.0 - - - +
178E ALA* 3.9 12.6 - - + +
180E GLY* 4.0 11.0 - - - +
181E THR 2.7 26.6 + - - +
182E PRO* 4.2 1.1 - - + -
184E ASP* 1.3 72.1 - - - +
186E PHE* 1.3 57.1 + - - +
188E GLN* 3.3 10.3 + - - +
189E LEU* 2.9 27.2 + - + +
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Residues in contact with PHE 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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27E GLN* 3.4 18.6 - - - +
30E LYS* 3.3 54.3 - - + +
31E LEU* 3.7 20.2 - - + -
34E LYS* 4.0 20.4 - - + -
182E PRO 2.9 18.8 + - - +
183E GLU* 3.5 6.7 - - - +
184E ASP 3.2 0.2 - - - -
185E VAL* 1.3 73.3 - - - +
187E LEU* 1.3 76.3 + - + +
189E LEU* 3.1 5.8 + - + +
190E CYS* 2.8 43.4 + - - -
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Residues in contact with LEU 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 GLU* 3.1 22.4 + - + +
184E ASP* 3.7 18.6 - - + +
186E PHE* 1.3 89.8 - - + +
188E GLN* 1.3 58.4 + - + +
190E CYS* 3.0 8.5 + - + +
191E THR* 2.8 34.6 + - - +
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Residues in contact with GLN 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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176E ILE* 3.8 18.7 - - + +
177E ASN* 3.2 46.8 + - - +
180E GLY* 5.5 1.2 - - - -
184E ASP* 3.1 44.4 + - - +
185E VAL* 3.4 8.3 - - - +
186E PHE 3.3 0.2 - - - -
187E LEU* 1.3 79.2 - - + +
189E LEU* 1.3 62.1 + - - +
191E THR* 3.4 8.6 + - - -
192E ALA* 3.2 21.5 + - - +
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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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16E ILE* 4.4 5.4 - - + -
27E GLN* 3.2 48.7 - - + +
31E LEU* 4.4 21.1 - - + -
119E ILE* 3.3 42.6 - - + +
121E MET* 4.1 10.3 - - + -
176E ILE* 4.0 13.0 - - + +
185E VAL* 2.9 18.4 + - + +
186E PHE* 3.1 8.5 + - + +
188E GLN* 1.3 75.6 - - - +
190E CYS* 1.3 57.9 + - - +
192E ALA* 3.4 4.0 + - - +
193E ILE* 3.0 33.2 + - + +
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Residues in contact with CYS 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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31E LEU* 4.6 0.7 - - - -
34E LYS* 3.4 32.5 - - - -
35E TYR* 3.3 20.0 - - - +
186E PHE* 2.8 42.5 + - - +
187E LEU* 3.5 9.9 - - + +
189E LEU* 1.3 73.8 - - - +
191E THR* 1.3 58.4 + - - +
193E ILE* 4.4 1.1 - - - +
194E ASP* 2.7 45.3 + - - +
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Residues in contact with THR 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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187E LEU* 2.8 17.3 + - - +
188E GLN* 3.6 12.9 - - - -
190E CYS* 1.3 76.3 - - - +
192E ALA* 1.3 61.0 + - - +
194E ASP* 4.0 6.0 - - - +
195E SER* 3.2 21.0 + - - -
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Residues in contact with ALA 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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117E LEU* 3.8 16.0 - - + +
119E ILE* 5.0 2.7 - - + -
174E HIS* 3.7 39.3 - - + +
176E ILE* 4.4 8.7 - - + -
188E GLN 3.2 10.5 + - - +
189E LEU 3.8 7.0 - - - +
190E CYS 3.2 0.4 - - - -
191E THR* 1.3 78.2 - - - +
193E ILE* 1.3 65.2 + - - +
195E SER* 2.5 27.0 + - - -
196E ILE* 3.7 1.9 + - - +
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Residues in contact with ILE 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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14E ILE* 5.1 6.7 - - + -
31E LEU* 3.3 37.9 - - + -
35E TYR* 3.6 30.7 - - + +
37E PHE* 4.3 17.7 - - + -
94E LEU* 5.7 0.2 - - + -
117E LEU* 3.9 10.8 - - + -
119E ILE* 3.9 26.9 - - + -
189E LEU* 3.0 19.5 + - + +
190E CYS 3.8 2.5 - - - +
192E ALA* 1.3 76.1 - - - +
194E ASP* 1.3 62.3 + - - +
196E ILE* 3.3 14.1 + - + +
197E PHE* 3.2 26.4 - - + -
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Residues in contact with ASP 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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34E LYS* 5.7 1.9 - - - -
35E TYR* 2.7 31.3 + - - -
190E CYS* 2.7 29.2 + - - +
191E THR* 4.0 6.3 - - - +
193E ILE* 1.3 71.5 - - - +
195E SER* 1.3 61.9 + - - +
197E PHE* 3.2 27.6 + - - +
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Residues in contact with SER 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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172E GLN* 4.6 8.6 + - - -
174E HIS* 4.1 16.9 + - - -
191E THR 3.2 13.8 + - - -
192E ALA* 2.5 25.0 + - - -
194E ASP* 1.3 76.4 - - - +
196E ILE* 1.3 63.9 + - - +
197E PHE 3.4 3.9 + - - +
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Residues in contact with ILE 196 (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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12E LYS* 5.0 9.0 - - + -
14E ILE* 4.1 20.0 - - + -
37E PHE* 6.4 0.2 - - + -
116E GLN* 4.3 27.6 - - + +
117E LEU* 4.2 30.5 - - + -
172E GLN* 4.8 13.9 - - + +
192E ALA 4.1 4.0 - - - +
193E ILE* 3.3 17.0 + - + +
194E ASP 3.2 1.0 - - - -
195E SER* 1.3 86.6 + - - +
197E PHE* 1.3 70.8 + - + +
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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