Contacts of the helix formed by residues 199 - 214 (chain E) in PDB entry 3EBL
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 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E HIS 3.5 2.8 + - - -
121E GLY 3.8 1.6 - - - -
123E SER* 3.5 8.7 + - - -
124E PHE* 3.1 52.6 + - - -
154E TYR* 2.7 26.3 + - - -
198E SER* 1.3 79.8 + - - +
200E GLY* 1.3 56.0 + - - +
202E ASN* 3.2 5.5 + - - +
203E ILE* 3.0 30.8 + - - +
227E MET* 3.4 13.1 - - - +
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Residues in contact with GLY 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E PHE* 3.1 39.5 - - - +
120E HIS 3.5 6.2 + - - -
196E GLY* 3.5 7.6 - - - -
197E ASP 2.7 13.6 + - - -
199E SER* 1.3 77.5 + - - +
201E GLY* 1.3 54.4 + - - -
203E ILE* 3.5 3.9 + - - -
204E ALA* 3.0 26.7 + - - +
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Residues in contact with GLY 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E GLY* 3.3 22.7 - - - -
198E SER 2.8 10.0 + - - -
200E GLY* 1.3 73.6 - - - +
202E ASN* 1.3 65.8 + - - +
204E ALA* 3.3 2.9 + - - +
205E HIS* 3.0 23.0 + - - +
223E LEU* 3.8 13.4 - - - +
226E ALA* 4.0 18.2 - - - -
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Residues in contact with ASN 202 (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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124E PHE* 3.6 11.8 - - + -
166E TYR* 2.4 29.5 + - - -
198E SER 3.5 4.2 + - - -
199E SER* 3.2 12.1 + - - +
201E GLY* 1.3 74.8 - - - +
203E ILE* 1.3 63.9 + - - +
205E HIS* 3.1 11.3 + - - +
206E HIS* 3.0 23.3 + - - -
226E ALA* 4.3 2.8 - - - +
227E MET 3.0 29.4 + - - +
228E PHE* 3.7 19.9 - - - -
255E TRP* 3.9 8.1 - - - -
269E ALA 2.8 23.8 + - - -
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Residues in contact with ILE 203 (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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119E PHE* 3.8 22.2 - - + -
124E PHE* 4.1 6.1 - - + -
154E TYR* 3.4 52.5 - - + +
165E ALA* 3.9 22.7 - - + +
166E TYR* 3.7 23.1 - - + -
199E SER 3.0 19.4 + - - +
200E GLY* 3.8 8.1 - - - +
201E GLY 3.4 0.2 - - - -
202E ASN* 1.3 75.4 - - - +
204E ALA* 1.3 53.7 + - - +
206E HIS* 3.3 1.6 + - - +
207E VAL* 2.8 55.8 + - + +
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Residues in contact with ALA 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E PHE* 4.0 11.2 - - + -
194E LEU* 3.7 11.8 - - + +
195E SER 4.0 26.2 - - - +
200E GLY 3.0 15.3 + - - +
201E GLY 3.5 8.3 - - - +
202E ASN 3.2 0.2 - - - -
203E ILE* 1.3 74.8 - - - +
205E HIS* 1.3 56.7 + - - +
207E VAL* 3.2 2.5 + - - -
208E ALA* 2.8 30.6 + - - +
221E ASN* 4.3 2.9 + - - -
223E LEU* 3.8 18.2 - - + -
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Residues in contact with HIS 205 (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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201E GLY 3.0 12.9 + - - +
202E ASN 3.1 6.7 + - - +
204E ALA* 1.3 76.3 - - - +
206E HIS* 1.3 85.0 + + - +
208E ALA* 3.0 9.2 + - - +
209E VAL* 3.0 48.7 + - + +
221E ASN* 4.3 5.4 - - - +
223E LEU* 4.7 2.6 - - + +
228E PHE* 4.3 13.7 - + + -
272E PRO* 4.0 16.3 - - + +
273E PHE* 4.7 4.7 - + - -
280E LEU* 4.1 15.5 - - + -
285E PHE* 3.9 6.7 - + - -
305E TYR* 2.9 41.7 + + - +
309E LEU* 4.8 0.2 - - + -
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Residues in contact with HIS 206 (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 TYR* 3.2 37.1 + + + -
202E ASN* 3.0 41.6 + - - -
205E HIS* 1.3 95.1 + + - +
207E VAL* 1.3 66.3 + - - +
209E VAL* 3.4 8.9 + - - +
210E ARG* 3.1 22.7 + - - +
228E PHE* 4.8 1.8 - - - -
268E PRO* 3.8 9.6 + - + -
269E ALA* 3.2 38.4 + - - -
272E PRO* 4.5 3.4 - - + -
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Residues in contact with VAL 207 (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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119E PHE* 4.2 3.8 - - + -
166E TYR* 4.1 11.9 - - + +
169E GLY* 3.8 34.3 - - - +
170E TRP* 4.1 6.9 - - + +
173E LEU* 3.9 21.9 - - + +
194E LEU* 3.9 16.8 - - + +
203E ILE* 2.8 40.0 + - + +
204E ALA* 3.7 5.2 - - - +
206E HIS* 1.3 76.5 - - - +
208E ALA* 1.3 56.8 + - - +
210E ARG* 3.6 7.0 + - - +
211E ALA* 3.1 26.5 + - - +
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Residues in contact with ALA 208 (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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194E LEU* 3.6 9.2 - - + +
204E ALA 2.8 9.3 + - - +
205E HIS 3.0 12.8 + - - +
207E VAL* 1.3 74.9 - - - +
209E VAL* 1.3 57.4 + - - +
211E ALA* 3.3 5.9 + - - +
212E ALA* 3.0 27.9 + - - +
218E VAL* 4.9 3.0 - - - +
221E ASN* 3.2 35.7 - - - +
285E PHE* 3.2 16.4 - - + -
286E ALA* 4.9 5.4 + - + +
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Residues in contact with VAL 209 (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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205E HIS* 3.0 40.2 + - + +
206E HIS* 3.8 10.1 - - - +
208E ALA* 1.3 73.5 - - - +
210E ARG* 1.3 66.4 + - - +
212E ALA* 3.1 7.1 + - - +
213E ASP* 2.9 26.3 + - - +
278E ARG* 3.8 28.9 - - - +
280E LEU* 4.0 28.7 - - + -
283E LEU* 5.0 2.0 - - + -
285E PHE* 4.0 5.8 - - + -
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Residues in contact with ARG 210 (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 TYR* 5.1 1.4 + - - +
167E ASP* 3.3 25.3 + - - +
170E TRP* 3.4 66.1 - - + +
206E HIS 3.1 16.9 + - - +
207E VAL* 3.8 5.6 - - - +
208E ALA 3.4 0.2 - - - -
209E VAL* 1.3 76.2 - - - +
211E ALA* 1.3 56.9 + - - +
213E ASP* 3.8 8.2 - - + +
214E GLU* 3.1 29.4 + - + +
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Residues in contact with ALA 211 (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* 3.8 8.5 - - - -
173E LEU* 3.8 16.4 - - + -
207E VAL 3.1 17.9 + - - +
208E ALA 3.6 5.4 - - - +
209E VAL 3.2 0.2 - - - -
210E ARG* 1.3 75.0 - - - +
212E ALA* 1.3 59.3 + - - +
214E GLU 3.6 0.4 + - - +
215E GLY 3.0 5.5 + - - -
216E VAL* 2.5 43.7 + - + +
218E VAL* 3.7 26.7 - - + -
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Residues in contact with ALA 212 (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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208E ALA 3.0 14.5 + - - +
209E VAL* 3.4 10.1 - - - +
211E ALA* 1.3 73.2 - - - +
213E ASP* 1.3 67.2 + - - +
215E GLY* 2.8 16.3 + - - -
216E VAL 4.6 1.3 - - - -
283E LEU* 4.0 26.0 - - + +
284E PRO* 3.6 38.1 - - + +
285E PHE* 4.3 8.3 - - + -
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Residues in contact with ASP 213 (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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209E VAL* 2.9 20.5 + - - +
210E ARG* 3.8 8.4 - - + +
212E ALA* 1.3 77.1 - - - +
214E GLU* 1.3 58.2 + - - +
215E GLY 3.4 2.1 + - - -
278E ARG* 2.7 45.8 + - - -
283E LEU* 3.3 16.7 - - - +
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Residues in contact with GLU 214 (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* 4.2 20.9 - - + -
210E ARG* 3.1 20.1 + - + +
211E ALA 4.4 0.7 - - - +
212E ALA 3.2 0.4 - - - -
213E ASP* 1.3 74.3 - - + +
215E GLY* 1.3 63.4 + - - +
216E VAL* 3.3 9.0 + - + +
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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