Contacts of the helix formed by residues 196 - 214 (chain E) in PDB entry 3EGC
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 LEU 196 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 3.8 25.1 - - + +
154E ARG* 3.6 49.4 - - + +
192E GLY* 5.5 1.3 - - - -
193E SER* 3.2 36.1 + - - +
195E GLY* 1.3 80.1 - - - +
197E MET* 1.3 64.2 + - - +
198E THR* 3.8 13.0 - - - +
199E SER* 3.7 11.7 - - - +
200E ARG* 3.0 23.7 + - - +
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Residues in contact with MET 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ASN 3.4 24.9 - - - +
154E ARG* 4.3 13.5 - - + +
155E GLU* 3.7 50.5 - - + +
165E LEU* 4.0 14.4 - - + -
168E ASN* 3.8 11.4 - - - +
196E LEU* 1.3 72.6 - - - +
198E THR* 1.3 64.1 + - + +
200E ARG* 3.2 20.4 + - - +
201E GLU* 2.9 65.7 + - + +
325E ARG* 4.2 3.8 - - - +
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Residues in contact with THR 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ASN* 3.3 45.1 - - - +
154E ARG* 4.2 9.4 + - + -
168E ASN* 4.4 8.5 - - - +
196E LEU* 3.8 15.3 - - - +
197E MET* 1.3 79.3 - - + +
199E SER* 1.3 69.4 + - - +
201E GLU* 3.8 0.3 - - - -
202E ARG* 2.9 60.1 + - - +
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Residues in contact with SER 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E VAL* 4.1 20.2 - - - +
192E GLY* 3.3 23.3 + - - +
193E SER 2.7 28.9 + - - -
194E ALA* 4.3 5.4 - - - -
196E LEU* 3.6 12.7 + - - +
197E MET 3.4 0.2 - - - -
198E THR* 1.3 81.4 + - - +
200E ARG* 1.3 62.6 + - - +
202E ARG* 4.0 3.2 - - - +
203E LEU* 3.0 27.3 + - - +
252E SER* 5.3 2.2 - - - -
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Residues in contact with ARG 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 5.6 2.2 + - - -
157E ARG* 4.6 16.8 - - - +
194E ALA 3.7 16.6 - - - +
195E GLY* 2.7 28.0 + - - -
196E LEU 3.0 8.4 + - - +
197E MET* 3.6 26.4 - - - +
198E THR 3.2 0.2 - - - -
199E SER* 1.3 79.9 - - - +
201E GLU* 1.3 58.9 + - + +
203E LEU* 3.3 6.3 + - - +
204E LYS* 3.0 27.1 + - - +
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Residues in contact with GLU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 5.6 0.2 - - - +
168E ASN* 2.6 43.5 + - + +
169E VAL* 3.6 26.8 - - + -
197E MET* 2.9 32.7 + - + +
198E THR 4.2 0.2 - - - +
200E ARG* 1.3 77.5 - - + +
202E ARG* 1.3 64.9 + - - +
204E LYS* 3.3 11.2 + - + +
205E GLY 3.1 17.2 + - - -
325E ARG* 2.8 38.3 + - - -
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Residues in contact with ARG 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ASN* 4.5 4.8 - - - +
168E ASN* 3.0 32.9 + - + -
172E ALA* 3.2 23.8 - - + +
191E VAL* 4.9 2.2 - - + -
198E THR* 2.9 48.4 + - - +
199E SER 4.1 2.0 - - - +
201E GLU* 1.3 73.4 - - - +
203E LEU* 1.3 62.3 + - - +
206E PHE* 3.2 11.1 + - - +
250E LEU* 3.8 6.8 - - + +
252E SER* 2.6 53.3 + - - -
253E SER* 4.5 6.1 - - - -
280E PHE* 3.5 42.2 - - + +
298E GLN* 3.4 28.3 + - - +
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Residues in contact with LEU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E ALA* 3.7 29.6 - - + +
191E VAL* 3.7 22.6 - - + +
199E SER 3.0 18.2 + - - +
200E ARG* 3.6 6.1 - - - +
202E ARG* 1.3 78.4 - - - +
204E LYS* 1.3 57.7 + - - +
206E PHE* 3.0 9.6 + - + +
207E ARG* 3.0 51.3 + - - +
222E ILE* 3.7 34.5 - - + -
250E LEU* 5.5 0.4 - - - -
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Residues in contact with LYS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E VAL* 4.2 27.5 - - + +
200E ARG 3.0 13.7 + - - +
201E GLU* 3.5 13.2 - - + +
203E LEU* 1.3 74.8 - - - +
205E GLY* 1.3 59.3 + - - +
207E ARG* 3.4 9.6 + - - +
208E ALA* 2.9 30.0 + - + +
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Residues in contact with GLY 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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169E VAL* 3.6 33.1 - - - +
173E ARG* 3.5 23.1 - - - +
201E GLU 3.1 8.7 + - - -
202E ARG 3.9 3.4 - - - -
203E LEU 3.3 0.2 - - - -
204E LYS* 1.3 76.3 - - - +
206E PHE* 1.3 64.4 + - - +
208E ALA* 3.5 2.0 + - - +
209E ALA* 3.1 18.5 + - - +
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Residues in contact with PHE 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ALA* 4.2 1.4 - - - +
176E VAL* 3.7 26.7 - - + -
187E ILE* 3.3 45.3 - - + -
188E GLY* 4.0 12.8 - - - -
189E ALA* 4.2 11.4 - - + -
202E ARG 3.2 12.6 + - - +
203E LEU* 3.0 16.3 + - + +
205E GLY* 1.3 78.4 - - - +
207E ARG* 1.3 71.9 + - + +
209E ALA* 3.2 2.9 + - - +
210E MET* 3.1 45.3 + - + +
217E VAL* 4.0 15.3 - - + -
222E ILE* 3.5 30.1 - - + -
250E LEU* 3.9 10.8 - - + -
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Residues in contact with ARG 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E LEU* 3.0 34.8 + - + +
204E LYS* 3.9 10.5 - - - +
205E GLY 3.3 0.2 - - - -
206E PHE* 1.3 84.0 - - + +
208E ALA* 1.3 63.1 + - - +
210E MET* 3.3 5.4 + - - +
211E SER* 2.8 33.5 + - - -
217E VAL* 4.1 30.3 + - + +
219E GLN* 2.7 29.9 + - - +
222E ILE* 4.5 12.6 - - - +
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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
----------------------------------------------------------
169E VAL* 5.6 3.4 - - + -
173E ARG* 4.2 26.2 - - - +
204E LYS* 2.9 19.1 + - + +
205E GLY* 3.9 5.6 - - - +
207E ARG* 1.3 78.4 - - - +
209E ALA* 1.3 62.4 + - - +
211E SER* 3.7 5.5 - - - -
212E ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 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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173E ARG* 3.9 21.2 - - + +
176E VAL* 3.5 31.6 - - + -
177E GLU* 3.9 15.5 - - + +
180E ILE* 4.2 5.0 - - + +
205E GLY 3.1 14.6 + - - +
206E PHE 3.2 4.0 + - - +
208E ALA* 1.3 72.1 - - - +
210E MET* 1.3 67.5 + - - +
212E ALA* 3.0 13.9 + - - +
213E ALA* 3.1 14.2 + - - +
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Residues in contact with MET 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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176E VAL* 4.2 4.9 - - + -
180E ILE* 3.9 22.2 - - - -
185E THR 3.7 22.9 - - - +
187E ILE* 4.0 33.0 - - + +
206E PHE* 3.1 35.6 + - + +
207E ARG* 3.7 5.8 - - - +
209E ALA* 1.3 76.1 - - - +
211E SER* 1.3 61.3 + - - +
213E ALA* 3.2 3.1 + - - -
214E GLY 2.9 4.2 + - - -
215E LEU* 2.9 52.3 + - + +
216E PRO 4.0 13.0 - - - +
217E VAL* 4.8 8.5 - - + -
221E TRP* 4.7 1.3 - - + -
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Residues in contact with SER 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ARG 2.8 23.0 + - - -
208E ALA* 3.7 6.7 - - - -
210E MET* 1.3 73.1 - - - +
212E ALA* 1.3 58.1 + - - +
214E GLY* 3.0 19.0 + - - +
215E LEU 4.6 4.0 - - - +
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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
----------------------------------------------------------
173E ARG* 3.8 21.8 - - - +
177E GLU* 5.4 2.7 - - - +
208E ALA 3.1 16.6 + - - +
209E ALA* 3.0 6.2 + - - +
211E SER* 1.3 76.1 - - - +
213E ALA* 1.3 59.7 + - - +
214E GLY 3.3 0.2 - - - -
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ILE* 4.1 31.9 - - + -
209E ALA 3.1 14.9 + - - +
210E MET 3.8 3.4 - - - +
212E ALA* 1.3 78.9 - - - +
214E GLY* 1.3 60.8 + - - +
215E LEU* 3.2 13.1 + - + +
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Residues in contact with GLY 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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210E MET 2.9 3.4 + - - -
211E SER 3.0 14.5 + - - -
212E ALA 3.3 1.2 + - - -
213E ALA* 1.3 79.7 - - - +
215E LEU* 1.3 62.2 + - - +
216E PRO* 3.6 7.6 - - - +
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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
------------------------------------------------------------
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