Contacts of the helix formed by residues 197 - 213 (chain E) in PDB entry 3E2A
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 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E TRP* 3.4 29.4 - - - -
195E ALA* 3.9 0.5 - - - +
196E THR* 1.3 79.5 + - - +
198E ARG* 1.3 64.3 + - - +
199E GLU* 3.7 19.8 + - - -
200E THR* 2.7 43.1 + - - +
201E LEU 3.0 8.5 + - - -
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Residues in contact with ARG 198 (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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156E TYR* 3.5 6.3 + - - -
159E GLY 4.6 2.5 - - - -
160E ARG* 3.6 18.0 - - - +
165E LYS* 3.7 24.0 - - + +
168E TRP* 3.4 16.5 - - + +
197E SER* 1.3 75.3 - - - +
199E GLU* 1.3 71.7 + - + +
201E LEU* 3.1 17.2 + - - +
202E GLU* 2.9 51.7 + - + +
231E SO4 2.6 44.9 + - - -
128F PHE* 6.0 0.4 - - - -
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Residues in contact with GLU 199 (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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197E SER* 3.7 14.6 + - - +
198E ARG* 1.3 91.6 + - + +
200E THR* 1.3 63.0 + - + +
202E GLU* 3.2 8.4 + - - +
203E ILE* 3.1 34.2 + - + +
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Residues in contact with THR 200 (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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217B GLU* 5.8 9.0 - - + -
194E MET 4.5 3.6 - - - -
195E ALA* 4.3 3.6 - - - -
196E THR* 3.0 29.4 + - - +
197E SER* 2.7 32.6 + - - +
199E GLU* 1.3 75.1 - - + +
201E LEU* 1.3 56.2 + - - +
203E ILE* 4.6 7.6 - - + +
204E SER* 2.6 37.5 + - - -
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Residues in contact with LEU 201 (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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155E VAL* 3.9 19.5 - - + +
156E TYR* 3.8 29.6 - - + +
159E GLY* 3.4 39.0 - - - +
160E ARG* 4.0 2.0 - - + +
168E TRP* 4.4 1.3 - - + -
193E VAL* 4.3 12.3 - - + -
195E ALA* 3.5 22.9 - - + +
197E SER 3.0 14.4 + - - +
198E ARG* 3.1 26.2 + - - +
200E THR* 1.3 76.5 + - - +
202E GLU* 1.3 62.4 + - - +
204E SER* 3.5 1.5 + - - -
205E TYR* 2.9 28.6 + - - +
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Residues in contact with GLU 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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156E TYR* 2.3 36.6 + - - -
198E ARG* 2.9 38.4 + - + +
199E GLU* 3.5 10.3 - - - +
201E LEU* 1.3 77.6 - - - +
203E ILE* 1.3 60.1 + - + +
205E TYR* 3.8 4.0 - - - +
206E ARG* 3.0 57.4 + - - +
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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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215B LEU 5.0 1.8 - - - +
217B GLU* 3.2 53.2 - - + +
199E GLU* 3.1 23.5 + - + +
200E THR* 4.3 6.7 - - + +
202E GLU* 1.3 81.5 - - + +
204E SER* 1.3 58.7 + - - +
206E ARG* 3.3 6.0 + - - +
207E ASN* 2.9 54.3 + - - +
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Residues in contact with SER 204 (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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192E GLY 3.7 21.7 - - - +
193E VAL* 3.9 4.1 - - - +
194E MET* 3.0 28.9 + - - -
200E THR 2.6 24.3 + - - -
201E LEU* 3.5 3.1 + - - -
203E ILE* 1.3 78.4 - - - +
205E TYR* 1.3 59.4 + - - +
207E ASN* 3.9 6.6 - - - +
208E ALA* 2.8 31.8 + - - +
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Residues in contact with TYR 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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129E LYS* 2.9 19.3 + - - -
130E HIS* 4.2 1.7 - - - -
152E ALA 4.0 12.1 - - - -
153E GLU* 2.6 39.7 + - - -
156E TYR* 3.7 52.9 - + + -
193E VAL* 4.1 15.5 - - + +
201E LEU 2.9 19.8 + - - +
202E GLU* 3.8 5.6 - - - +
204E SER* 1.3 79.0 + - - +
206E ARG* 1.3 73.9 + - + +
208E ALA* 3.2 1.9 + - - +
209E ILE* 3.1 45.8 + - + +
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Residues in contact with ARG 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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202E GLU* 3.0 40.2 + - - +
203E ILE* 3.7 6.1 - - - +
205E TYR* 1.3 86.8 - - + +
207E ASN* 1.3 62.7 + - - +
209E ILE* 3.8 4.6 - - - +
210E ALA* 3.0 27.9 + - - +
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Residues in contact with ASN 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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214B ILE* 3.6 23.3 - - + +
215B LEU 3.0 27.2 + - - +
216B ASP* 4.6 7.2 + - - +
203E ILE* 2.9 37.7 + - - +
204E SER* 3.9 6.3 - - - +
206E ARG* 1.3 77.5 - - - +
208E ALA* 1.3 60.5 + - - +
210E ALA* 3.6 5.0 - - - +
211E ARG* 2.9 44.2 + - - +
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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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152E ALA* 4.8 5.6 - - + -
191E GLN 3.9 13.5 - - - +
193E VAL* 3.4 27.4 - - + +
204E SER 2.8 19.7 + - - +
205E TYR 3.5 3.1 - - - +
207E ASN* 1.3 74.4 - - - +
209E ILE* 1.3 66.2 + - - +
211E ARG* 3.3 16.6 + - - +
212E LEU* 2.9 33.0 + - + +
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Residues in contact with ILE 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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130E HIS* 3.8 33.2 - - + +
132E HIS* 6.1 1.1 - - - +
133E LEU* 4.6 4.1 - - + +
149E ILE* 4.8 12.1 - - + -
152E ALA* 4.2 18.8 - - + -
153E GLU* 4.3 1.3 - - - +
205E TYR* 3.1 46.1 + - + +
206E ARG* 3.8 4.9 - - - +
208E ALA* 1.3 77.7 - - - +
210E ALA* 1.3 53.2 + - - +
212E LEU* 3.4 7.6 + - + +
213E SER* 2.6 43.4 + - - +
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Residues in contact with ALA 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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214B ILE* 4.0 17.4 - - + +
206E ARG 3.0 17.7 + - - +
207E ASN* 3.6 8.7 - - - +
208E ALA 3.3 0.2 - - - -
209E ILE* 1.3 78.3 - - - +
211E ARG* 1.3 62.0 + - - +
213E SER* 3.2 21.2 + - - -
214E ILE* 3.4 14.4 + - - +
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Residues in contact with ARG 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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211B ARG* 4.8 27.7 + - + +
214B ILE* 3.4 33.2 - - + +
216B ASP* 5.5 8.1 + - - -
191E GLN 3.5 20.8 + - - -
192E GLY* 3.5 28.6 + - - -
204E SER* 5.5 0.4 - - - +
207E ASN* 2.9 18.5 + - - +
208E ALA* 3.3 25.6 + - - +
210E ALA* 1.3 74.7 - - - +
212E LEU* 1.3 65.2 + - + +
214E ILE* 3.0 29.0 + - - +
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Residues in contact with LEU 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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133E LEU* 4.1 8.6 - - + +
145E MET* 3.6 42.2 - - + +
148E LYS* 4.0 36.8 - - + +
149E ILE* 5.1 9.0 - - + +
191E GLN* 4.2 21.5 - - + +
208E ALA* 2.9 29.3 + - + +
209E ILE* 3.8 8.3 - - + +
211E ARG* 1.3 84.4 - - + +
213E SER* 1.3 60.7 + - - +
214E ILE 3.2 3.3 + - - +
215E LEU* 3.9 7.1 - - - +
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Residues in contact with SER 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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132E HIS* 6.1 0.5 - - - -
133E LEU* 3.5 22.8 - - - +
136E LYS* 6.1 0.7 - - - +
209E ILE* 2.6 26.2 + - - +
210E ALA* 3.3 14.3 - - - -
211E ARG 3.1 0.4 - - - -
212E LEU* 1.3 76.2 - - - +
214E ILE* 1.3 61.4 + - - +
215E LEU* 3.2 16.1 + - - +
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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