Contacts of the helix formed by residues 211 - 222 (chain E) in PDB entry 3ECS
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 GLY 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D ALA* 3.1 28.5 + - - -
128E HIS* 3.6 14.7 + - - -
183E VAL* 6.1 0.9 - - - +
210E ILE* 1.3 72.8 - - - +
212E THR* 1.3 63.9 + - - +
213E ASN 3.3 2.2 - - - -
214E GLN* 3.5 8.4 + - - +
215E MSE 3.4 19.9 + - - +
274E ASP* 2.7 10.2 + - - -
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Residues in contact with THR 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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128E HIS* 3.5 12.6 - - - -
195E VAL* 4.2 11.1 - - + +
206E ILE* 4.2 4.5 - - + -
208E ASN* 2.8 37.1 + - + +
209E LYS 2.9 15.7 + - - -
211E GLY* 1.3 78.4 - - - +
213E ASN* 1.3 62.8 + - - +
215E MSE 3.3 7.3 + - + +
216E ALA* 3.1 20.1 + - - +
226E PHE* 3.9 20.5 - - + -
274E ASP* 3.5 7.8 + - - -
276E THR* 3.6 13.7 - - - +
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Residues in contact with ASN 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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184D GLY* 3.0 42.9 + - - -
185D TYR 4.7 1.8 - - - +
222D GLN* 5.7 0.8 - - - +
211E GLY 3.3 0.2 - - - -
212E THR* 1.3 78.4 - - - +
214E GLN* 1.3 63.0 + - - +
216E ALA* 3.1 7.5 + - - +
217E VAL* 3.0 30.3 + - - +
243E GLN* 4.1 6.2 + - - +
274E ASP* 3.2 25.9 + - + +
275E TYR 3.1 20.8 - - - +
276E THR* 3.6 14.3 + - - -
277E ALA 4.9 0.5 + - - -
280E LEU* 4.3 10.0 - - - +
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Residues in contact with GLN 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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180D ASP 3.2 13.2 + - - +
181D ALA* 2.9 25.8 + - - +
183D VAL* 2.3 45.7 - - + +
184D GLY* 2.9 19.7 - - - +
214D GLN* 3.5 24.1 - - + +
218D CYS* 3.9 18.6 - - - -
180E ASP 4.6 3.1 - - - +
183E VAL* 5.1 3.6 - - + +
211E GLY* 3.5 8.6 + - - +
212E THR 3.4 0.2 - - - -
213E ASN* 1.3 78.7 - - - +
215E MSE 1.3 62.4 + - - +
217E VAL* 3.3 2.2 + - - +
218E CYS* 3.0 29.3 + - - -
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Residues in contact with MSE 215 (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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126E LEU* 3.7 23.1 - - + -
127E THR 3.7 13.7 - - - +
128E HIS* 3.9 22.4 - - + +
153E THR* 3.7 15.3 - - + -
183E VAL* 3.6 39.9 - - + +
187E MSE 3.5 14.3 - - + +
193E VAL* 3.7 31.6 - - + -
195E VAL* 4.4 3.6 - - - -
211E GLY 3.4 8.3 + - - +
212E THR* 3.3 10.7 + - - +
213E ASN 3.3 0.6 - - - -
214E GLN* 1.3 78.5 - - - +
216E ALA* 1.3 59.4 + - - +
218E CYS 3.2 1.6 + - - -
219E ALA* 2.8 29.3 + - - +
226E PHE* 4.3 2.7 - - + -
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Residues in contact with ALA 216 (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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212E THR 3.1 6.8 + - - +
213E ASN 3.1 9.3 + - - +
215E MSE 1.3 80.3 - - - +
217E VAL* 1.3 57.1 + - - +
219E ALA* 3.1 3.0 + - - +
220E LYS* 2.9 29.6 + - - +
226E PHE* 3.7 25.1 - - + -
276E THR* 3.5 30.7 - - + -
280E LEU* 3.9 17.3 - - + +
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Residues in contact with VAL 217 (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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217D VAL* 3.9 18.8 - - + +
218D CYS* 4.0 17.3 - - + -
221D ALA* 3.9 28.5 - - + -
213E ASN* 3.0 30.1 + - - +
214E GLN 3.8 5.8 - - - +
215E MSE 3.2 0.2 - - - -
216E ALA* 1.3 76.5 - - - +
218E CYS* 1.3 56.1 + - - +
220E LYS* 3.4 2.3 + - - +
221E ALA* 3.0 27.8 + - + +
280E LEU* 3.9 26.7 - - + -
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Residues in contact with CYS 218 (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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214D GLN* 4.0 17.7 - - - -
217D VAL* 4.1 29.4 - - + -
218D CYS* 5.1 2.2 - - - -
183E VAL* 4.6 1.6 - - + -
184E GLY* 3.7 29.8 - - - -
187E MSE 3.5 28.7 - - + +
214E GLN 3.0 21.6 + - - +
215E MSE 3.8 3.4 - - - +
217E VAL* 1.3 76.1 - - - +
219E ALA* 1.3 61.0 + - - +
221E ALA* 3.7 1.4 + - - +
222E GLN* 3.4 19.2 + - - +
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Residues in contact with ALA 219 (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 MSE 3.8 19.0 - - + +
193E VAL* 4.4 4.3 - - + -
215E MSE 2.8 13.7 + - - +
216E ALA* 3.3 12.8 - - - +
218E CYS* 1.3 75.1 - - - +
220E LYS* 1.3 60.9 + - - +
222E GLN 3.2 1.9 + - - -
223E ASN 2.8 23.6 + - - -
224E LYS* 2.9 30.7 + - + +
226E PHE* 4.4 15.5 - - + -
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Residues in contact with LYS 220 (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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216E ALA 2.9 15.4 + - - +
217E VAL* 3.8 4.7 - - - +
219E ALA* 1.3 75.0 - - - +
221E ALA* 1.3 60.0 + - - +
223E ASN* 2.9 35.5 + - - +
224E LYS 4.7 1.8 + - - +
279E SER* 3.7 28.0 + - - +
280E LEU* 3.8 24.6 - - + +
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Residues in contact with ALA 221 (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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217D VAL* 3.6 25.1 - - + -
217E VAL* 3.0 17.8 + - + +
218E CYS 3.9 5.2 - - - +
219E ALA 3.3 0.2 - - - -
220E LYS* 1.3 76.8 - - - +
222E GLN* 1.3 62.9 + - + +
223E ASN* 3.9 4.7 - - - +
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Residues in contact with GLN 222 (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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213D ASN* 5.6 0.7 + - - -
184E GLY 4.1 8.0 - - - +
187E MSE 3.6 21.1 - - - +
188E GLU* 3.2 40.0 + - - +
218E CYS* 3.4 12.9 + - - +
219E ALA 3.2 3.3 + - - +
220E LYS 3.1 0.6 - - - -
221E ALA* 1.3 82.6 - - + +
223E ASN* 1.3 72.8 + - - +
224E LYS* 3.3 26.3 + - + +
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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