Contacts of the helix formed by residues 211 - 222 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B HIS* 3.8 12.4 + - - -
183B VAL* 5.8 1.7 - - - +
210B ILE* 1.3 73.3 - - - +
212B THR* 1.3 64.5 + - - +
213B ASN 3.3 2.5 - - - -
214B GLN* 3.3 19.7 + - - +
215B MSE 3.3 11.3 + - - +
274B ASP* 2.7 9.6 + - - -
181H ALA* 2.9 31.7 + - - -
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B HIS* 3.2 14.1 + - - -
195B VAL* 4.1 16.1 - - + +
206B ILE* 4.2 11.9 - - + -
208B ASN* 3.0 23.4 + - + +
209B LYS 2.9 17.9 + - - -
211B GLY* 1.3 78.4 - - - +
213B ASN* 1.3 64.3 + - - +
215B MSE 3.2 8.2 + - - +
216B ALA* 3.0 19.8 + - - +
226B PHE* 4.1 19.6 - - + -
274B ASP* 3.2 10.3 + - - -
276B THR* 3.7 12.3 - - - +
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Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B THR* 1.3 78.7 - - - +
214B GLN* 1.3 59.8 + - - +
216B ALA* 3.0 6.0 + - - +
217B VAL* 2.9 42.1 + - - +
243B GLN* 3.7 12.6 - - - +
274B ASP* 3.2 18.8 + - + +
275B TYR* 3.0 28.4 + - - +
276B THR* 3.4 15.8 + - - +
277B ALA 4.9 0.8 - - - +
280B LEU* 4.2 11.9 - - - +
184H GLY* 3.6 23.8 - - - +
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Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ASP* 4.1 7.3 + - - +
183B VAL* 5.1 4.5 - - + +
211B GLY* 3.3 17.1 - - - +
213B ASN* 1.3 81.0 + - - +
215B MSE 1.3 60.8 + - - +
217B VAL* 3.3 1.8 + - - +
218B CYS* 3.0 30.8 + - - -
274B ASP* 5.6 0.2 - - - +
180H ASP 2.8 20.8 + - - -
181H ALA* 3.2 21.2 - - - +
183H VAL* 2.8 35.5 + - - +
184H GLY* 2.8 14.5 + - - +
214H GLN* 3.5 24.3 - - + +
218H CYS* 3.6 23.6 - - - -
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Residues in contact with MSE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.6 32.1 - - + -
127B THR 3.8 8.7 - - - +
128B HIS* 3.8 23.3 - - + +
153B THR* 3.5 32.3 - - + -
183B VAL* 3.6 30.3 - - + +
187B MSE 4.9 0.7 - - - +
193B VAL* 4.1 18.8 - - + -
195B VAL* 4.1 6.7 - - - -
211B GLY 3.3 12.4 + - - +
212B THR* 3.2 10.9 + - - +
213B ASN 3.1 0.6 - - - -
214B GLN* 1.3 77.7 - - - +
216B ALA* 1.3 64.6 + - - +
218B CYS* 3.1 3.8 + - - +
219B ALA* 2.9 22.5 + - - +
226B PHE* 4.2 8.5 - - + -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B THR 3.0 6.8 + - - +
213B ASN 3.0 8.7 + - - +
215B MSE 1.3 77.6 - - - +
217B VAL* 1.3 60.4 + - - +
219B ALA* 3.5 2.1 + - - +
220B LYS* 3.1 23.2 + - - +
226B PHE* 3.5 36.7 - - + -
276B THR* 3.6 23.1 - - + -
280B LEU* 3.9 17.8 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASN* 2.9 36.4 + - - +
214B GLN* 3.8 6.1 - - - +
215B MSE 3.2 0.2 - - - -
216B ALA* 1.3 77.1 - - - +
218B CYS* 1.3 59.3 + - - +
220B LYS* 3.6 2.8 + - + +
221B ALA* 3.3 21.0 + - - +
280B LEU* 3.8 25.6 - - + -
217H VAL* 3.9 15.9 - - + +
218H CYS* 4.2 17.5 - - - -
221H ALA* 3.9 27.6 - - + -
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Residues in contact with CYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 4.4 9.2 - - + -
184B GLY* 3.9 29.6 - - - -
187B MSE 3.7 17.4 - - + +
214B GLN 3.0 22.1 + - - +
215B MSE 3.7 3.4 - - - +
217B VAL* 1.3 74.0 - - - +
219B ALA* 1.3 65.7 + - - +
221B ALA* 3.6 2.8 + - - +
222B GLN* 3.4 18.6 + - - +
214H GLN* 4.1 26.0 - - - -
217H VAL* 4.2 20.6 - - + -
218H CYS* 5.1 2.5 - - - -
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B MSE 3.7 22.6 - - - -
193B VAL* 4.0 15.3 - - + -
215B MSE 2.9 15.3 + - - +
216B ALA 3.7 5.2 - - - +
217B VAL 3.3 0.2 - - - -
218B CYS* 1.3 76.8 - - - +
220B LYS* 1.3 61.7 + - - +
222B GLN 3.2 2.9 + - - -
223B ASN 3.2 3.8 + - - -
224B LYS* 2.8 44.7 + - + +
226B PHE* 4.2 11.7 - - + -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA 3.1 14.6 + - - +
217B VAL* 3.6 7.4 - - + +
219B ALA* 1.3 72.2 - - - +
221B ALA* 1.3 66.1 + - - +
222B GLN 3.0 1.8 - - - -
223B ASN* 2.9 16.2 + - - +
224B LYS 5.0 2.2 - - - +
279B SER* 3.1 32.8 + - - +
280B LEU* 3.7 26.9 - - + +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL 3.3 6.3 + - - +
218B CYS 3.6 4.0 + - - +
219B ALA 3.5 0.2 - - - -
220B LYS* 1.3 79.3 - - - +
222B GLN* 1.3 60.4 + - + +
223B ASN* 3.4 1.1 + - - +
217H VAL* 3.8 30.1 - - + -
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLY 4.3 5.5 - - - +
187B MSE 3.3 22.0 - - + +
188B GLU* 2.8 43.8 + - - +
218B CYS* 3.4 11.2 + - - +
219B ALA 3.2 1.6 + - - -
220B LYS 3.0 1.2 - - - -
221B ALA* 1.3 82.7 - - + +
223B ASN* 1.3 68.0 + - - +
224B LYS* 3.1 31.3 + - + +
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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