Contacts of the helix formed by residues 211 - 222 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ALA* 2.9 34.0 + - - -
128C HIS* 3.8 12.6 + - - -
183C VAL* 6.0 0.5 - - - +
210C ILE* 1.3 73.4 - - - +
212C THR* 1.3 62.7 + - - +
213C ASN 3.3 2.2 - - - -
214C GLN* 3.1 21.6 + - - +
215C MSE 3.3 10.6 + - - +
274C ASP* 2.7 8.7 + - - -
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C HIS* 3.2 13.5 + - - -
195C VAL* 4.3 9.6 - - + -
206C ILE* 4.3 7.4 - - + -
208C ASN* 2.7 35.6 + - + +
209C LYS 2.5 22.4 + - - -
211C GLY* 1.3 76.2 - - - +
213C ASN* 1.3 65.2 + - - +
215C MSE 3.4 7.3 + - - +
216C ALA* 3.2 19.8 + - - +
226C PHE* 4.1 17.0 - - + -
274C ASP* 3.6 7.4 - - - -
276C THR* 3.8 12.1 - - - +
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Residues in contact with ASN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLY* 3.4 28.6 + - - +
185A TYR 4.8 0.2 - - - +
212C THR* 1.3 78.1 - - - +
214C GLN* 1.3 60.3 + - - +
216C ALA* 2.9 20.3 + - - +
217C VAL* 3.1 21.9 + - - +
243C GLN* 3.6 11.9 - - - +
274C ASP* 3.1 27.0 + - + +
275C TYR 2.7 24.5 + - - +
276C THR* 3.6 13.6 - - - +
277C ALA 4.8 1.0 - - - +
280C LEU* 4.6 11.1 - - - +
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Residues in contact with GLN 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP 3.3 17.5 + - - +
181A ALA* 3.3 21.6 - - - +
183A VAL* 3.1 17.8 + - - +
184A GLY* 3.1 22.8 + - - +
214A GLN* 3.6 28.1 - - + +
218A CYS* 3.8 24.1 - - - -
180C ASP* 3.7 9.3 + - - +
183C VAL* 4.9 4.0 - - + +
211C GLY* 3.1 19.9 + - - +
213C ASN* 1.3 80.8 + - - +
215C MSE 1.3 63.8 + - - +
217C VAL* 3.9 2.0 - - - +
218C CYS* 3.0 29.1 + - - +
274C ASP* 4.8 0.2 + - - -
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Residues in contact with MSE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.4 36.3 - - + -
127C THR 3.7 20.9 - - - +
128C HIS* 3.7 26.0 - - + +
153C THR* 3.8 6.5 - - + -
183C VAL* 3.4 41.5 - - + -
187C MSE 3.4 7.5 - - + +
193C VAL* 4.0 14.1 - - + -
195C VAL* 4.2 6.5 - - - -
211C GLY 3.3 11.7 + - - +
212C THR* 3.6 9.9 - - - +
213C ASN 3.1 0.6 - - - -
214C GLN* 1.3 80.7 - - - +
216C ALA* 1.3 56.2 - - - +
218C CYS 3.4 0.3 + - - -
219C ALA* 3.1 23.9 + - - +
226C PHE* 4.2 7.9 - - + -
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C THR 3.2 8.7 + - - +
213C ASN 2.9 10.2 + - - +
215C MSE 1.3 74.7 - - - +
217C VAL* 1.3 60.0 + - - +
219C ALA* 3.2 2.6 + - - +
220C LYS* 2.9 30.8 + - - +
226C PHE* 3.6 22.3 - - + +
276C THR* 3.6 29.4 - - + -
280C LEU* 3.8 18.5 - - + +
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.1 8.3 - - + +
218A CYS* 4.1 26.0 - - - -
221A ALA* 3.7 30.5 - - + -
213C ASN* 3.1 26.0 + - - +
214C GLN* 3.9 6.3 - - - +
216C ALA* 1.3 74.9 - - - +
218C CYS* 1.3 62.6 + - - +
220C LYS* 3.4 3.1 + - - +
221C ALA* 3.1 22.5 + - - +
280C LEU* 3.9 27.8 - - + -
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Residues in contact with CYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLN* 3.9 26.2 - - - -
217A VAL* 4.2 19.7 - - - +
218A CYS* 5.5 1.6 - - - -
183C VAL* 4.2 5.4 - - + -
184C GLY* 3.7 28.9 - - - -
187C MSE 3.7 21.9 - - + +
214C GLN* 3.0 21.2 + - - +
215C MSE 3.7 4.5 - - - +
217C VAL* 1.3 75.2 - - - +
219C ALA* 1.3 61.4 + - - +
221C ALA* 3.6 3.5 + - - +
222C GLN* 3.3 17.7 + - - +
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C MSE 3.4 21.1 - - + +
193C VAL* 3.9 17.7 - - + -
215C MSE 3.1 17.5 + - - +
216C ALA 3.7 4.0 - - - +
218C CYS* 1.3 74.7 - - - +
220C LYS* 1.3 65.0 + - - +
222C GLN 3.2 1.0 + - - -
223C ASN 3.0 3.8 + - - -
224C LYS* 2.7 43.0 + - + +
226C PHE* 4.3 9.6 - - + -
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Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA 2.9 17.1 + - - +
217C VAL* 3.7 5.2 - - - +
219C ALA* 1.3 76.3 - - - +
221C ALA* 1.3 56.3 + - - +
223C ASN* 2.7 27.6 + - - +
224C LYS 4.8 3.1 - - - -
279C SER* 3.2 33.6 + - - +
280C LEU* 3.9 26.4 - - + +
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 3.7 23.1 - - + -
280A LEU* 6.5 0.2 - - + -
217C VAL 3.1 14.0 + - - +
218C CYS 3.8 4.0 - - - +
219C ALA 3.3 0.2 - - - -
220C LYS* 1.3 79.9 - - - +
222C GLN* 1.3 62.6 + - + +
223C ASN* 3.3 1.1 + - - +
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Residues in contact with GLN 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY 4.2 7.6 - - - +
187C MSE 3.7 15.0 - - + +
188C GLU* 3.2 45.3 + - - +
218C CYS 3.3 12.6 + - - +
219C ALA 3.2 2.2 + - - -
220C LYS 3.1 0.8 - - - -
221C ALA* 1.3 81.5 - - + +
223C ASN* 1.3 70.0 + - - +
224C LYS* 3.3 32.6 + - + +
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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
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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