Contacts of the helix formed by residues 211 - 222 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A HIS* 3.8 13.3 + - - -
183A VAL* 6.0 0.9 - - - +
210A ILE* 1.3 73.7 - - - +
212A THR* 1.3 65.3 + - - +
213A ASN 3.3 2.0 - - - -
214A GLN* 3.3 11.3 + - - +
215A MSE 3.3 19.8 + - - +
274A ASP* 2.7 10.6 + - - -
181C ALA* 3.1 28.6 + - - -
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A HIS* 3.7 12.9 + - - +
195A VAL* 4.4 5.8 - - + +
206A ILE* 4.1 17.9 - - + -
208A ASN* 3.0 30.4 + - + +
209A LYS 3.0 14.6 + - - -
211A GLY* 1.3 77.8 - - - +
213A ASN* 1.3 62.7 + - - +
215A MSE 3.0 9.2 + - - +
216A ALA* 2.9 19.6 + - - +
226A PHE* 4.0 19.4 - - + -
274A ASP* 3.8 8.1 - - - -
276A THR* 3.5 15.0 - - - +
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Residues in contact with ASN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 3.3 0.2 - - - -
212A THR* 1.3 78.2 - - - +
214A GLN* 1.3 58.9 + - - +
216A ALA* 3.1 4.5 + - - +
217A VAL* 2.8 44.9 + - - +
243A GLN* 3.6 12.9 - - - +
274A ASP* 3.5 17.5 + - + +
275A TYR 2.7 30.1 + - - +
276A THR* 3.4 16.2 + - - +
277A ALA 4.7 1.2 - - - +
280A LEU* 4.2 11.1 - - - +
184C GLY* 3.5 25.4 - - - +
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Residues in contact with GLN 214 (chain A).
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 4.6 4.0 + - - -
183A VAL* 5.1 4.5 - - + +
211A GLY* 3.3 8.2 + - - +
212A THR 3.3 0.4 - - - -
213A ASN* 1.3 78.6 + - - +
215A MSE 1.3 58.7 + - - +
217A VAL* 3.8 1.3 - - - +
218A CYS* 2.9 35.8 + - - +
180C ASP 3.0 20.8 + - - +
181C ALA* 3.1 22.0 + - - +
183C VAL* 2.5 38.5 + - + +
184C GLY* 3.2 21.8 - - - +
185C TYR 5.0 0.2 - - - +
214C GLN* 3.6 22.0 + - + +
218C CYS* 3.9 17.7 - - - -
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Residues in contact with MSE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.7 20.9 - - + -
127A THR 3.2 27.8 - - - +
128A HIS* 3.6 22.0 - - + +
153A THR* 3.5 25.8 - - + -
183A VAL* 3.7 28.9 - - + +
187A MSE 3.3 11.2 - - + +
193A VAL* 3.5 28.9 - - + -
195A VAL* 4.1 4.5 - - - -
211A GLY 3.3 8.6 + - - +
212A THR* 3.0 10.8 + - - +
214A GLN* 1.3 79.7 - - - +
216A ALA* 1.3 57.6 + - - +
218A CYS 3.3 0.3 + - - -
219A ALA* 2.8 26.2 + - - +
226A PHE* 4.0 1.8 - - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR 2.9 7.6 + - - +
213A ASN 3.4 7.6 - - - +
215A MSE 1.3 74.3 - - - +
217A VAL* 1.3 65.8 + - - +
219A ALA* 3.1 1.9 + - - +
220A LYS* 3.0 24.4 + - - +
226A PHE* 3.4 35.0 - - + +
276A THR* 3.7 25.1 - - + -
280A LEU* 3.9 17.0 - - + +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ASN* 2.8 38.1 + - - +
214A GLN* 3.8 5.8 - - - +
216A ALA* 1.3 75.8 - - - +
218A CYS* 1.3 62.9 + - - +
220A LYS* 3.3 2.9 + - - +
221A ALA* 3.1 22.3 + - - +
280A LEU* 3.7 26.0 - - + +
217C VAL* 4.1 14.8 - - + +
218C CYS* 4.2 18.8 - - - -
221C ALA* 3.7 29.2 - - + -
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.4 5.2 - - + -
184A GLY* 3.7 28.9 - - - -
187A MSE 3.8 23.3 - - + +
214A GLN* 2.9 21.9 + - - +
215A MSE 3.7 4.0 - - - +
217A VAL* 1.3 78.3 - - - +
219A ALA* 1.3 61.5 + - - +
221A ALA* 3.5 9.7 + - - +
222A GLN* 3.5 11.1 + - - +
214C GLN* 3.8 23.6 - - - -
217C VAL* 4.1 20.4 - - - -
218C CYS* 5.5 1.3 - - - -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A MSE 3.5 21.5 - - + +
193A VAL* 4.0 15.3 - - + -
215A MSE 2.8 17.2 + - - +
216A ALA 3.1 4.4 + - - +
218A CYS* 1.3 73.2 - - - +
220A LYS* 1.3 66.7 + - - +
222A GLN 3.2 2.9 + - - -
223A ASN 2.9 17.7 + - - -
224A LYS* 2.9 27.6 + - + +
226A PHE* 4.1 11.7 - - + -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA 3.0 16.0 + - - +
217A VAL 3.8 3.8 - - - +
219A ALA* 1.3 77.5 - - - +
221A ALA* 1.3 66.0 + - - +
223A ASN* 2.9 22.7 + - - +
224A LYS 4.9 2.2 - - - +
279A SER* 3.0 35.0 + - - +
280A LEU* 4.0 22.2 - - + +
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Residues in contact with ALA 221 (chain A).
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 3.1 9.3 + - - +
218A CYS 3.7 5.2 - - - +
219A ALA 3.2 0.6 - - - -
220A LYS* 1.3 79.5 - - - +
222A GLN* 1.3 62.5 + - + +
223A ASN* 5.2 0.3 - - - +
217C VAL* 3.7 34.3 - - + -
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Residues in contact with GLN 222 (chain A).
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 4.0 8.7 - - - +
187A MSE 3.7 23.0 - - + +
188A GLU* 3.1 39.2 + - - +
218A CYS 3.5 12.9 + - - +
219A ALA 3.2 4.0 + - - +
220A LYS 3.1 0.4 - - - -
221A ALA* 1.3 80.3 - - + +
223A ASN* 1.3 71.8 + - - +
224A LYS* 3.5 24.5 + - + +
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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