Contacts of the helix formed by residues 212 - 225 (chain A) in PDB entry 1TFZ
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 GLU 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A VAL* 3.6 4.2 - - - +
211A PRO* 1.3 97.8 - - + +
213A LEU* 1.3 65.3 + - - +
214A GLY 3.4 1.3 - - - -
215A PRO* 3.5 27.0 - - + +
216A ALA* 3.4 21.5 + - - +
262A GLU* 3.6 3.8 - - - -
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Residues in contact with LEU 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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210A VAL* 3.9 6.1 - - - -
212A GLU* 1.3 70.2 - - - +
214A GLY* 1.3 55.1 - - - +
216A ALA* 3.2 2.4 + - - +
217A LEU* 2.8 58.4 + - + +
245A ASN* 3.5 35.7 - - + +
246A SER 3.8 12.6 - - - +
247A ALA* 4.3 5.8 - - + +
260A ILE* 3.3 46.2 - - + +
261A ASN* 4.2 1.3 - - - +
262A GLU* 2.7 30.7 + - + +
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Residues in contact with GLY 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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213A LEU* 1.3 79.3 - - - +
215A PRO* 1.3 63.4 - - - +
217A LEU* 3.6 7.3 - - - +
218A THR* 3.0 34.8 + - - -
262A GLU* 4.3 1.8 + - - -
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Residues in contact with PRO 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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212A GLU* 3.5 35.9 - - + +
214A GLY* 1.3 88.3 - - - +
216A ALA* 1.3 55.8 + - - +
218A THR* 3.9 6.6 - - - -
219A TYR* 2.9 30.7 + - - +
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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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160A LEU 6.0 0.4 - - - +
161A TYR* 5.6 4.5 - - + -
210A VAL* 3.8 25.8 - - + -
212A GLU 3.4 12.2 + - - +
213A LEU 3.2 8.6 + - - +
215A PRO* 1.3 76.1 - - - +
217A LEU* 1.3 67.3 + - - +
219A TYR* 3.4 5.9 + - - +
220A VAL* 3.0 32.5 + - + +
260A ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 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 LEU* 2.8 45.0 + - + +
214A GLY* 3.6 6.1 - - - +
216A ALA* 1.3 70.8 - - - +
218A THR* 1.3 62.3 + - - +
221A ALA* 2.9 37.4 + - + +
228A GLN* 4.7 13.5 - - + +
247A ALA* 3.5 38.4 - - + +
249A LEU* 3.9 32.7 - - + +
260A ILE* 4.5 8.5 - - + -
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Residues in contact with THR 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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214A GLY 3.0 18.2 + - - -
215A PRO* 3.9 8.1 - - - -
217A LEU* 1.3 76.6 - - - +
219A TYR* 1.3 57.9 + - - +
221A ALA* 4.9 2.2 - - - -
222A GLY* 3.0 25.8 + - - -
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Residues in contact with TYR 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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138A ASN 5.2 0.3 - - - +
139A GLY 3.1 27.5 - - - -
140A ALA* 3.5 4.8 - - - -
141A ILE* 2.8 43.9 + - + +
159A LYS* 2.9 32.1 + - + +
160A LEU 3.7 18.4 - - - -
215A PRO 2.9 19.8 + - - +
216A ALA* 3.7 5.4 - - - +
218A THR* 1.3 77.1 - - - +
220A VAL* 1.3 70.0 + - + +
222A GLY* 3.3 2.3 + - - -
223A PHE* 3.2 38.4 + + - +
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Residues in contact with VAL 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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160A LEU* 3.8 48.5 - - + +
166A LEU* 5.7 0.2 - - + -
216A ALA* 3.0 18.3 + - + +
219A TYR* 1.3 79.0 - - + +
221A ALA* 1.3 63.8 + - - +
223A PHE* 3.5 13.4 + - + -
224A THR* 2.8 37.2 + - + +
226A PHE* 5.2 0.9 - - + -
249A LEU* 3.7 21.3 - - + -
258A LEU* 4.7 12.1 - - + -
260A ILE* 4.4 11.9 - - + -
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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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20A LYS* 4.3 1.6 + - - -
217A LEU 2.9 22.8 + - - +
218A THR* 4.5 2.0 - - - +
220A VAL* 1.3 73.1 - - - +
222A GLY* 1.3 64.4 + - - +
224A THR* 4.0 3.4 - - - -
225A GLY* 2.9 24.1 + - - -
226A PHE 3.6 22.0 - - - +
249A LEU* 3.8 16.4 - - + +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.2 30.5 + - - -
138A ASN* 3.6 12.6 - - - +
218A THR 3.0 21.7 + - - -
219A TYR* 3.7 1.8 - - - -
220A VAL 3.2 0.4 - - - -
221A ALA* 1.3 78.1 - - - +
223A PHE* 1.3 57.3 + - - +
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Residues in contact with PHE 223 (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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20A LYS* 3.7 9.1 - - - +
21A PHE* 3.6 5.0 - - - -
135A SER* 3.2 55.5 + - - +
138A ASN* 3.6 13.9 + - - +
140A ALA* 3.3 15.7 - - + +
158A VAL* 3.6 12.3 - - + -
159A LYS 3.8 12.3 - - - -
160A LEU* 4.6 3.6 - - + -
166A LEU* 3.8 11.2 - - + -
168A TYR* 3.3 13.7 - - - -
219A TYR* 3.2 52.6 + + - +
220A VAL* 3.5 18.6 + - + -
221A ALA 3.4 0.2 - - - -
222A GLY* 1.3 75.4 - - - +
224A THR* 1.3 80.0 + - + +
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Residues in contact with THR 224 (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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19A ASP* 3.5 4.5 - - - +
20A LYS* 2.8 27.0 + - - +
21A PHE* 3.9 13.6 - - + -
166A LEU* 4.1 11.0 - - + -
168A TYR* 4.1 8.5 - - - +
220A VAL* 2.8 22.6 + - + +
223A PHE* 1.3 106.7 - - + +
225A GLY* 1.3 61.8 + - - +
226A PHE* 3.1 45.9 + - + +
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Residues in contact with GLY 225 (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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18A SER* 2.8 49.3 + - - +
19A ASP* 3.7 2.2 + - - +
20A LYS* 4.0 13.6 - - - +
221A ALA 2.9 16.1 + - - -
223A PHE 3.7 0.6 - - - -
224A THR* 1.3 78.3 - - - +
226A PHE* 1.3 63.4 + - - +
227A HIS 3.4 0.9 + - - -
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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