Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 1PUF
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 THR 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PRO 5.3 1.6 - - - +
212A TYR* 1.3 76.9 - - - +
214A LYS* 1.3 68.4 + - - +
215A HIS* 3.7 9.1 + - - +
216A GLN* 2.6 40.4 + - - +
217A THR* 2.8 23.1 + - - -
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Residues in contact with LYS 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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212A TYR 4.1 0.2 + - - -
213A THR* 1.3 72.8 - - - +
215A HIS* 1.3 56.1 + - - +
217A THR* 3.4 3.7 + - - -
218A LEU* 2.7 52.5 + - + +
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Residues in contact with HIS 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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213A THR* 3.0 9.2 + - - +
214A LYS* 1.3 76.8 - - - +
216A GLN* 1.3 71.5 + - + +
218A LEU* 3.9 4.2 - - - +
219A GLU* 3.0 48.3 + - + +
241A LEU* 4.9 6.7 + - + +
242A LEU* 3.8 21.3 - - + +
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Residues in contact with GLN 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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211A PRO 4.7 0.2 - - - +
212A TYR* 3.2 19.8 - - + -
213A THR* 2.6 45.2 + - - +
215A HIS* 1.3 79.9 - - + +
217A THR* 1.3 59.3 + - - +
219A GLU* 3.7 1.4 - - - +
220A LEU* 2.9 35.7 + - + +
242A LEU* 3.6 41.6 + - + +
243A ASN 4.7 1.4 + - - -
244A LEU* 3.3 33.0 - - + +
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Residues in contact with THR 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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212A TYR* 4.2 13.9 + - - +
213A THR 2.8 17.2 + - - -
214A LYS* 3.6 5.8 - - - -
216A GLN* 1.3 77.9 - - - +
218A LEU* 1.3 66.1 + - + +
220A LEU* 3.2 9.6 + - - +
221A GLU* 2.8 31.9 + - + +
252A TRP* 4.4 13.1 + - + +
12D T 4.5 9.0 + - - -
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Residues in contact with LEU 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 LYS* 2.7 52.2 + - + +
215A HIS* 4.0 5.2 - - - +
217A THR* 1.3 84.4 - - + +
219A GLU* 1.3 63.9 + - + +
221A GLU* 3.4 9.7 + - + +
222A LYS* 3.1 31.6 + - + +
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Residues in contact with GLU 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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215A HIS* 3.0 47.1 + - + +
216A GLN 3.7 2.9 - - - +
218A LEU* 1.3 76.3 - - + +
220A LEU* 1.3 66.4 + - - +
222A LYS* 3.2 35.3 + - - +
223A GLU* 3.1 21.3 + - - +
238A VAL* 5.5 1.1 - - + +
241A LEU* 4.3 16.6 - - + +
242A LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 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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212A TYR* 4.1 16.2 - - + -
216A GLN 2.9 21.9 + - - +
217A THR* 3.7 4.0 - - - +
219A GLU* 1.3 73.2 - - - +
221A GLU* 1.3 68.8 + - - +
223A GLU* 3.0 6.1 + - - +
224A PHE* 2.9 22.0 + - - +
238A VAL* 3.8 25.1 - - + -
242A LEU* 3.8 7.6 - - + -
244A LEU* 4.1 11.7 - - + -
249A VAL* 4.3 13.5 - - + -
252A TRP* 3.7 50.4 - - + +
253A PHE* 4.2 19.1 - - + -
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Residues in contact with GLU 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 THR* 2.8 19.8 + - + +
218A LEU* 3.6 12.6 - - + +
219A GLU 3.3 0.2 - - - -
220A LEU* 1.3 77.6 - - - +
222A LYS* 1.3 62.9 + - + +
224A PHE* 3.1 15.6 + - - +
225A LEU* 3.1 37.7 + - + +
252A TRP* 3.5 12.6 - - + -
256A ARG* 2.9 44.2 + - - -
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Residues in contact with LYS 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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218A LEU* 3.1 18.7 + - + +
219A GLU* 3.2 34.7 + - - +
220A LEU 3.2 0.4 - - - -
221A GLU* 1.3 76.7 - - + +
223A GLU* 1.3 61.3 + - - +
225A LEU* 3.6 9.7 + - + +
226A PHE* 3.3 20.3 + - - +
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Residues in contact with GLU 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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219A GLU 3.1 12.2 + - - +
220A LEU* 3.0 10.5 + - - +
222A LYS* 1.3 73.8 - - - +
224A PHE* 1.3 65.2 + - - +
226A PHE* 3.3 11.3 + - - +
227A ASN* 3.2 24.1 + - - +
230A LEU* 4.1 7.0 - - + +
234A ARG* 2.7 60.4 + - - +
238A VAL* 3.5 25.0 - - + +
253A PHE* 3.6 18.6 - - + -
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Residues in contact with PHE 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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220A LEU 2.9 11.2 + - - +
221A GLU* 3.2 20.9 - - - +
223A GLU* 1.3 77.2 - - - +
225A LEU* 1.3 64.8 + - + +
227A ASN 3.1 25.3 - - - -
228A MET* 3.1 61.6 + - + +
252A TRP* 4.2 3.4 - + + -
253A PHE* 3.5 26.9 - + + -
256A ARG* 3.4 60.8 - - + -
257A ARG* 3.8 22.2 - - + -
260A MET* 4.6 2.5 - - - -
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Residues in contact with LEU 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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221A GLU* 3.1 36.0 + - + +
222A LYS* 4.1 8.7 - - + +
223A GLU 3.4 0.2 - - - -
224A PHE* 1.3 82.9 - - + +
226A PHE* 1.3 65.6 + - - +
227A ASN* 4.6 0.2 - - - -
228A MET* 5.3 7.7 - - + +
256A ARG* 5.4 2.0 - - - +
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Residues in contact with PHE 226 (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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222A LYS 3.3 11.3 + - - +
223A GLU* 3.3 23.0 + - - +
224A PHE 3.2 0.6 - - - -
225A LEU* 1.3 81.4 - - - +
227A ASN* 1.3 69.2 + - + +
234A ARG* 3.8 37.9 - - + +
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Residues in contact with ASN 227 (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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223A GLU* 3.2 12.0 + - - +
224A PHE 3.1 6.2 + - - +
225A LEU 4.6 0.2 - - - -
226A PHE* 1.3 98.1 - - + +
228A MET* 1.3 59.0 + - - +
229A TYR 3.0 25.4 + - - +
230A LEU* 5.0 1.2 - - - +
231A THR* 6.2 2.2 - - + -
234A ARG* 6.2 1.8 - - + -
253A PHE* 3.6 8.5 - - - -
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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