Contacts of the helix formed by residues 221 - 236 (chain A) in PDB entry 4CSC
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 ASP 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A TYR* 3.6 4.6 - - + +
220A THR* 1.3 80.7 + - - +
222A ALA* 1.3 65.4 + - - +
223A GLN* 2.6 37.9 + - - +
224A PHE* 3.3 26.3 + - + +
225A THR* 3.6 8.0 + - - -
385A TYR* 4.0 24.1 - - + +
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Residues in contact with ALA 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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220A THR 3.1 7.1 + - - +
221A ASP* 1.3 77.3 + - - +
223A GLN* 1.3 60.8 + - - +
225A THR* 3.4 17.9 + - - -
226A GLU* 3.5 14.9 + - - +
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Residues in contact with GLN 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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86A GLU* 5.3 0.6 + - - -
221A ASP* 2.6 18.0 + - - +
222A ALA* 1.3 73.5 - - - +
224A PHE* 1.3 58.3 + - - +
226A GLU* 3.3 22.2 + - - +
227A LEU* 2.8 26.9 + - - +
336A PHE* 3.5 19.9 - - - -
340A HIS* 3.0 45.0 + - + +
385A TYR* 3.6 22.0 - - + +
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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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214A THR* 3.4 29.4 - - + -
217A LEU* 4.9 1.8 - - + -
219A TYR* 3.4 41.1 - + + -
221A ASP* 3.3 24.5 + - + +
223A GLN* 1.3 80.9 - - - +
225A THR* 1.3 51.7 + - - +
227A LEU* 3.2 9.6 + - + +
228A MET* 2.8 40.8 + - - +
382A LEU* 4.4 18.6 - - + -
385A TYR* 3.2 39.6 - + + -
387A MET* 3.9 32.1 - - + -
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Residues in contact with THR 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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210A SER 4.5 0.9 - - - -
211A HIS* 3.7 39.9 + - + +
214A THR* 3.8 15.6 + - - +
219A TYR 5.2 2.4 + - - -
220A THR 5.3 1.0 + - - -
221A ASP 3.6 10.1 + - - -
222A ALA* 3.4 12.6 + - - -
223A GLN 3.2 0.6 - - - -
224A PHE* 1.3 74.0 - - - +
226A GLU* 1.3 61.2 + - - +
228A MET* 3.3 7.0 + - - +
229A ARG* 2.9 61.3 + - - +
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Residues in contact with GLU 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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81A GLY 5.2 0.3 + - - -
84A GLY* 2.9 20.4 + - - +
85A GLY* 2.7 25.3 + - - -
86A GLU* 3.1 28.2 + - - +
222A ALA 3.5 11.4 + - - +
223A GLN* 3.3 32.3 + - - +
225A THR* 1.3 76.4 - - - +
227A LEU* 1.3 65.2 + - - +
229A ARG* 2.7 41.9 + - - +
230A LEU* 3.1 22.0 + - - +
336A PHE* 4.5 0.2 - - - -
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Residues in contact with LEU 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 GLN 2.8 11.3 + - - +
224A PHE* 3.5 14.6 - - + +
226A GLU* 1.3 76.0 - - - +
228A MET* 1.3 60.1 + - - +
230A LEU* 3.2 7.6 + - + +
231A TYR* 2.8 42.6 + - + +
336A PHE* 3.7 31.4 - - + -
381A LEU* 3.7 58.8 - - + +
382A LEU* 3.9 23.8 - - + -
385A TYR* 3.9 12.3 - - + -
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Residues in contact with MET 228 (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 SER* 4.4 7.6 - - - +
213A PHE* 4.1 9.4 - - + -
214A THR* 3.9 22.4 - - + -
217A LEU* 5.1 2.5 - - - -
224A PHE* 2.8 33.4 + - - +
225A THR 3.5 6.7 - - - +
227A LEU* 1.3 78.9 - - - +
229A ARG* 1.3 56.2 + - - +
231A TYR* 3.7 15.1 - - + +
232A LEU* 3.0 84.9 + - + +
382A LEU* 5.2 4.7 - - - -
396A LEU* 3.9 32.1 - - + -
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Residues in contact with ARG 229 (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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81A GLY* 4.5 12.9 - - - +
84A GLY 4.4 5.3 - - - +
86A GLU* 4.2 9.4 - - + -
87A PRO 3.5 13.9 - - - +
88A LEU* 3.5 20.7 - - + +
89A PRO* 3.8 4.9 - - + +
208A ASP* 2.9 36.3 + - - +
210A SER* 3.8 20.4 + - - +
211A HIS* 4.1 10.3 + - - +
225A THR* 2.9 46.3 + - + +
226A GLU* 2.7 47.7 + - - +
228A MET* 1.3 73.1 - - - +
230A LEU* 1.3 63.9 + - - +
232A LEU 3.8 0.2 + - - -
233A THR* 2.9 29.1 + - - -
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Residues in contact with LEU 230 (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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71A ILE* 5.8 0.4 - - + -
75A GLN* 4.4 8.5 - - + +
86A GLU* 3.4 40.5 - - + +
87A PRO* 4.4 9.0 - - + -
226A GLU 3.1 6.3 + - - +
227A LEU* 3.5 12.1 - - + +
229A ARG* 1.3 75.9 - - - +
231A TYR* 1.3 57.3 + - - +
233A THR* 2.8 8.3 + - - -
234A ILE* 2.7 55.0 + - + +
332A CYS* 3.9 25.6 - - - +
333A GLN* 5.5 4.0 - - + -
336A PHE* 3.8 28.7 - - + -
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Residues in contact with TYR 231 (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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227A LEU* 2.8 31.2 + - + +
228A MET* 3.7 20.6 - - + +
230A LEU* 1.3 75.0 - - - +
232A LEU* 1.3 67.4 + - - +
234A ILE* 3.2 5.8 + - - -
235A HIS* 2.8 68.1 + + + +
278A ASN* 3.4 27.4 + - - -
333A GLN* 4.6 3.6 - - - -
378A SER* 3.7 18.8 + - - -
381A LEU* 6.2 0.7 - - + -
382A LEU* 4.1 28.7 - - + +
393A TYR 3.4 9.2 + - - -
396A LEU* 3.8 30.7 - - + +
397A PHE* 3.7 2.6 + - - -
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Residues in contact with LEU 232 (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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89A PRO* 3.9 15.0 - - + -
209A TRP* 3.9 15.3 - - + -
210A SER* 3.2 26.0 - - - +
213A PHE* 4.3 10.5 - - + -
228A MET* 3.0 49.9 + - + +
231A TYR* 1.3 79.0 - - + +
233A THR* 1.3 59.2 + - - +
236A SER* 3.8 1.4 + - - -
396A LEU 4.0 9.6 - - - +
399A VAL* 4.2 13.2 - - + -
400A SER* 2.6 48.7 + - - +
403A LEU* 3.9 12.0 - - - +
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Residues in contact with THR 233 (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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66A PHE* 4.4 6.2 - - + -
74A CYS* 5.4 4.5 - - + -
78A LEU* 4.8 3.6 - - + -
87A PRO* 3.3 31.5 + - + -
88A LEU 3.9 1.2 - - - -
89A PRO* 3.5 15.1 - - - +
92A LEU* 3.0 46.5 - - + +
229A ARG 2.9 16.9 + - - -
230A LEU* 2.8 11.5 + - - -
232A LEU* 1.3 79.7 - - - +
234A ILE* 1.3 72.8 + - + +
236A SER* 3.0 7.1 - - - -
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Residues in contact with ILE 234 (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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66A PHE* 4.4 11.4 - - + -
71A ILE* 4.2 26.0 - - + -
230A LEU* 2.7 42.3 + - + +
231A TYR* 3.2 5.1 + - - +
233A THR* 1.3 83.6 - - + +
235A HIS* 1.3 75.8 - - + +
236A SER* 3.2 2.0 + - - -
237A ASP 4.8 0.9 - - - +
329A ARG* 3.6 53.1 + - + +
332A CYS* 4.1 16.2 - - - -
333A GLN* 4.0 23.1 - - + +
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Residues in contact with HIS 235 (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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231A TYR* 2.8 61.6 + + + +
234A ILE* 1.3 84.2 - - + +
236A SER* 1.3 53.1 + - - +
237A ASP 3.4 2.5 - - - -
278A ASN* 5.3 0.2 + - - -
329A ARG* 5.2 2.5 - - - +
333A GLN* 3.8 17.0 - - - -
374A VAL* 3.5 26.2 - - + +
375A ASP* 5.0 1.4 + - - -
378A SER* 4.1 6.5 + - - -
397A PHE* 3.6 43.4 - + + -
400A SER* 2.9 23.7 + - - +
401A ARG* 2.8 40.3 + - - +
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Residues in contact with SER 236 (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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66A PHE* 4.2 8.7 - - - -
92A LEU* 2.7 27.1 - - - +
96A LEU* 3.9 5.8 - - - +
232A LEU 4.1 0.9 - - - -
233A THR 3.0 18.6 + - - -
235A HIS* 1.3 73.6 - - - +
237A ASP* 1.3 63.3 + - - -
400A SER* 2.7 17.8 + - - -
401A ARG* 3.1 17.0 - - - +
403A LEU* 3.8 16.1 - - - +
404A GLY* 2.9 21.0 + - - -
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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