Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 3CVW
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.4 0.8 - - - -
67A THR* 3.4 24.1 + - - -
70A ASP* 3.5 12.1 - - - -
221A PRO 4.0 0.2 + - - -
222A GLY* 1.3 74.1 - - - -
224A GLU* 1.3 64.9 - - - -
225A THR 3.3 2.5 - - - -
226A GLU 3.6 3.4 + - - -
227A ALA* 3.2 20.4 + - - +
264A TYR* 3.6 6.6 - - - -
269A CYS* 3.9 12.5 - - - -
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Residues in contact with GLU 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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16A LEU 4.2 11.5 + - - +
17A ARG* 3.4 3.5 - - + -
18A LEU* 2.8 39.3 + - - +
19A HIS* 2.7 40.4 + - + +
67A THR* 5.2 0.4 + - - +
70A ASP* 2.8 9.3 + - - +
71A LEU* 4.8 4.9 - - + +
74A GLN* 4.3 13.2 - - + +
177A VAL* 4.9 2.9 - - - +
223A GLY* 1.3 68.7 - - - -
225A THR* 1.3 67.2 + - - +
227A ALA* 3.2 3.5 + - - +
228A LEU* 3.0 33.0 + - + +
269A CYS* 3.4 27.8 - - - +
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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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70A ASP* 2.8 29.9 + - - -
74A GLN* 3.0 18.1 + - - +
223A GLY* 5.8 0.2 - - - -
224A GLU* 1.3 77.9 - - - +
226A GLU* 1.3 57.0 + - - +
228A LEU* 3.5 9.7 + - - +
229A ARG* 3.0 31.3 + - + +
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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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219A LYS 5.4 0.3 - - - +
221A PRO* 3.4 39.6 - - + +
222A GLY 4.7 4.0 - - - +
223A GLY* 3.6 6.7 + - - +
224A GLU 3.3 0.4 - - - -
225A THR* 1.3 76.4 - - - +
227A ALA* 1.3 56.3 + - - +
229A ARG* 3.3 43.0 + - - +
230A ARG* 2.7 42.9 + - + +
264A TYR* 3.4 23.6 + - + +
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Residues in contact with ALA 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 GLY 3.2 7.0 + - - +
224A GLU 3.2 9.8 + - - +
226A GLU* 1.3 77.7 - - - +
228A LEU* 1.3 57.1 + - - +
230A ARG* 4.7 0.7 - - - -
231A MET* 2.9 29.7 + - - +
261A LEU* 3.7 7.5 - - - +
264A TYR* 3.6 40.3 - - + -
269A CYS 3.7 17.3 - - - +
270A LEU* 3.8 11.7 - - + +
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Residues in contact with LEU 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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19A HIS* 3.6 31.6 - - + +
224A GLU* 3.0 38.4 + - + +
225A THR* 3.8 7.4 - - - +
227A ALA* 1.3 73.3 - - - +
229A ARG* 1.3 61.0 + - - +
231A MET* 3.2 11.3 + - + +
232A GLU* 2.9 39.9 + - + +
270A LEU* 4.1 6.3 - - + -
274A LEU* 4.1 17.7 - - + -
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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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225A THR* 3.0 21.1 + - + +
226A GLU* 3.3 40.9 + - - +
228A LEU* 1.3 77.4 - - - +
230A ARG* 1.3 94.9 + - - +
232A GLU* 3.5 5.8 + - - +
233A GLU* 3.1 51.0 + - - +
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Residues in contact with ARG 230 (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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219A LYS 5.4 2.0 + - - -
220A PHE* 3.7 22.9 - - - -
226A GLU* 2.7 25.5 + - - +
227A ALA* 3.9 4.0 - - - +
229A ARG* 1.3 97.9 - - - +
231A MET* 1.3 60.1 + - - +
233A GLU* 3.5 4.4 + - + +
234A SER* 2.8 35.1 + - - +
256A PRO* 4.3 10.5 - - - +
258A THR 4.8 1.0 + - - -
259A THR 2.8 27.9 + - - +
260A VAL* 3.2 37.7 + - - +
261A LEU* 3.9 7.2 - - + -
264A TYR* 4.2 16.8 - - - -
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Residues in contact with MET 231 (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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227A ALA 2.9 19.2 + - - +
228A LEU* 3.2 10.1 + - + +
230A ARG* 1.3 74.5 - - - +
232A GLU* 1.3 83.8 + - + +
234A SER* 2.9 3.8 + - - -
235A LEU* 2.8 48.0 + - + +
261A LEU* 3.8 15.0 - - + +
270A LEU* 3.7 22.4 - - + -
274A LEU* 4.6 10.8 - - + -
275A PHE* 3.6 43.3 - - + -
278A LYS* 4.0 24.0 - - + -
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Residues in contact with GLU 232 (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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228A LEU* 2.9 25.9 + - + +
229A ARG* 3.9 5.6 - - - +
231A MET* 1.3 96.6 - - + +
233A GLU* 1.3 60.3 + - - +
235A LEU* 3.5 9.7 + - - +
236A LYS* 3.1 22.7 + - - +
278A LYS* 3.7 19.4 + - - +
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Residues in contact with GLU 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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229A ARG* 3.1 38.1 + - - +
230A ARG* 3.6 9.6 - - + +
232A GLU* 1.3 77.0 - - - +
234A SER* 1.3 61.6 + - - +
236A LYS* 3.4 35.9 + - - +
237A ASP 4.7 0.7 + - - -
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Residues in contact with SER 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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230A ARG* 2.8 21.3 + - - +
231A MET* 2.9 9.2 + - - -
233A GLU* 1.3 77.9 - - - +
235A LEU* 1.3 61.6 + - - +
236A LYS 3.3 1.6 + - - -
237A ASP* 4.4 3.8 + - - +
240A TRP* 3.8 13.9 - - - -
241A VAL* 3.3 16.9 - - - +
259A THR* 3.8 42.9 + - - +
261A LEU* 4.8 2.1 - - - +
275A PHE* 5.9 0.4 - - - -
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Residues in contact with LEU 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 MET* 2.8 42.5 + - + +
232A GLU* 3.7 10.3 - - - +
234A SER* 1.3 77.8 - - - +
236A LYS* 1.3 64.6 + - - +
237A ASP 3.5 2.9 - - - -
238A GLU* 3.8 17.3 + - - +
241A VAL* 3.8 15.5 - - + -
275A PHE* 4.2 10.5 - - + -
278A LYS* 3.7 32.8 - - + -
279A LEU* 3.9 22.9 - - + -
282A ILE* 3.8 24.5 - - + +
296A LEU* 5.5 1.3 - - + -
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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