Contacts of the helix formed by residues 222 - 232 (chain A) in PDB entry 3EJW
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY* 4.6 1.2 - - - -
15A PHE* 3.5 41.3 + - + +
196A ALA* 5.2 0.8 - - + +
221A SER* 1.3 80.6 + - - +
223A PRO* 1.3 71.6 - - - +
224A ASN* 5.1 0.2 - - - +
225A VAL* 3.3 26.0 + - - +
226A MET* 3.0 23.4 + - - +
238A PHE* 4.2 2.5 - - - -
240A LEU* 4.0 5.6 - - + -
243A VAL* 5.1 0.2 - - + -
315A PHE* 3.6 36.2 + - + +
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Residues in contact with PRO 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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221A SER 4.3 3.4 - - - +
222A THR* 1.3 83.5 - - - +
224A ASN* 1.3 56.4 + - - +
227A ARG* 2.9 48.8 + - - +
238A PHE* 4.0 11.2 - - + -
305A PHE* 3.8 24.5 - - + -
310A ILE* 3.9 12.6 - - + +
313A PHE* 3.9 12.6 - - + +
315A PHE* 3.4 48.5 - - + +
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Residues in contact with ASN 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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222A THR* 5.1 0.7 - - - +
223A PRO* 1.3 73.1 - - - +
225A VAL* 1.3 62.5 + - + +
227A ARG* 2.8 36.6 + - - +
228A PRO* 4.4 3.6 - - - +
314A ASP* 2.9 26.2 + - - +
315A PHE* 2.9 41.4 + - - +
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Residues in contact with VAL 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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13A VAL* 6.4 0.4 - - + -
14A GLY* 5.0 14.6 - - - +
196A ALA 4.5 2.0 - - - +
200A PRO* 3.7 33.9 - - + -
221A SER* 3.9 9.9 - - - +
222A THR* 3.3 23.8 + - - +
223A PRO 3.2 0.4 - - - -
224A ASN* 1.3 80.2 - - + +
226A MET* 1.3 61.7 + - - +
228A PRO* 3.5 11.4 - - - +
229A TYR* 3.9 10.9 - - - -
137B THR* 5.7 9.0 - - + -
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Residues in contact with MET 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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199A LEU* 3.8 22.4 - - + -
200A PRO* 3.8 33.4 - - + -
203A ALA* 4.5 4.3 - - + -
221A SER* 3.6 16.6 - - - -
222A THR 3.0 18.9 + - - +
225A VAL* 1.3 74.1 - - - +
227A ARG* 1.3 66.5 + - - +
228A PRO* 3.3 4.9 - - - -
229A TYR* 3.0 36.9 + - + +
230A ILE* 3.1 10.9 + - - +
235A ILE* 3.8 26.9 - - + -
238A PHE* 3.4 31.4 - - + -
310A ILE* 4.5 1.8 - - - -
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Residues in contact with ARG 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 PRO* 2.9 23.1 + - - +
224A ASN* 2.8 35.8 + - - +
225A VAL 3.4 0.2 - - - -
226A MET* 1.3 76.2 - - - +
228A PRO* 1.3 65.5 - - + +
230A ILE* 3.2 2.9 + - - +
231A GLU* 2.8 62.1 + - + +
310A ILE* 2.9 47.8 + - + +
311A GLY* 3.9 7.9 + - - -
313A PHE 2.8 21.4 + - - -
314A ASP* 4.4 0.4 - - - +
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Residues in contact with PRO 228 (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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224A ASN 4.4 3.6 - - - +
225A VAL 3.5 13.5 - - - +
226A MET 3.3 4.9 - - - -
227A ARG* 1.3 96.9 - - + +
229A TYR* 1.3 70.6 + - + +
231A GLU* 3.9 8.8 - - - +
232A ARG* 3.0 42.5 + - + +
136B PRO* 6.4 2.0 - - + -
146B GLU* 6.0 1.8 - - - +
166B TYR* 6.0 2.2 - - - +
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Residues in contact with TYR 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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200A PRO* 3.8 24.0 + - + +
203A ALA* 3.5 21.3 - - + -
204A GLN* 2.6 49.5 + - - +
207A GLU* 3.4 24.0 - - - -
225A VAL 3.9 16.6 - - - -
226A MET* 3.0 31.9 + - + +
228A PRO* 1.3 85.6 - - + +
230A ILE* 1.3 62.8 + - - +
232A ARG* 5.8 0.4 - - - -
233A GLY 3.2 1.7 + - - -
234A THR* 2.9 36.2 + - - -
235A ILE* 3.3 9.6 + - + -
136B PRO* 5.0 10.6 - - + +
166B TYR* 4.8 4.9 - - - -
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Residues in contact with ILE 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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226A MET 3.1 9.1 + - - +
227A ARG 3.7 6.1 - - - +
229A TYR* 1.3 74.2 - - - +
231A GLU* 1.3 65.7 + - + +
233A GLY* 3.1 13.0 + - - -
235A ILE* 3.7 24.6 - - + +
236A GLN 3.5 28.0 - - - +
237A ARG 4.0 1.3 - - - +
238A PHE* 3.8 28.7 - - + -
305A PHE 4.1 7.0 - - - +
306A THR* 3.8 4.3 - - - -
307A LYS* 3.5 40.6 - - + +
310A ILE* 4.0 19.1 - - + -
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Residues in contact with GLU 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 ARG* 2.8 53.0 + - + +
228A PRO* 4.0 6.7 - - + +
230A ILE* 1.3 78.9 - - + +
232A ARG* 1.3 61.9 + - + +
307A LYS* 5.6 2.9 - - + -
310A ILE* 5.2 7.4 - - + +
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Residues in contact with ARG 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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207A GLU* 2.8 50.6 + - - +
210A LYS* 5.5 4.2 - - - +
228A PRO* 3.0 22.9 + - + +
229A TYR 4.2 0.2 - - - +
231A GLU* 1.3 78.8 - - + +
233A GLY* 1.3 59.6 + - - +
234A THR* 3.2 16.8 + - - +
161B ILE 5.3 4.0 + - - -
162B VAL 3.0 27.7 + - - -
163B THR* 4.3 11.4 - - - +
164B THR* 5.1 6.7 - - - +
185B TYR* 4.9 2.6 + - - -
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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