Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 4D88
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 LYS 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TYR* 6.3 0.4 - - - -
223A LEU 3.6 1.2 + - - -
224A PRO* 1.3 71.0 - - - +
226A LYS* 1.3 61.6 + - + +
228A PHE* 3.3 1.3 + - - +
229A GLU* 2.9 65.1 + - - +
313A GLN* 3.5 39.3 - - + +
314A SER 4.2 3.2 + - - +
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Residues in contact with LYS 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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202A MET* 3.5 20.8 - - + +
206A GLU* 3.5 36.7 + - - +
209A TYR* 6.5 0.2 - - + -
224A PRO* 3.0 3.0 + - + +
225A LYS* 1.3 81.3 - - + +
227A VAL* 1.3 63.4 + - + +
229A GLU* 3.6 11.8 + - - +
230A ALA* 3.3 22.5 + - - +
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Residues in contact with VAL 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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193A VAL* 5.1 5.6 - - + -
200A LEU* 4.3 15.2 - - + +
202A MET* 4.0 18.2 - - + -
206A GLU 3.7 23.3 - - - +
207A TYR* 3.9 30.1 - - + -
223A LEU* 4.1 23.8 - - + -
224A PRO* 2.9 19.0 + - + +
226A LYS* 1.3 75.0 - - + +
228A PHE* 1.3 66.3 + - - +
230A ALA* 3.3 3.3 + - - +
231A ALA* 2.9 23.7 + - + +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 3.8 20.9 - - + +
224A PRO 2.8 16.7 + - - +
225A LYS* 3.5 4.9 - - - +
227A VAL* 1.3 76.3 - - - +
229A GLU* 1.3 71.5 + - + +
231A ALA* 3.2 2.3 + - - +
232A VAL* 3.0 53.1 + - + +
249A TRP 3.8 18.2 - - - -
250A LEU* 5.7 7.4 - - + -
309A PHE* 4.5 0.7 - + - -
311A ILE* 3.6 28.0 - - + -
312A SER* 3.5 20.0 - - - -
313A GLN* 3.5 43.3 - - + -
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Residues in contact with GLU 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 LYS* 2.9 55.4 + - + +
226A LYS* 4.0 10.3 - - - +
228A PHE* 1.3 86.6 - - + +
230A ALA* 1.3 59.0 + - - +
232A VAL* 3.5 4.9 + - - +
233A LYS* 3.0 52.8 + - - +
313A GLN* 5.1 3.3 + - - +
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Residues in contact with ALA 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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195A ILE* 4.6 0.3 - - - +
200A LEU* 4.3 26.3 - - + +
202A MET* 4.9 7.0 - - + -
226A LYS 3.3 11.8 + - - +
227A VAL* 3.3 9.3 + - - +
228A PHE 3.2 0.4 - - - -
229A GLU* 1.3 79.1 - - - +
231A ALA* 1.3 62.6 + - - +
233A LYS* 3.5 13.2 + - - +
234A SER* 3.1 22.9 + - - -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 3.4 25.1 - - + +
200A LEU* 4.9 2.4 - - + +
223A LEU* 4.0 20.0 - - + -
227A VAL 2.9 17.0 + - - +
228A PHE 3.2 4.2 + - - +
230A ALA* 1.3 75.1 - - - +
232A VAL* 1.3 62.0 + - + +
234A SER* 3.2 2.8 + - - -
235A ILE* 3.0 41.5 + - + +
270A ILE* 5.8 2.0 - - + -
311A ILE* 5.3 5.6 - - + -
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Residues in contact with VAL 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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228A PHE* 3.0 53.8 + - + +
229A GLU* 3.9 4.9 - - - +
231A ALA* 1.3 72.7 - - + +
233A LYS* 1.3 62.4 + - + +
235A ILE* 4.0 6.6 - - - +
236A LYS* 2.8 61.3 + - + +
249A TRP* 4.1 20.0 - - + +
309A PHE* 4.2 15.5 - - + -
311A ILE* 5.8 0.2 - - + -
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Residues in contact with LYS 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 GLU* 3.0 46.3 + - - +
230A ALA* 3.6 10.3 - - - +
231A ALA 3.3 0.2 - - - -
232A VAL* 1.3 78.1 - - + +
234A SER* 1.3 56.8 - - - +
236A LYS* 3.8 7.6 - - + +
237A ALA* 3.0 29.1 + - - +
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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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195A ILE* 3.2 37.2 + - - +
196A ASN* 5.7 0.5 - - - +
198A GLN* 6.0 0.5 - - - +
200A LEU* 5.3 4.0 - - - -
230A ALA 3.1 11.3 + - - -
231A ALA 3.6 7.6 - - - -
232A VAL 3.2 0.2 - - - -
233A LYS* 1.3 81.0 - - - +
235A ILE* 1.3 61.0 + - - +
237A ALA* 3.5 6.1 + - - +
238A ALA* 3.1 24.3 + - - +
268A PRO* 4.8 1.3 - - - +
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Residues in contact with ILE 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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195A ILE* 4.4 5.8 - - + -
231A ALA* 3.0 21.6 + - + +
232A VAL 4.0 2.7 - - - +
234A SER* 1.3 74.1 - - - +
236A LYS* 1.3 57.5 + - - +
238A ALA* 3.4 2.1 + - - +
239A SER* 2.8 34.0 + - - -
249A TRP* 3.8 22.9 - - + -
267A PHE* 4.2 14.4 - - + -
268A PRO* 3.9 30.5 - - + +
270A ILE* 4.4 8.7 - - + -
292A TYR* 4.2 15.9 - - + +
309A PHE* 4.1 11.9 - - + -
311A ILE* 3.8 28.3 - - + -
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Residues in contact with LYS 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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232A VAL* 2.8 44.6 + - + +
233A LYS* 3.8 7.4 - - + +
235A ILE* 1.3 76.8 - - - +
237A ALA* 1.3 62.3 + - - +
239A SER* 3.3 7.2 + - - -
240A SER* 3.2 23.6 + - - -
249A TRP* 3.5 46.4 - - + +
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Residues in contact with ALA 237 (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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233A LYS 3.0 19.2 + - - +
234A SER* 3.7 7.0 - - - +
235A ILE 3.3 0.2 - - - -
236A LYS* 1.3 77.0 - - - +
238A ALA* 1.3 61.6 + - - +
240A SER* 3.3 21.8 + - - -
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Residues in contact with ALA 238 (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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196A ASN* 5.1 5.8 - - + +
234A SER* 3.1 17.9 + - - +
235A ILE 3.8 0.4 - - - +
237A ALA* 1.3 78.6 - - - +
239A SER* 1.3 57.2 + - - +
240A SER* 3.3 2.9 + - - -
241A THR* 5.1 3.8 + - - +
266A ILE* 3.0 25.2 - - - +
268A PRO* 3.7 26.0 - - + -
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Residues in contact with SER 239 (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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235A ILE 2.8 21.5 + - - -
236A LYS* 3.5 8.8 + - - -
237A ALA 3.3 0.2 - - - -
238A ALA* 1.3 76.2 - - - +
240A SER* 1.3 55.8 + - - +
241A THR* 3.1 7.0 - - - -
242A GLU* 2.9 29.5 + - - +
244A PHE* 3.5 20.6 - - - -
249A TRP* 3.9 4.5 - - - -
266A ILE* 3.5 28.7 - - - -
267A PHE* 3.9 12.7 - - - -
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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