Contacts of the helix formed by residues 227 - 237 (chain A) in PDB entry 1AX4
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 PHE 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 4.7 5.8 - - + -
89A PHE* 3.6 23.8 - + - -
191A VAL* 3.5 15.2 + - + -
224A SER* 3.2 17.2 + - - +
225A ALA 4.7 0.2 - - - -
226A ARG* 1.3 79.1 - - - +
228A CYS* 1.3 83.9 + - - +
230A ASN* 3.5 3.4 + - - +
231A ALA* 3.0 25.3 + - - +
250A ILE* 3.9 26.5 - - + -
253A MET* 3.9 4.9 - - + +
254A TYR* 3.1 31.4 - + + +
262A MET* 3.7 17.5 - - + -
267A ASP* 4.4 4.9 - - + -
268A PRO* 4.3 12.3 - - + -
316A LEU* 4.0 24.7 - - + -
320A THR* 5.1 2.0 - - + -
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Residues in contact with CYS 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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227A PHE* 1.3 104.4 - - - +
229A GLU* 1.3 57.7 + - - +
231A ALA* 3.2 8.0 + - - +
232A TYR* 2.9 29.3 + - - +
250A ILE* 4.3 3.1 - - - -
267A ASP* 2.7 25.2 + - + +
316A LEU 5.2 0.2 - - - -
319A GLY* 3.2 37.7 - - - +
320A THR* 4.0 11.4 - - - -
325A LEU* 3.9 14.0 - - + +
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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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192A THR* 3.9 10.6 + - + -
226A ARG* 3.6 17.2 - - - +
228A CYS* 1.3 71.0 - - - +
230A ASN* 1.3 61.9 + - - +
232A TYR* 3.2 4.5 + - - +
233A PHE* 3.2 26.8 + - - -
267A ASP* 2.8 28.9 + - - +
324A TYR* 5.0 0.5 + - - -
325A LEU* 4.4 11.7 - - + -
328A ARG* 2.7 32.8 + - - +
329A ILE* 4.2 12.6 - - + -
352A GLY* 3.3 35.0 - - - +
353A HIS* 3.4 9.9 - - - +
419A ARG* 3.2 10.9 + - - -
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Residues in contact with ASN 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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191A VAL* 3.8 22.4 - - + +
192A THR* 3.5 17.9 - - + +
200A PRO* 3.2 8.2 - - - +
201A VAL 2.9 44.8 + - - -
206A LEU* 4.7 1.0 - - - +
226A ARG 3.1 13.5 + - - +
227A PHE 3.6 8.7 - - - +
229A GLU* 1.3 76.6 - - - +
231A ALA* 1.3 57.4 + - - +
233A PHE* 3.2 6.6 + - - +
234A ILE* 3.0 37.7 + - - +
253A MET* 3.9 10.8 - - + +
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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
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227A PHE 3.0 17.7 + - - +
228A CYS 3.2 4.9 + - - +
230A ASN* 1.3 73.4 - - - +
232A TYR* 1.3 65.4 + - - +
234A ILE* 3.2 3.5 + - - +
235A LYS* 3.0 21.7 + - - +
246A ILE* 4.2 11.7 - - + -
249A VAL* 3.6 31.9 - - + +
250A ILE* 3.8 22.9 - - + -
253A MET* 4.1 4.9 - - - -
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Residues in contact with TYR 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 CYS 2.9 13.1 + - - +
229A GLU 3.4 8.3 - - - +
231A ALA* 1.3 76.3 - - - +
233A PHE* 1.3 67.1 + + - +
235A LYS* 3.1 6.9 + - + +
236A ALA* 2.9 41.5 + - + +
246A ILE* 3.9 17.9 - - + +
322A GLU* 4.6 14.8 - - + -
325A LEU* 3.9 20.2 - - + -
326A HIS* 2.8 51.5 + - + -
329A ILE* 3.2 42.1 - - + +
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Residues in contact with PHE 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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163A TRP* 3.8 3.4 - - + -
192A THR* 4.4 3.1 - - + -
198A GLY 4.3 5.6 - - - -
200A PRO* 3.6 37.5 - - + -
229A GLU 3.2 22.4 + - - -
230A ASN 3.2 2.2 + - - +
232A TYR* 1.3 84.1 - + - +
234A ILE* 1.3 66.2 + - - +
236A ALA* 4.3 4.0 - - + -
237A ARG* 2.9 64.2 + - - +
329A ILE* 3.8 31.0 - - + -
350A THR 3.9 7.2 - - - -
351A GLY* 3.8 16.6 - - - -
352A GLY* 3.6 24.0 - - - -
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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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163A TRP* 3.8 15.0 - - + -
201A VAL 3.7 15.5 - - - +
203A MET* 3.8 21.5 - - + +
206A LEU* 4.8 0.9 - - + -
230A ASN* 3.0 35.6 + - - +
231A ALA 3.2 6.5 + - - +
233A PHE* 1.3 77.6 - - - +
235A LYS* 1.3 59.5 + - - +
238A ASP* 2.8 42.3 + - + +
241A TYR* 3.6 31.3 - - + +
249A VAL* 3.8 11.4 - - + -
253A MET* 4.0 24.7 - - + -
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Residues in contact with LYS 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 ALA 3.0 12.8 + - - +
232A TYR* 3.1 9.4 + - + +
234A ILE* 1.3 80.9 - - - +
236A ALA* 1.3 61.4 + - - +
238A ASP 4.2 2.6 - - - +
241A TYR* 3.5 24.3 - - - +
242A LYS* 3.8 29.0 + - - +
243A ASN* 4.4 2.8 - - - +
244A ALA 2.6 30.2 + - - +
245A THR* 4.4 3.2 - - - +
246A ILE* 4.2 14.4 - - + -
249A VAL* 4.3 8.0 - - + +
322A GLU* 3.0 42.7 + - - +
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Residues in contact with ALA 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 TYR* 2.9 35.8 + - + +
233A PHE* 3.7 9.0 - - + +
234A ILE 3.3 0.2 - - - -
235A LYS* 1.3 79.4 - - - +
237A ARG* 1.3 66.7 + - + +
238A ASP 5.4 0.2 - - - -
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Residues in contact with ARG 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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160A TYR* 3.6 13.9 + - - +
161A ASP 4.2 0.2 + - - -
162A ASP* 2.8 65.5 + - - +
163A TRP* 3.7 18.4 - - + -
199A GLN* 4.7 1.0 + - - -
200A PRO* 3.5 21.0 - - - +
233A PHE* 2.9 46.7 + - - +
236A ALA* 1.3 82.9 - - + +
238A ASP* 1.3 62.4 + - - +
239A PRO* 3.2 11.0 - - - +
349A PRO* 3.7 30.4 - - - +
350A THR 4.5 2.2 + - - -
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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