Contacts of the helix formed by residues 225 - 236 (chain A) in PDB entry 4XK8
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 VAL 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A SER 3.7 8.3 - - - +
157A GLY* 4.7 1.1 - - - +
221A HIS* 2.7 53.2 + - + +
224A HIS* 1.3 83.7 - - + +
226A SER* 1.3 67.1 + - - +
228A PRO* 3.3 14.6 - - - +
229A ILE* 3.4 21.4 + - + +
245A PRO* 3.7 37.7 - - + +
249A ILE* 4.9 8.7 - - + -
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Residues in contact with SER 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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155A ALA 3.0 25.8 + - - -
156A SER* 3.7 6.3 + - - -
157A GLY 4.8 0.2 - - - +
218A TRP* 4.6 1.6 - - - -
221A HIS* 3.1 27.3 + - - -
222A GLN* 3.3 24.9 + - - +
225A VAL* 1.3 77.0 - - - +
227A LEU* 1.3 65.5 + - - +
230A ASN* 2.9 33.8 + - - +
296A LEU* 4.4 9.0 - - - -
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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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222A GLN* 2.9 23.0 + - + +
223A VAL* 3.9 18.8 - - + +
226A SER* 1.3 73.4 - - - +
228A PRO* 1.3 63.2 - - + +
230A ASN* 3.8 3.1 - - - +
231A GLN* 2.9 30.8 + - - +
259A TYR* 3.4 20.9 + - + +
280A PHE* 3.7 36.3 - - + +
296A LEU* 3.6 31.4 - - + +
297A THR* 3.7 23.8 - - + +
300A ALA* 4.4 8.1 - - + -
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Residues in contact with PRO 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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223A VAL 4.0 4.7 - - - +
224A HIS 3.5 21.3 - - - +
225A VAL* 3.3 17.7 - - - +
226A SER 4.0 0.2 - - - +
227A LEU* 1.3 94.3 - - + +
229A ILE* 1.3 66.2 + - - +
231A GLN* 3.0 4.8 + - + +
232A PHE* 2.9 30.7 + - - -
248A PHE* 3.5 35.7 - - + -
255A LEU* 3.8 12.3 - - + -
258A LEU* 3.6 15.5 - - + -
259A TYR* 4.4 2.0 - - + -
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Residues in contact with ILE 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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157A GLY* 3.4 35.7 - - - +
159A THR* 4.1 18.6 - - + +
225A VAL* 3.4 21.0 + - + +
226A SER 4.2 0.7 - - - +
228A PRO* 1.3 79.5 - - - +
230A ASN* 1.3 58.4 + - - +
232A PHE* 3.3 8.8 + - - +
233A LEU* 2.9 35.0 + - + +
242A ILE* 4.3 9.0 - - + -
243A PRO 4.2 5.8 - - - +
245A PRO* 4.0 37.5 - - + -
248A PHE* 4.0 19.1 - - + -
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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
----------------------------------------------------------
154A ARG* 3.1 39.2 + - - +
155A ALA* 3.3 18.9 + - - -
157A GLY* 4.1 4.6 - - - +
226A SER* 2.9 28.5 + - - +
227A LEU 4.0 2.0 - - - +
229A ILE* 1.3 74.8 - - - +
231A GLN* 1.3 60.0 + - - +
233A LEU* 3.7 8.2 - - - +
234A ASN* 2.9 48.1 + - - +
296A LEU* 3.7 25.4 - - + +
383A PRO* 4.3 8.8 - - - +
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Residues in contact with GLN 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 2.9 14.3 + - - +
228A PRO* 3.2 10.5 - - + +
230A ASN* 1.3 76.6 - - - +
232A PHE* 1.3 58.3 + - - +
234A ASN* 3.5 11.2 + - - +
235A ALA* 2.9 29.3 + - + +
258A LEU* 3.8 27.4 - - + +
259A TYR* 3.5 22.8 + - + +
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Residues in contact with PHE 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 PRO 2.9 24.1 + - - -
229A ILE 3.4 7.6 - - - +
231A GLN* 1.3 73.8 - - - +
233A LEU* 1.3 65.8 + - - +
235A ALA* 3.0 15.1 + - + +
236A GLY 3.1 9.4 + - - -
237A VAL* 3.1 35.9 - - + +
242A ILE* 3.7 14.1 - - + -
243A PRO* 3.7 29.8 - - + -
248A PHE* 3.6 18.8 - + - -
254A LEU* 5.6 3.8 - - + -
257A GLN* 5.8 3.4 - - - -
258A LEU* 3.5 34.1 - - + -
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Residues in contact with LEU 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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110A LEU* 4.3 10.8 - - + +
154A ARG* 3.5 64.4 + - + +
157A GLY* 5.7 0.2 - - - -
158A ILE 5.4 1.1 - - - +
159A THR* 5.0 6.1 - - + -
229A ILE* 2.9 32.7 + - + +
230A ASN* 3.7 9.9 - - - +
232A PHE* 1.3 72.7 - - - +
234A ASN* 1.3 64.0 + - - +
236A GLY* 3.1 14.9 + - - -
237A VAL 4.5 5.3 - - - +
239A PRO* 4.1 23.1 - - + -
242A ILE* 3.7 20.8 - - + +
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Residues in contact with ASN 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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154A ARG* 4.1 13.7 + - - +
230A ASN* 2.9 37.8 + - - +
231A GLN* 3.8 12.6 + - - +
233A LEU* 1.3 75.7 - - - +
235A ALA* 1.3 65.3 + - - +
236A GLY* 3.4 0.9 + - - -
288A ASP* 4.7 12.5 + - - -
290A LEU* 3.6 33.7 - - + +
291A THR* 4.5 15.9 + - - +
296A LEU* 5.1 8.1 - - - +
383A PRO* 5.8 1.0 - - - +
384A TYR* 4.5 7.1 + - - -
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Residues in contact with ALA 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 GLN* 2.9 15.0 + - + +
232A PHE* 3.0 16.3 + - + +
234A ASN* 1.3 78.8 - - - +
236A GLY* 1.3 55.2 + - - +
237A VAL* 3.6 6.1 - - + +
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Residues in contact with GLY 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 PHE 3.1 0.4 + - - -
233A LEU 3.1 14.5 + - - -
234A ASN 3.2 1.1 - - - -
235A ALA* 1.3 79.4 - - - +
237A VAL* 1.3 66.5 + - - +
238A ASP* 3.5 1.9 + - - -
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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