Contacts of the helix formed by residues 229 - 236 (chain B) in PDB entry 5X6E
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 CYS 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LYS* 4.0 21.7 - - - +
224B TRP* 4.0 23.1 - - - -
225B PHE* 3.1 18.6 - - + +
228B ALA* 1.3 73.5 - - - +
230B PRO* 1.3 71.9 - - - +
231B ALA* 3.3 3.1 - - - -
232B THR* 3.3 21.3 + - - +
233B TRP 3.2 12.3 + - - -
301B GSH 3.4 30.1 - - - +
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Residues in contact with PRO 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B PHE 3.5 10.3 - - - +
226B TYR 3.3 15.7 - - - +
227B LEU 3.8 6.7 - - - +
228B ALA* 4.3 0.4 - - - -
229B CYS* 1.3 85.2 - - - +
231B ALA* 1.3 63.8 + - + +
233B TRP* 3.0 4.2 + - + +
234B GLY* 2.9 26.5 + - - -
10F LYS* 3.7 36.1 - - + +
13F GLU* 4.5 11.2 - - + +
14F THR* 3.7 22.1 - - + -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B CYS* 3.3 1.1 - - - -
230B PRO* 1.3 82.1 - - + +
232B THR* 1.3 60.5 + - - +
234B GLY* 3.5 7.8 + - - -
235B LYS* 3.7 20.5 + - - +
13F GLU* 3.4 38.9 - - + +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.8 31.4 - - + +
153B VAL* 4.7 6.7 - - + +
225B PHE* 5.1 4.9 - - + -
229B CYS* 3.3 25.7 + - + +
230B PRO 3.2 0.4 - - - -
231B ALA* 1.3 77.4 - - - +
233B TRP* 1.3 63.7 + - - +
235B LYS* 3.8 22.4 + - - +
236B LEU* 3.4 21.1 - - - +
301B GSH 4.9 3.8 + - - -
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Residues in contact with TRP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.3 15.2 + + - -
215B LYS* 3.5 18.4 - - - -
222B ASP* 2.5 39.0 + - - -
225B PHE* 3.1 48.9 - - + +
226B TYR* 3.4 29.3 - + - +
229B CYS 3.2 4.0 + - - -
230B PRO* 3.0 9.3 + - + +
232B THR* 1.3 78.4 - - - +
234B GLY* 1.3 64.5 + - - +
236B LEU* 3.4 6.1 + - - +
237B ASN* 3.4 37.5 + - - +
14F THR* 3.9 26.2 - - + -
15F ASN* 5.3 2.0 - - - -
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PRO 2.9 11.4 + - - -
231B ALA 3.5 2.1 + - - -
232B THR 3.4 0.4 - - - -
233B TRP* 1.3 75.8 - - - +
235B LYS* 1.3 60.0 + - - +
237B ASN* 2.9 21.3 + - - +
13F GLU 3.9 7.0 - - - -
14F THR 3.2 30.4 - - - +
15F ASN 5.6 0.2 - - - -
16F GLY* 4.9 7.8 + - - -
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Residues in contact with LYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR 5.0 2.6 + - - -
155B GLY 5.4 5.4 + - - -
156B LYS* 5.5 10.7 - - - +
157B GLU* 5.3 3.8 - - - +
231B ALA 3.7 17.3 + - - +
232B THR* 4.0 26.7 - - - +
233B TRP 3.4 0.4 - - - -
234B GLY* 1.3 74.6 - - - +
236B LEU* 1.3 77.5 + - + +
237B ASN* 3.2 4.2 + - - +
18F LYS* 6.4 2.7 - - + -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B THR* 4.0 12.8 - - + +
152B TYR* 3.9 41.5 - - + +
155B GLY 4.6 14.1 - - - +
156B LYS* 5.4 0.2 - - - -
157B GLU* 5.2 12.6 - - + +
162B ILE* 4.1 26.7 - - + +
211B LEU* 4.3 15.7 - - + +
232B THR 3.4 20.4 - - - +
233B TRP 3.4 2.5 + - - +
234B GLY 3.2 0.6 - - - -
235B LYS* 1.3 95.1 - - + +
237B ASN* 1.3 80.3 + - - +
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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