Contacts of the helix formed by residues 222 - 232 (chain A) in PDB entry 5T0H
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A THR 4.1 0.6 + - - -
221A GLY* 1.3 71.4 + - - +
223A THR* 1.3 58.1 + - - +
224A LEU* 3.4 4.4 - - - +
225A CYS* 3.3 18.1 - - + +
226A ALA* 2.9 18.4 + - - +
273A PHE* 4.3 19.4 - - + -
275A ASP* 3.2 23.8 - - + +
320A ALA* 5.4 4.0 - - - +
314B ASN* 3.8 11.4 - - - -
317B ASP* 3.5 28.5 + - - -
318B GLY 3.2 27.9 + - - -
319B PHE* 3.3 45.3 - - + +
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Residues in contact with THR 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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172A VAL* 3.8 25.1 - - + -
176A ASP* 5.3 7.6 - - + +
220A THR* 3.1 28.9 + - + +
221A GLY 2.7 13.9 + - - -
222A LYS* 1.3 71.9 + - - +
224A LEU* 1.3 55.1 + - + +
225A CYS 3.1 1.6 - - - -
226A ALA* 2.9 6.2 + - + -
227A ARG* 2.3 37.5 + - + +
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Residues in contact with LEU 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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184A ILE* 3.6 33.2 - - + -
187A LEU* 4.0 18.8 - - + -
214A LEU* 4.3 9.6 - - + -
220A THR* 3.4 39.3 - - + +
221A GLY* 5.5 0.2 - - - -
222A LYS 3.4 3.6 - - - +
223A THR* 1.3 76.3 - - + +
225A CYS* 1.3 58.2 + - - +
227A ARG* 3.3 22.2 + - + +
228A ALA* 2.9 24.3 + - - +
318A LEU* 5.8 6.4 - - + +
343A PHE* 3.8 20.4 - - + -
344A SER* 5.8 1.3 - - - +
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Residues in contact with CYS 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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222A LYS* 3.3 17.6 + - + +
223A THR 3.1 0.2 - - - -
224A LEU* 1.3 76.3 - - - +
226A ALA* 1.3 53.8 + - - +
228A ALA* 2.9 10.8 + - - +
229A VAL* 2.6 37.8 + - - +
237A PHE* 3.4 7.9 - - + -
273A PHE* 3.4 54.3 - - + -
318A LEU* 3.8 13.2 - - - -
320A ALA* 6.0 0.2 - - - -
319B PHE* 3.9 13.9 - - + -
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Residues in contact with ALA 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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171A ASP 2.8 12.7 - - - +
172A VAL* 2.7 38.9 - - + +
222A LYS 2.9 15.7 + - - +
223A THR* 2.9 13.4 + - + +
225A CYS* 1.3 72.1 - - - +
227A ARG* 1.3 58.8 + - - +
229A VAL* 2.9 22.5 + - - +
230A ALA 3.2 0.9 + - - -
319B PHE* 3.5 10.0 - - + -
320B ASP* 4.0 11.7 - - + +
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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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172A VAL* 3.1 12.1 + - + +
173A THR 4.4 2.5 - - - +
174A TYR* 3.1 52.1 + - + +
177A VAL* 6.0 3.4 - - - -
184A ILE* 3.3 29.7 - - - +
187A LEU* 3.3 30.7 + - - +
188A ARG* 4.2 13.5 - - - +
191A VAL* 4.5 10.7 - - - +
192A GLU* 4.5 11.5 + - - +
223A THR* 2.3 30.3 + - + +
224A LEU* 3.3 22.2 + - + +
226A ALA* 1.3 68.2 - - - +
228A ALA* 1.3 64.1 + - - +
230A ALA 3.8 0.3 + - - -
231A ASN* 2.7 42.8 + - - +
318A LEU* 5.4 2.0 - - - +
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Residues in contact with ALA 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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191A VAL* 5.6 9.0 - - + -
192A GLU* 3.6 18.5 - - + +
224A LEU 2.9 14.1 + - - +
225A CYS* 2.9 13.4 + - - +
227A ARG* 1.3 82.0 - - - +
229A VAL* 1.3 58.9 + - - +
232A ARG* 2.9 31.7 + - - +
237A PHE* 3.2 14.1 - - + -
318A LEU* 6.4 1.6 - - + -
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Residues in contact with VAL 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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168A GLU 5.2 0.2 - - - +
169A LYS 3.1 26.0 - - - +
170A PRO* 3.5 11.0 - - + +
171A ASP* 3.1 23.3 - - - +
225A CYS 2.6 20.4 + - - +
226A ALA* 2.9 13.2 + - - +
228A ALA* 1.3 77.2 - - - +
230A ALA* 1.3 63.8 + - - +
232A ARG* 3.6 11.4 + - - +
237A PHE* 3.4 21.3 - - + -
319B PHE* 3.4 24.2 - - + -
320B ASP* 4.8 1.3 - - - +
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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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170A PRO* 3.5 19.0 - - + +
171A ASP* 3.1 28.9 + - - +
172A VAL 4.0 0.2 - - - +
173A THR* 3.6 27.4 - - - +
226A ALA 3.2 3.4 + - - -
229A VAL* 1.3 79.7 - - - +
231A ASN* 1.3 62.3 + - - +
232A ARG 3.2 6.9 + - - +
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Residues in contact with ASN 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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173A THR* 2.6 23.9 + - - -
174A TYR* 3.1 51.1 + - + -
192A GLU* 3.3 32.3 - - - +
227A ARG* 2.7 21.9 + - - +
230A ALA* 1.3 74.8 - - - +
232A ARG* 1.3 64.7 + - - +
233A THR* 3.2 9.2 + - - +
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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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170A PRO* 6.0 0.3 - - - +
192A GLU* 4.4 3.6 - - - -
195A LEU* 3.3 25.9 - - - +
228A ALA 2.9 20.0 + - - +
229A VAL 3.6 10.2 - - - +
230A ALA 3.2 7.4 - - - +
231A ASN* 1.3 77.4 - - - +
233A THR* 1.3 59.4 + - - +
234A ASP* 3.8 12.1 + - - +
235A ALA* 2.4 55.3 + - - +
236A CYS* 4.7 2.9 - - - +
237A PHE* 4.2 15.5 - - + -
269A ALA 4.4 2.2 + - - -
270A CYS* 3.5 24.6 - - - +
271A LEU* 3.2 40.2 - - - +
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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