Contacts of the helix formed by residues 225 - 232 (chain A) in PDB entry 5H1C
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 THR 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 1.3 86.7 - - + +
226A ALA* 1.3 66.4 + - - +
227A LEU 3.3 3.1 - - - -
228A TYR* 3.0 26.6 + - - +
229A ARG* 3.5 4.2 + - - +
245A LEU* 5.3 7.0 - - + -
265A ILE* 5.3 2.7 - - + -
266A THR 4.1 2.4 + - - +
267A ASN* 4.0 17.6 - - + -
268A GLN* 3.8 23.7 + - - +
287A ILE* 3.5 25.7 - - + +
292A ILE* 3.7 30.5 - - + -
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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
----------------------------------------------------------
162A THR 5.6 0.4 - - - +
163A GLU* 4.0 9.9 - - + +
223A SER* 3.5 29.3 + - - +
224A ALA 3.5 1.2 - - - -
225A THR* 1.3 81.9 + - - +
227A LEU* 1.3 67.1 + - + +
228A TYR 3.3 0.3 + - - -
229A ARG* 3.4 18.7 + - - +
230A THR* 3.7 14.4 + - - +
268A GLN* 3.5 16.8 - - - +
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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
----------------------------------------------------------
162A THR* 4.3 27.6 - - + +
194A ALA* 4.7 0.7 - - + -
195A PHE* 3.2 33.2 - - - +
196A ASN 3.6 16.4 - - - +
197A THR* 3.6 16.2 - - + -
200A GLN* 3.3 33.2 - - + +
223A SER 4.8 0.7 - - - +
224A ALA 4.6 0.2 + - - -
225A THR 3.3 0.6 - - - -
226A ALA* 1.3 79.2 - - + +
228A TYR* 1.3 62.2 + - + +
230A THR* 3.1 7.4 + - - -
231A ASP* 3.0 33.8 + - - +
250B ARG* 3.5 14.8 - - - +
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Residues in contact with TYR 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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197A THR* 4.2 14.3 + - + -
200A GLN* 3.6 18.7 + - - -
224A ALA 3.0 28.7 - - - -
225A THR* 3.0 12.7 + - - +
227A LEU* 1.3 76.9 - - + +
229A ARG* 1.3 65.1 + - - +
231A ASP 4.1 0.4 - - - -
232A TYR* 3.3 36.0 + + - +
241A ARG* 3.3 41.2 - - + +
244A HIS* 2.7 48.4 + + + -
245A LEU* 3.4 33.1 - - + +
248A PHE* 4.3 8.2 - + - +
287A ILE* 5.5 0.9 - - + -
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Residues in contact with ARG 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 THR 3.5 7.2 + - - +
226A ALA* 3.4 13.3 + - - +
227A LEU 3.2 0.8 - - - -
228A TYR* 1.3 82.4 - - - +
230A THR* 1.3 68.0 + - + +
231A ASP 3.2 0.3 + - - -
232A TYR 3.5 15.5 + - - +
233A SER* 4.1 3.8 + - - -
241A ARG* 5.3 2.0 - - - +
268A GLN* 3.9 12.5 - - - +
269A VAL 2.4 43.9 + - - +
270A VAL* 3.3 2.6 - - - +
287A ILE* 3.3 31.1 - - + +
246B ALA* 5.1 7.5 - - + +
290B ASN* 4.7 1.0 - - - +
291B ILE* 3.2 41.7 - - - +
294B HIS* 4.1 9.7 - - - +
3D T 3.6 32.9 + - - +
4D T 5.3 1.5 + - - -
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Residues in contact with THR 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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226A ALA 3.7 9.3 + - - +
227A LEU 3.1 9.0 + - - -
229A ARG* 1.3 82.5 - - + +
231A ASP* 1.3 61.7 + - - +
233A SER* 5.0 1.2 + - - -
246B ALA* 3.4 38.1 - - + +
247B ARG* 4.0 21.4 + - - +
250B ARG* 3.0 49.2 + - + +
291B ILE* 6.1 1.1 - - + -
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Residues in contact with ASP 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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197A THR* 3.1 35.8 + - + +
227A LEU* 3.0 16.9 + - - +
230A THR* 1.3 78.6 - - - +
232A TYR* 1.3 62.8 + - + +
233A SER* 3.5 4.9 + - - -
237A GLU* 5.2 0.9 - - - +
56B PRO* 4.3 14.5 - - - +
58B LYS* 2.6 42.8 + - - +
247B ARG* 5.3 3.3 + - - -
250B ARG* 3.0 41.8 + - - -
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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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197A THR* 3.9 20.8 + - + -
198A ASP* 4.7 2.9 + - - -
228A TYR* 3.3 42.2 + + - +
229A ARG* 3.6 9.2 - - - +
231A ASP* 1.3 75.6 - - + +
233A SER* 1.3 58.9 + - - +
234A GLY* 2.8 9.2 + - - -
237A GLU* 4.1 23.6 - - + -
238A LEU 4.6 0.6 + - - +
240A ALA* 5.1 12.6 - - + -
241A ARG* 3.5 49.4 + - + -
244A HIS* 4.5 15.4 - - + +
58B LYS* 3.4 36.1 - - + +
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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