Contacts of the helix formed by residues 228 - 235 (chain A) in PDB entry 2CT8
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 TYR 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.5 22.6 - - + +
205A SER 3.5 19.5 - - - +
206A VAL* 2.9 30.8 + - - +
207A THR* 3.8 5.8 - - - +
208A ARG* 5.4 11.4 - - + -
226A THR 3.5 3.4 + - - -
227A ILE* 1.3 71.8 - - - +
229A VAL* 1.3 94.4 + - + +
230A TRP* 3.6 34.8 - + + -
231A PHE* 2.9 22.4 + - + +
232A ASP* 3.1 9.0 + - - +
263A PHE* 3.6 14.5 - + - -
267A TYR* 5.4 2.2 - + - -
271A PHE* 6.3 0.9 - + - -
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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
----------------------------------------------------------
15A TYR* 5.4 9.4 - - + +
52A ASP* 4.9 11.0 - - - +
54A HIS* 3.8 13.9 - - + +
55A GLY* 3.4 38.8 - - - +
227A ILE 3.4 4.8 + - - +
228A TYR* 1.3 87.0 - - + +
230A TRP* 1.3 61.3 + - + +
232A ASP* 3.0 9.5 + - - +
233A ALA* 2.6 39.0 + - - +
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Residues in contact with TRP 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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15A TYR* 3.5 19.2 + - - -
52A ASP* 5.3 1.1 - - - -
228A TYR* 3.3 27.6 - + + -
229A VAL* 1.3 85.4 - - + +
231A PHE* 1.3 60.3 + - - +
233A ALA* 3.8 4.0 - - + -
234A LEU* 3.1 44.8 + - + +
260A ILE* 3.5 32.5 - - + -
263A PHE* 3.2 63.3 - + + -
264A HIS* 3.9 13.7 - + - -
267A TYR* 5.7 0.9 - - + -
271A PHE* 5.4 0.7 - - - -
501A MSP 3.4 50.5 - - + -
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Residues in contact with PHE 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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106A VAL* 3.9 22.2 - - + -
109A VAL* 4.0 12.1 - - + -
110A PHE* 3.7 25.6 - + - -
113A CYS* 5.0 9.4 - - + -
119A ILE* 5.3 5.8 - - + -
206A VAL* 3.5 28.9 - - + -
227A ILE* 3.5 20.2 - - + -
228A TYR* 2.9 19.1 + - + +
230A TRP* 1.3 80.1 - - - +
232A ASP* 1.3 63.0 + - - +
234A LEU* 4.3 0.3 - - - +
235A PHE* 3.3 49.7 + + - -
271A PHE* 3.6 37.9 - + + -
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Residues in contact with ASP 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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52A ASP* 4.3 4.2 - - - +
54A HIS* 3.2 34.0 - - - +
97A THR* 3.6 9.6 - - - -
102A HIS* 2.7 42.1 + - - -
106A VAL* 3.9 21.7 - - + +
217A ILE* 3.8 9.7 + - + +
227A ILE* 4.5 8.0 - - + +
228A TYR 3.1 7.7 + - - +
229A VAL* 3.0 13.1 + - - +
231A PHE* 1.3 81.7 - - - +
233A ALA* 1.3 62.8 + - - +
235A PHE 3.8 2.8 + - - -
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Residues in contact with ALA 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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13A ILE* 3.5 10.7 - - + +
52A ASP* 3.1 35.9 - - - +
229A VAL 2.6 21.2 + - - +
230A TRP* 4.1 6.7 - - + -
232A ASP* 1.3 75.1 - - - +
234A LEU* 1.3 65.6 + - - +
236A ASN* 2.9 29.5 + - - +
501A MSP 3.5 12.7 - - + +
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Residues in contact with LEU 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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230A TRP* 3.1 43.6 + - + +
231A PHE* 4.3 3.1 - - - +
232A ASP 3.5 0.2 - - - -
233A ALA* 1.3 78.7 - - - +
235A PHE* 1.3 59.3 + - + +
236A ASN 2.9 5.9 + - - -
237A TYR* 3.1 28.6 - - + -
263A PHE* 3.7 21.8 - - + +
264A HIS* 3.7 37.2 - - + +
267A TYR* 4.8 6.3 - - + -
268A TRP* 3.3 46.7 - - + +
271A PHE* 4.8 7.2 - - + -
501A MSP 3.8 4.5 - - + -
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Residues in contact with PHE 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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102A HIS* 4.1 6.3 - - + -
105A PHE* 3.7 27.6 - + + -
106A VAL* 4.7 6.3 - - + -
109A VAL* 3.4 20.2 - - + -
231A PHE* 3.3 54.3 + + - +
232A ASP 4.4 3.8 - - - +
233A ALA 3.2 1.6 + - - -
234A LEU* 1.3 74.0 - - + +
236A ASN* 1.3 64.8 + - - +
237A TYR 3.1 0.7 - - - -
238A ILE* 3.1 9.7 + - + +
239A SER* 3.0 22.0 + - - -
268A TRP* 3.6 28.0 - + - -
271A PHE* 4.1 17.9 - + + -
272A LEU* 4.6 5.4 - - + -
275A LEU* 3.5 27.4 - - + -
277A TYR* 4.5 5.4 - + - -
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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