Contacts of the strand formed by residues 224 - 230 (chain A) in PDB entry 1TFF
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 HIS 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 3.1 29.1 + - - -
46A LYS 3.7 1.6 - - - -
47A GLY* 3.4 29.6 - - - -
51A CYS* 4.0 9.3 - - - -
219A LEU 3.4 0.7 - - - +
220A TYR* 3.4 7.3 - - - -
221A LYS* 3.1 37.1 + - - +
222A THR* 3.9 4.9 - - - +
223A SER* 1.3 78.7 - - - +
225A TYR* 1.3 80.8 + - - +
226A ASN* 2.9 37.1 + - - -
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Residues in contact with TYR 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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45A THR* 2.6 30.8 + - - +
51A CYS* 3.6 10.9 - - - +
52A PHE* 3.7 36.6 - + + +
55A ALA* 4.1 3.2 - - + +
175A CYS* 3.6 23.0 - - - -
176A ASP* 5.6 1.0 - - - -
180A ILE* 2.9 30.2 - - + +
193A VAL* 4.4 12.5 - - + +
195A TYR* 5.6 1.9 + - - -
218A LEU* 4.1 30.7 - - + -
219A LEU 3.3 2.2 - - - -
220A TYR* 3.3 45.4 - + + -
223A SER* 4.6 5.2 - - - -
224A HIS* 1.3 80.4 - - - +
226A ASN* 1.3 58.1 + - - +
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Residues in contact with ASN 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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42A ILE* 3.8 25.3 - - + +
43A ARG 3.3 12.1 - - - +
44A LYS* 3.4 13.7 - - - +
45A THR* 3.0 19.6 + - - -
218A LEU* 3.2 11.0 - - - +
219A LEU* 2.8 37.5 + - + +
224A HIS* 2.9 32.1 + - - -
225A TYR* 1.3 73.9 - - - +
227A ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 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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9A ILE* 4.7 3.6 - - + -
42A ILE* 3.2 7.2 - - - +
43A ARG* 2.8 51.3 + - + +
45A THR* 4.3 11.0 - - + -
55A ALA* 3.9 34.1 - - + +
58A TYR* 3.8 28.5 - - + -
59A SER* 3.7 18.2 - - - +
217A TYR 3.7 5.4 - - - +
218A LEU* 4.0 5.6 - - + -
226A ASN* 1.3 76.0 - - - +
228A LEU* 1.3 67.5 + - - +
229A TYR* 3.5 28.6 - - + +
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Residues in contact with LEU 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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15A ILE* 3.8 28.5 - - + -
18A ILE* 5.6 0.2 - - + -
35A LEU* 4.7 5.6 - - + -
39A PHE* 3.7 27.6 - - + -
41A ALA 3.7 4.0 - - - +
42A ILE* 4.4 10.1 - - + -
59A SER* 5.3 0.3 + - - -
194A GLU* 3.8 30.1 - - + -
217A TYR* 2.9 35.5 + - + +
218A LEU 4.1 2.2 - - - +
219A LEU* 3.6 40.6 - - + +
227A ILE* 1.3 75.8 - - - +
229A TYR* 1.3 69.5 + - - +
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Residues in contact with TYR 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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12A LYS* 3.8 29.4 - - + +
39A PHE* 3.2 5.9 - - - +
40A THR* 2.8 33.4 + - - +
41A ALA* 3.3 31.4 + - + +
43A ARG* 2.9 38.6 + - + -
58A TYR* 3.9 1.7 - - - -
59A SER* 5.5 1.3 - - - -
62A GLU* 2.6 31.6 + - - -
217A TYR* 5.4 0.4 - - - -
227A ILE* 3.5 31.4 - - + +
228A LEU* 1.3 76.4 - - - +
230A ALA* 1.3 62.7 + - - +
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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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38A ARG 3.8 4.5 - - - +
39A PHE* 3.7 12.2 - - + -
40A THR* 4.4 3.8 + - - -
217A TYR* 3.8 26.8 - - + +
228A LEU 4.5 0.2 + - - -
229A TYR* 1.3 73.5 - - - +
231A ALA* 1.4 58.1 + - - +
232A ASP* 3.1 35.1 + - + +
233A LYS* 5.5 0.9 - - - +
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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