Contacts of the helix formed by residues 202 - 210 (chain A) in PDB entry 1TK5
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 GLY 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLY 3.5 13.2 - - - -
54A GLY* 5.0 2.0 - - - -
55A LEU* 4.2 1.8 - - - -
201A VAL* 1.3 80.0 - - - +
203A TYR* 1.3 65.6 + - - -
204A THR 3.3 2.7 - - - -
205A THR* 3.3 9.4 + - - -
206A PHE* 3.2 17.3 + - - +
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Residues in contact with TYR 203 (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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50A VAL 5.9 0.2 - - - -
53A GLY* 3.1 32.5 + - - -
54A GLY 3.7 5.8 - - - +
55A LEU* 3.5 32.3 - - + +
86A GLU* 3.5 45.5 + - + +
87A ASN* 3.5 21.1 - - - +
202A GLY* 1.3 71.2 - - - -
204A THR* 1.3 93.5 + - - +
206A PHE* 3.2 2.8 + - - +
207A TRP* 3.1 31.5 + + - -
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Residues in contact with THR 204 (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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202A GLY 3.3 0.8 - - - -
203A TYR* 1.3 105.8 + - - +
205A THR* 1.3 61.6 + - - +
207A TRP* 4.1 4.2 - - - +
208A SER* 3.0 32.0 + - - +
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Residues in contact with THR 205 (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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196A ILE* 5.0 5.6 - - + -
201A VAL* 3.9 26.7 - - + -
202A GLY* 3.3 11.9 + - - -
203A TYR 3.3 0.6 - - - -
204A THR* 1.3 76.1 - - - +
206A PHE* 1.3 61.2 + - - +
208A SER* 3.6 6.1 - - - -
209A GLU* 2.8 56.3 + - + +
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Residues in contact with PHE 206 (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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1A MET* 4.2 2.2 - - + -
55A LEU* 3.6 28.5 - - + -
89A ILE* 3.5 34.8 - - + -
94A LEU* 5.2 1.8 - - + -
182A LEU* 5.9 0.9 - - + -
186A LEU* 4.2 10.3 - - + -
192A PHE* 3.9 19.1 - + - -
198A PHE* 3.7 44.7 - + + -
201A VAL* 3.9 7.1 - - + +
202A GLY 3.2 4.5 + - - +
203A TYR* 3.5 8.3 - - - +
205A THR* 1.3 80.5 - - - +
207A TRP* 1.3 93.3 + + - +
210A SER* 2.9 28.9 + - - -
214A VAL* 4.2 11.7 - - + -
218A HIS* 5.4 0.2 - + - -
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Residues in contact with TRP 207 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 4.7 1.3 - - + -
85A ARG* 4.6 15.3 - - - -
86A GLU* 2.8 33.7 + - + +
88A CYS 3.5 20.6 - - - -
89A ILE* 4.2 8.7 - - + -
203A TYR* 3.1 32.8 + + - +
204A THR* 4.2 3.6 - - - +
206A PHE* 1.3 105.2 - + - +
208A SER* 1.3 63.4 + - - +
210A SER* 3.4 16.9 + - - +
211A LEU 5.0 0.3 - - - +
212A GLU* 5.7 0.9 - - - -
214A VAL* 3.9 11.7 - - + -
215A ASP* 3.9 40.7 - - - +
218A HIS* 3.6 42.4 - + + -
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Residues in contact with SER 208 (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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204A THR* 3.0 25.9 + - - +
205A THR* 3.3 8.7 + - - -
207A TRP* 1.3 77.8 - - - +
209A GLU* 1.3 75.2 + - - +
210A SER 3.9 3.5 + - - +
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Residues in contact with GLU 209 (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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193A PRO* 3.4 24.1 - - - +
196A ILE* 3.2 32.1 - - + +
198A PHE* 4.0 8.1 - - + -
205A THR* 2.8 43.3 + - + +
208A SER* 1.3 84.1 + - - +
210A SER* 1.3 62.7 + - - +
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Residues in contact with SER 210 (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 TYR 3.6 13.2 - - - -
192A PHE* 3.7 25.1 - - - -
198A PHE* 4.0 4.7 - - - -
206A PHE* 2.9 23.6 + - - -
207A TRP* 3.4 17.5 + - - +
208A SER 4.1 3.6 - - - +
209A GLU* 1.3 80.4 - - - +
211A LEU* 1.3 71.6 + - - +
212A GLU* 3.4 1.7 + - - -
214A VAL* 3.7 14.8 - - - +
215A ASP 5.0 0.3 + - - -
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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