Contacts of the helix formed by residues 200 - 211 (chain A) in PDB entry 5TSQ
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A LEU* 3.1 27.2 + - + +
199A ALA* 1.3 74.7 - - - +
201A PRO* 1.3 75.5 - - - +
202A GLU* 3.7 9.1 + - - +
203A VAL* 3.0 31.2 + - - +
204A LEU* 3.0 12.7 + - - +
236A TYR* 4.2 15.9 - - + -
296A PHE* 4.0 14.9 - - + -
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Residues in contact with PRO 201 (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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200A THR* 1.3 87.1 - - - +
202A GLU* 1.3 57.4 + - - +
204A LEU* 3.3 11.7 + - + +
205A GLN* 2.9 30.2 + - - +
236A TYR* 3.5 36.8 - - + +
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Residues in contact with GLU 202 (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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200A THR* 3.2 9.6 + - - +
201A PRO* 1.3 78.2 - - - +
203A VAL* 1.3 63.5 + - + +
205A GLN* 3.4 8.0 + - - +
206A ARG* 3.0 30.3 + - + +
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Residues in contact with VAL 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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198A LEU 3.9 3.4 - - - +
199A ALA* 4.2 7.6 - - + -
200A THR* 3.0 25.7 + - - +
202A GLU* 1.3 79.1 - - + +
204A LEU* 1.3 65.9 + - + +
206A ARG* 3.1 12.8 + - - +
207A VAL* 3.0 27.7 + - + +
222A LEU* 5.6 0.7 - - + -
296A PHE* 4.0 6.3 - - + -
300A TRP* 3.6 71.8 - - + +
304A ILE* 5.7 1.8 - - + -
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Residues in contact with LEU 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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199A ALA* 4.1 24.5 - - + +
200A THR 3.0 15.8 + - - +
201A PRO* 3.8 11.7 - - + +
203A VAL* 1.3 75.5 - - + +
205A GLN* 1.3 57.9 + - - +
207A VAL* 3.2 6.5 + - + +
208A LYS* 2.9 27.2 + - - +
219A LEU* 3.8 19.0 - - + +
222A LEU* 4.0 33.7 - - + -
223A GLU* 4.9 12.8 - - + +
226A THR* 3.9 25.1 - - + +
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Residues in contact with GLN 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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201A PRO 2.9 17.6 + - - +
202A GLU* 3.5 8.7 - - - +
204A LEU* 1.3 77.9 - - - +
206A ARG* 1.3 61.7 + - + +
208A LYS* 3.2 22.0 + - - +
209A GLU* 2.4 64.8 + - - +
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Residues in contact with ARG 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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202A GLU* 3.0 20.7 + - + +
203A VAL* 3.1 13.6 + - - +
205A GLN* 1.3 73.9 - - + +
207A VAL* 1.3 66.3 + - - +
209A GLU* 3.2 18.8 + - - +
210A VAL* 3.3 16.5 + - - +
297A SER* 4.8 1.6 + - - +
300A TRP* 4.1 11.8 - - - +
301A ASP* 2.8 41.8 + - - +
304A ILE* 3.8 42.4 - - + +
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Residues in contact with VAL 207 (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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203A VAL* 3.0 28.3 + - + +
204A LEU* 3.6 9.4 - - - +
206A ARG* 1.3 75.8 - - - +
208A LYS* 1.3 63.9 + - - +
210A VAL* 3.1 21.0 + - - +
215A ALA* 3.4 31.7 - - - +
218A ILE* 4.2 9.9 - - + -
219A LEU* 3.9 19.7 - - + +
222A LEU* 4.7 13.7 - - + -
300A TRP* 5.4 3.6 - - + -
303A VAL* 5.6 2.0 - - + -
304A ILE* 3.7 19.3 - - + -
307A LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 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 LEU 2.9 11.5 + - - +
205A GLN* 3.2 28.5 + - - +
207A VAL* 1.3 76.3 - - - +
209A GLU* 1.3 62.0 + - + +
211A ARG* 3.3 19.9 + - - +
215A ALA 6.2 0.4 - - - -
216A ASP* 5.0 7.9 - - - +
219A LEU* 3.7 29.1 - - + +
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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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205A GLN* 2.4 53.8 + - - +
206A ARG* 3.8 12.0 - - - +
207A VAL 3.2 0.6 - - - -
208A LYS* 1.3 74.7 - - + +
210A VAL* 1.3 65.4 + - - +
211A ARG* 3.1 34.4 + - - +
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Residues in contact with VAL 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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206A ARG 3.3 15.7 + - - +
207A VAL* 3.1 15.0 + - - +
209A GLU* 1.3 77.3 - - - +
211A ARG* 1.3 66.8 - - - +
212A THR* 3.6 20.0 - - + +
215A ALA* 3.7 17.9 - - + -
304A ILE* 4.0 23.1 - - + -
307A LEU* 4.0 30.5 - - + +
308A GLN* 4.1 16.2 - - + +
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Residues in contact with ARG 211 (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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207A VAL 4.2 1.0 + - - -
208A LYS 3.3 16.9 + - - +
209A GLU* 3.1 30.7 + - - +
210A VAL* 1.3 80.4 - - - +
212A THR* 1.3 62.1 + - - +
215A ALA* 4.6 0.6 - - - +
216A ASP* 5.0 5.8 + - - -
312A ASP* 3.9 6.4 - - - +
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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