Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 1TAD
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 ARG 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY 3.7 0.8 + - - -
200A GLN* 1.3 70.1 - - - +
202A SER* 1.3 62.7 + - - +
203A GLU 3.1 1.4 + - - -
204A ARG* 3.3 28.6 + - - +
205A LYS* 4.2 3.6 + - - +
230A LEU* 3.7 16.0 - - - +
232A GLU* 2.9 37.6 + - + +
233A ASP* 4.3 18.8 + - - +
236A VAL* 4.0 14.5 - - - +
241A GLU* 2.9 41.7 + - - +
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Residues in contact with SER 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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176A LYS* 5.4 2.9 + - - -
200A GLN* 4.1 8.5 - - - +
201A ARG* 1.3 76.3 - - - +
203A GLU* 1.3 78.2 + - - +
204A ARG 3.5 0.2 - - - -
205A LYS* 2.7 38.0 + - - +
206A LYS* 4.1 0.5 - - - +
232A GLU* 5.5 0.6 - - - +
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Residues in contact with GLU 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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176A LYS* 5.0 4.2 + - - -
178A THR* 3.1 50.1 - - - +
197A VAL* 4.7 0.4 - - + +
198A GLY* 3.4 34.8 - - - +
200A GLN* 2.9 22.2 + - - +
202A SER* 1.3 93.4 + - - +
204A ARG* 1.3 64.5 + - - +
205A LYS 3.3 2.7 - - - -
206A LYS* 2.9 35.3 + - - +
207A TRP* 3.4 11.0 - - - +
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Residues in contact with ARG 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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37A ALA* 3.9 11.5 - - - +
38A GLY 4.6 0.4 - - - +
199A GLY 2.9 23.8 + - - -
200A GLN 3.4 9.7 + - - +
201A ARG* 3.3 21.9 + - - +
203A GLU* 1.3 75.2 - - - +
205A LYS* 1.3 65.3 + - - +
207A TRP* 3.0 47.4 + - + +
208A ILE 4.6 0.3 + - - -
230A LEU* 5.3 0.6 - - - +
232A GLU* 4.0 11.9 + - - -
241A GLU* 2.8 43.0 + - - +
245A LEU* 3.8 39.0 - - + +
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Residues in contact with LYS 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 ARG 4.2 3.5 + - - +
202A SER* 2.7 31.8 + - - +
204A ARG* 1.3 76.6 - - - +
206A LYS* 1.3 83.6 + - + +
207A TRP 3.6 0.3 + - - -
208A ILE* 3.7 16.8 + - - +
209A HIS* 5.2 0.7 + - - -
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Residues in contact with LYS 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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178A THR* 4.5 7.0 + - - -
179A GLY* 4.9 8.7 - - - -
180A ILE* 5.9 5.1 - - + +
197A VAL* 5.3 4.4 - - - +
202A SER 4.1 0.7 - - - +
203A GLU* 2.9 45.9 + - - +
204A ARG 3.1 1.0 - - - -
205A LYS* 1.3 107.7 - - + +
207A TRP* 1.3 63.8 + - - +
208A ILE 3.2 3.1 - - - -
209A HIS* 3.0 36.8 + - + +
210A CYS 4.4 0.2 + - - -
354A CAC 4.3 10.3 - - + +
167C GLU* 6.2 0.4 - - - +
353C CAC 5.6 2.3 - - + +
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Residues in contact with TRP 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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35A LEU* 4.0 20.2 - - + -
36A GLY 3.8 25.1 - - - -
42A LYS* 5.8 0.2 - - + -
197A VAL* 3.4 26.6 - - + +
198A GLY 3.2 27.8 + - - -
199A GLY* 4.2 0.4 - - - -
203A GLU 3.4 13.8 + - - -
204A ARG* 3.0 34.3 + - + +
206A LYS* 1.3 75.5 - - - +
208A ILE* 1.3 53.0 + - - +
210A CYS* 2.8 28.2 + - - +
211A PHE* 3.3 23.9 - + + -
245A LEU* 3.7 44.0 - - + -
249A ILE* 3.9 23.8 - - + -
354A CAC 3.5 12.8 - - - +
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Residues in contact with ILE 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 ARG 4.6 0.6 + - - -
205A LYS 3.7 19.0 + - - +
206A LYS 4.2 1.6 - - - +
207A TRP* 1.3 77.6 - - - +
209A HIS* 1.3 81.8 + - + +
210A CYS 3.0 1.7 + - - -
211A PHE* 3.1 40.7 + - + +
212A GLU* 4.8 4.2 + - - +
252A HIS* 4.1 14.6 - - + +
254A TYR* 4.3 19.1 + - + -
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Residues in contact with HIS 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 LYS 5.3 0.6 + - - -
206A LYS* 3.0 34.7 + - + +
207A TRP 3.0 0.4 + - - -
208A ILE* 1.3 88.2 - - + +
210A CYS* 1.3 58.0 + - - +
211A PHE 3.5 0.2 - - - -
212A GLU* 4.5 6.1 + - - +
55C ASP 3.2 27.6 + - - -
56C GLY* 4.4 4.5 - - - -
57C TYR 3.1 26.8 + - - +
58C SER* 3.6 9.3 - - - +
59C LEU* 2.9 23.6 + - - +
60C GLU* 4.7 1.9 - - - +
167C GLU* 4.6 14.0 + - - -
353C CAC 3.9 18.4 - - + -
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Residues in contact with CYS 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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31A LYS* 2.9 26.4 + - - -
33A LEU* 3.7 7.1 - - + +
180A ILE* 3.7 14.6 - - - -
206A LYS 4.5 2.0 - - - -
207A TRP 2.8 4.6 + - - +
209A HIS* 1.3 80.5 - - - +
211A PHE* 1.3 58.9 + - - +
212A GLU 3.3 5.3 + - - -
214A VAL* 3.6 5.4 - - - +
354A CAC 2.2 63.0 - - + +
59C LEU* 3.9 22.7 - - + -
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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