Contacts of the helix formed by residues 198 - 208 (chain A) in PDB entry 4TR8
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A SER 5.0 1.8 + - - -
146A MET* 3.6 43.6 + - + +
147A ALA 2.9 30.6 + - - -
148A GLN* 3.7 42.9 - - - +
149A GLN 5.1 0.7 - - - +
156A ASN* 2.9 26.7 + - + +
157A GLY* 3.5 0.6 - - - -
197A PRO* 1.3 71.6 - - + +
199A LYS* 1.3 67.1 + - + +
201A ILE* 3.3 0.9 - - - +
202A LEU* 3.2 52.6 + - - +
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Residues in contact with LYS 199 (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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20A VAL* 5.7 5.0 + - - +
22A GLU* 5.4 9.9 - - - +
48A ASP* 4.2 22.8 + - - +
50A GLU* 3.7 17.5 - - - +
51A VAL* 5.3 2.5 - - + -
197A PRO* 3.3 1.4 - - - +
198A ARG* 1.3 84.1 - - + +
200A GLY* 1.3 61.6 + - - +
202A LEU* 3.5 7.5 + - - +
203A GLU* 3.1 23.4 + - + +
206A ARG* 5.0 1.2 + - - -
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Residues in contact with GLY 200 (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 GLU* 3.2 9.9 + - - -
51A VAL* 3.8 27.1 - - - -
196A VAL* 4.2 2.7 - - - -
197A PRO 3.1 6.5 + - - -
199A LYS* 1.3 73.7 - - - +
201A ILE* 1.3 58.8 + - - +
203A GLU* 3.3 3.5 + - - +
204A LEU 2.9 24.1 + - - -
233A PHE* 3.2 15.7 - - - -
235A SER* 4.4 5.4 - - - -
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Residues in contact with ILE 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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139A ILE* 3.8 38.7 - - + +
146A MET* 3.6 30.1 - - + -
158A MET* 3.9 18.6 - - + -
160A LEU* 4.0 15.5 - - + -
196A VAL* 3.7 32.3 - - + +
197A PRO 2.9 15.6 + - - +
198A ARG 3.3 11.4 - - - +
200A GLY* 1.3 74.7 - - - +
202A LEU* 1.3 65.6 + - + +
204A LEU* 3.3 13.4 + - + +
205A ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 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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139A ILE* 5.2 2.0 - - + -
143A SER* 3.7 34.1 - - - +
146A MET* 4.0 7.4 - - + -
198A ARG* 3.2 46.4 + - - +
199A LYS* 3.9 6.5 - - - +
201A ILE* 1.3 74.1 - - + +
203A GLU* 1.3 62.4 + - - +
205A ALA* 3.4 7.9 + - + +
206A ARG* 3.3 51.3 + - - +
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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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16A LEU* 4.3 7.2 - - - +
19A GLY* 5.2 5.1 - - - +
20A VAL* 3.7 31.2 - - + +
51A VAL* 5.2 3.4 - - + -
53A LEU* 3.9 3.5 - - - +
199A LYS* 3.1 18.7 + - + +
200A GLY* 3.5 6.7 - - - +
201A ILE 3.2 0.2 - - - -
202A LEU* 1.3 73.5 - - - +
204A LEU* 1.4 64.2 + - - +
206A ARG* 3.2 36.5 + - - +
207A LEU* 3.3 43.5 + - + +
233A PHE* 4.0 15.5 - - + -
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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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135A LEU* 4.2 18.6 - - + -
139A ILE* 4.2 11.0 - - + -
160A LEU* 5.5 0.4 - - + -
196A VAL* 5.9 0.7 - - + -
200A GLY 2.9 13.6 + - - +
201A ILE* 3.3 20.8 + - + +
203A GLU* 1.4 75.9 - - - +
205A ALA* 1.4 61.5 + - - +
207A LEU* 3.1 19.7 + - - +
208A LEU* 3.3 37.2 + - + +
224A ILE* 4.9 13.7 - - + -
226A ALA* 3.7 28.0 - - + -
231A PHE* 4.5 6.7 - - + -
233A PHE* 3.9 29.1 - - + -
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Residues in contact with ALA 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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136A ARG* 3.2 31.8 + - + +
139A ILE* 3.6 38.1 - - + +
140A ASP* 3.7 17.0 - - - +
201A ILE 3.1 6.0 + - - +
202A LEU* 3.6 11.0 - - + +
203A GLU 3.3 0.2 - - - -
204A LEU* 1.4 74.9 - - - +
206A ARG* 1.3 61.5 + - + +
208A LEU* 3.3 12.9 + - - -
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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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16A LEU* 5.2 8.5 - - + +
136A ARG* 4.1 14.5 + - - +
199A LYS 5.0 1.4 + - - -
202A LEU* 3.3 35.7 + - - +
203A GLU* 3.2 47.6 + - - +
205A ALA* 1.3 76.2 - - + +
207A LEU* 1.3 57.9 + - + +
209A THR* 3.4 21.1 - - - +
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Residues in contact with LEU 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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16A LEU* 3.7 34.6 - - + +
53A LEU* 3.8 28.3 - - + -
132A GLN* 4.3 1.2 - - - +
203A GLU* 3.3 33.0 - - - +
204A LEU* 3.1 9.5 + - - +
206A ARG* 1.3 75.3 - - + +
208A LEU* 1.3 55.8 + - - +
209A THR* 3.0 19.6 + - - -
210A GLU* 5.6 0.7 - - - +
231A PHE* 3.2 51.0 - - + -
233A PHE* 3.8 20.9 - - + -
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Residues in contact with LEU 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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132A GLN* 3.6 45.0 - - + +
133A SER* 5.1 1.6 + - - -
135A LEU* 3.7 32.1 - - + -
136A ARG* 3.6 39.4 - - + +
139A ILE* 4.3 3.4 - - + -
204A LEU* 3.3 28.5 - - + +
205A ALA* 3.3 8.8 + - - +
207A LEU* 1.3 72.1 - - - +
209A THR* 1.3 59.9 + - - +
210A GLU 5.0 0.3 - - - +
215A VAL* 4.0 24.2 - - + -
231A PHE* 4.3 11.7 - - + -
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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