Contacts of the helix formed by residues 198 - 207 (chain A) in PDB entry 4IJ3
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 TYR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.5 56.8 + - + +
151A ILE* 3.8 28.5 - - + -
152A ASP* 2.6 37.5 + - - -
196A GLY* 3.5 19.7 + - - -
197A SER* 1.3 73.7 + - - +
199A LEU* 1.3 59.9 + - - +
200A GLY 3.4 2.2 - - - -
201A ARG* 3.2 29.4 + - - +
202A GLU* 2.8 45.6 + - + +
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Residues in contact with LEU 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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191A ILE* 4.1 6.5 - - + -
193A GLU* 4.0 0.7 - - - +
197A SER* 3.4 12.9 + - - +
198A TYR* 1.3 76.7 - - - +
200A GLY* 1.3 66.4 + - - +
202A GLU* 3.0 18.0 + - - +
203A VAL* 2.9 30.1 + - + +
235A PRO* 3.7 30.3 - - + -
254A GLU 4.1 0.9 - - - +
255A SER* 3.7 22.9 - - - -
256A ARG* 3.4 14.1 - - + +
259A TYR* 3.3 30.7 - - + -
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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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191A ILE* 3.8 29.9 - - - +
193A GLU* 3.0 21.2 + - - -
199A LEU* 1.3 76.3 - - - +
201A ARG* 1.3 57.2 + - - +
203A VAL* 3.1 4.2 + - - +
204A ALA* 2.8 29.8 + - - +
215A VAL* 4.3 2.5 - - - +
217A ARG* 4.8 7.9 - - - -
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Residues in contact with ARG 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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151A ILE* 3.9 21.5 - - + +
152A ASP* 4.7 1.0 + - - -
155A GLU* 2.9 40.4 + - - -
168A LEU* 3.6 33.4 - - + +
193A GLU* 4.7 1.4 + - - -
196A GLY* 4.9 3.4 - - - +
197A SER 2.9 28.9 + - - +
198A TYR* 3.2 43.1 + - - +
200A GLY* 1.3 75.3 - - - +
202A GLU* 1.3 62.6 + - - +
204A ALA* 3.8 6.9 - - + +
205A LEU* 3.1 29.8 + - - +
217A ARG* 3.6 31.4 - - - +
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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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90A TRP* 4.0 9.1 + - + -
147A ARG* 2.5 45.0 + - - -
148A GLU* 4.9 1.7 - - - +
151A ILE* 3.8 14.8 - - + -
198A TYR* 2.8 33.6 + - - +
199A LEU* 3.0 21.5 + - - +
201A ARG* 1.3 77.2 - - - +
203A VAL* 1.3 56.9 + - - +
205A LEU* 3.4 2.8 + - - +
206A ASP* 2.8 35.9 + - - +
256A ARG* 3.7 32.5 - - - +
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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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191A ILE* 3.6 19.3 - - + -
199A LEU* 2.9 37.1 + - + +
200A GLY 3.6 6.3 - - - +
202A GLU* 1.3 73.9 - - - +
204A ALA* 1.3 65.9 + - - +
206A ASP 3.1 0.3 + - - -
207A LEU* 2.9 46.5 + - + +
215A VAL* 4.3 3.4 - - + -
256A ARG* 3.6 20.6 - - + +
259A TYR* 4.0 8.5 - - + -
260A THR* 3.8 15.5 - - - +
263A LEU* 4.0 16.2 - - + -
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Residues in contact with ALA 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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166A PRO* 3.7 14.6 - - + +
167A PRO 4.8 4.5 - - - +
168A LEU* 4.5 13.2 - - + -
200A GLY 2.8 16.2 + - - +
201A ARG* 3.8 9.0 - - + +
202A GLU 3.3 0.2 - - - -
203A VAL* 1.3 78.6 - - - +
205A LEU* 1.3 61.5 + - - +
207A LEU* 3.3 3.6 + - - +
208A SER* 3.1 18.2 + - - -
215A VAL* 3.7 34.8 - - + +
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Residues in contact with LEU 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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89A ALA 3.7 4.5 - - - +
90A TRP* 3.3 65.9 - - + +
93A ALA* 5.1 5.2 - - + -
151A ILE* 3.9 14.4 - - + -
154A LEU* 4.0 21.5 - - + -
165A CYS* 4.3 7.2 - - - -
166A PRO* 3.8 22.2 - - + -
168A LEU* 4.2 11.2 - - + -
201A ARG 3.1 18.7 + - - +
202A GLU 3.7 0.4 - - - +
204A ALA* 1.3 76.0 - - - +
206A ASP* 1.3 67.5 + - - +
208A SER* 2.5 28.6 + - - +
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Residues in contact with ASP 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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86A ASP 4.6 1.0 - - - +
89A ALA* 3.7 23.9 - - + +
90A TRP* 2.9 24.2 + - - +
202A GLU 2.8 17.2 + - - +
203A VAL 3.1 9.4 + - - +
205A LEU* 1.3 75.9 - - - +
207A LEU* 1.3 62.4 + - + +
208A SER 3.4 0.6 + - - -
209A GLN* 4.8 1.0 - - - +
210A HIS* 4.4 7.3 + - - -
256A ARG* 2.8 36.7 + - - +
260A THR* 2.8 34.3 + - + +
264A GLN* 4.4 9.6 + - - +
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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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203A VAL* 2.9 44.3 + - + +
204A ALA 3.5 5.2 - - - +
205A LEU 3.1 0.2 - - - -
206A ASP* 1.3 85.6 - - + +
208A SER* 1.3 63.7 + - - +
209A GLN 3.3 2.2 - - - -
210A HIS* 3.2 40.7 + - + +
213A VAL* 4.4 13.1 - - + +
215A VAL* 4.2 16.6 - - + -
260A THR* 3.9 15.7 - - + +
263A LEU* 4.1 13.2 - - + -
264A GLN* 3.7 35.2 - - + +
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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