Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 4JBQ
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU 4.0 1.1 + - - +
216A GLY* 1.3 74.4 - - - -
218A VAL* 1.3 62.7 + - - +
219A TYR* 3.7 11.5 - - - +
220A ARG* 3.0 30.6 + - - +
221A GLU* 3.3 18.2 + - - +
259A PRO 4.2 0.2 - - - -
260A GLU* 3.4 25.4 - - - +
262A LEU 3.1 8.7 - - - +
263A LEU* 3.7 7.0 - - + -
264A LEU* 4.0 4.2 - - - +
501A VX6 3.5 32.4 + - + -
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Residues in contact with VAL 218 (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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217A THR* 1.3 69.0 - - - +
219A TYR* 1.3 59.8 + - - +
221A GLU* 3.2 7.2 + - - +
222A LEU* 2.9 29.1 + - + +
228A PHE* 3.8 16.4 - - + -
236A TYR* 4.3 10.8 - - + -
259A PRO* 4.2 7.0 - - + +
262A LEU* 2.7 35.5 + - + +
264A LEU* 3.8 28.3 - - + -
270A LEU* 4.5 9.9 - - + -
322A PHE* 3.6 33.2 - - + -
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Residues in contact with TYR 219 (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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217A THR* 3.7 5.4 - - - +
218A VAL* 1.3 78.2 - - - +
220A ARG* 1.3 65.8 + - + +
222A LEU* 3.4 8.4 + - + +
223A GLN* 3.2 52.7 + - + +
259A PRO* 3.6 15.7 + - + +
260A GLU* 3.6 53.8 - - + +
295A TYR* 5.9 0.7 - - - -
321A GLU* 5.6 5.2 - - - -
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Residues in contact with ARG 220 (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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216A GLY* 6.2 0.4 - - - -
217A THR* 3.0 24.7 + - - +
219A TYR* 1.3 81.8 - - + +
221A GLU* 1.3 57.5 + - - +
223A GLN* 3.1 15.0 + - + +
224A LYS* 3.0 67.7 + - + +
501A VX6 3.8 40.3 - - - -
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Residues in contact with GLU 221 (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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217A THR 3.3 10.4 + - - +
218A VAL* 3.2 9.4 + - - +
220A ARG* 1.3 79.4 - - - +
222A LEU* 1.3 56.4 + - - +
224A LYS* 3.3 10.4 + - + +
225A LEU* 2.9 39.9 + - + +
228A PHE* 3.8 17.0 - - + -
232A ARG* 2.7 33.0 + - - -
236A TYR* 2.6 26.4 + - - -
264A LEU* 3.5 17.9 - - + +
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Residues in contact with LEU 222 (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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218A VAL 2.9 11.3 + - - +
219A TYR* 3.6 10.5 - - + +
220A ARG 3.3 0.2 - - - -
221A GLU* 1.3 74.8 - - - +
223A GLN* 1.3 56.5 + - - +
226A SER* 2.8 53.5 + - - +
227A LYS* 4.1 2.7 - - - -
228A PHE* 3.7 31.8 - - + -
259A PRO* 4.7 9.4 - - + -
321A GLU* 3.8 50.9 - - + +
322A PHE* 4.1 21.1 - - + +
325A GLY* 4.6 5.4 - - - +
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Residues in contact with GLN 223 (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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219A TYR* 3.2 42.5 + - + +
220A ARG* 3.1 19.7 + - + +
222A LEU* 1.3 77.9 - - + +
224A LYS* 1.3 65.1 + - + +
226A SER* 4.1 4.9 + - - -
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Residues in contact with LYS 224 (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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220A ARG* 3.0 65.6 + - + +
221A GLU* 3.8 11.4 - - + +
223A GLN* 1.3 77.3 - - + +
225A LEU* 1.3 71.2 + - + +
226A SER* 3.8 1.4 + - - -
501A VX6 4.5 7.9 - - - -
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Residues in contact with LEU 225 (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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221A GLU* 2.9 35.1 + - + +
224A LYS* 1.3 84.1 - - + +
226A SER* 1.3 65.3 + - - +
227A LYS* 3.0 20.9 + - - +
228A PHE* 4.0 26.0 - - + -
232A ARG* 4.0 16.6 - - - +
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Residues in contact with SER 226 (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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222A LEU* 2.8 26.9 + - - +
223A GLN 4.1 4.3 + - - -
224A LYS 3.5 2.5 + - - -
225A LEU* 1.3 73.9 - - - +
227A LYS* 1.3 62.5 + - - -
325A GLY* 3.3 24.4 - - - +
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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