Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 1JPP
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 HIS 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A GLU* 5.6 4.8 + - - -
185A ARG* 5.0 13.8 + - - -
186A HIS* 6.1 4.5 - + - -
189A MET* 4.4 15.3 - - + -
221A LEU 3.7 2.2 + - - +
222A SER 3.1 2.4 + - - -
223A HIS* 1.3 99.0 + - + +
225A ARG* 1.3 67.3 + - - +
226A GLU* 3.3 17.0 + - - +
227A GLY* 2.9 15.1 + - - -
228A LEU* 3.2 15.9 + - - +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A HIS* 1.3 71.8 + - - +
226A GLU* 1.3 73.1 + - - +
228A LEU* 3.1 21.8 + - - +
229A LEU* 3.2 14.6 + - - +
266A GLN* 5.0 1.0 - - - +
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Residues in contact with GLU 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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186A HIS* 5.2 9.4 - - - +
189A MET* 3.8 19.3 - - + +
224A HIS* 3.7 19.6 + - - +
225A ARG* 1.3 85.8 - - + +
227A GLY* 1.3 60.7 + - - +
229A LEU* 3.6 6.4 + - - +
230A ALA* 3.4 20.1 + - - +
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Residues in contact with GLY 227 (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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189A MET* 3.3 24.8 - - - +
221A LEU* 3.2 25.4 - - - +
224A HIS 2.9 5.2 + - - -
226A GLU* 1.3 77.6 - - - +
228A LEU* 1.3 61.1 + - - +
230A ALA* 3.8 4.9 - - - +
231A ILE* 3.1 30.1 + - - +
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Residues in contact with LEU 228 (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 SER* 3.3 44.2 - - - +
224A HIS 3.2 14.8 + - - +
225A ARG* 3.1 15.0 + - - +
227A GLY* 1.3 73.9 - - - +
229A LEU* 1.3 67.2 + - - +
230A ALA 3.0 1.6 - - - -
231A ILE* 3.0 8.2 + - + +
232A PHE* 2.9 23.9 + - - +
261A ASN* 4.4 13.7 - - + +
262A LEU* 4.3 23.1 - - + +
265A HIS* 4.1 33.7 - - + +
266A GLN* 4.1 14.6 - - + +
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Residues in contact with LEU 229 (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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225A ARG 3.2 12.6 + - - +
226A GLU* 3.9 7.4 - - - +
227A GLY 3.5 0.2 - - - -
228A LEU* 1.3 78.5 - - - +
230A ALA* 1.3 61.4 + - - +
232A PHE* 3.5 10.4 - - + +
233A LYS* 3.2 54.0 + - + +
266A GLN* 3.7 29.5 + - - +
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Residues in contact with ALA 230 (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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189A MET* 4.5 14.8 - - + +
195A VAL* 4.0 23.7 - - + +
221A LEU* 5.9 0.9 - - + -
226A GLU 3.4 11.6 + - - +
227A GLY* 3.8 10.5 - - - +
228A LEU 3.0 0.4 - - - -
229A LEU* 1.3 79.0 - - - +
231A ILE* 1.3 67.9 + - + +
232A PHE 3.1 1.5 + - - -
233A LYS* 3.2 6.5 + - - +
234A SER* 2.9 24.7 + - - -
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Residues in contact with ILE 231 (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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195A VAL* 4.4 6.0 - - + +
199A VAL* 5.9 0.7 - - + -
218A LEU* 3.6 49.1 - - + +
221A LEU* 4.0 12.3 - - + -
222A SER* 4.3 13.7 - - - +
227A GLY 3.1 17.0 + - - +
228A LEU* 3.0 11.6 + - + +
230A ALA* 1.3 76.8 - - + +
232A PHE* 1.3 61.3 + - - +
234A SER* 2.9 18.4 + - - +
236A GLY* 3.2 27.9 + - - -
237A ILE* 4.9 0.8 + - + +
240A LEU* 4.9 7.4 - - + -
258A THR* 4.7 6.1 - - + -
262A LEU* 4.5 20.6 - - + -
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Residues in contact with PHE 232 (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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228A LEU 2.9 15.6 + - - +
229A LEU* 3.5 14.1 - - + +
230A ALA 3.1 0.2 - - - -
231A ILE* 1.3 79.0 - - - +
233A LYS* 1.3 67.2 + - + +
235A GLY* 3.3 13.2 + - - -
236A GLY 4.5 0.6 + - - +
237A ILE* 4.3 20.2 - - + -
262A LEU* 4.9 5.3 - - + +
266A GLN* 3.9 24.9 - - + -
267A GLU 4.0 9.2 - - - -
268A GLY* 3.8 23.8 - - - -
269A ALA* 3.7 22.4 - - - -
272A ALA* 4.7 6.7 - - + -
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Residues in contact with LYS 233 (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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229A LEU* 3.2 39.5 + - + +
230A ALA* 3.2 5.8 + - - +
232A PHE* 1.3 80.6 - - + +
234A SER* 1.3 56.9 + - - +
235A GLY* 3.0 10.9 + - - -
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Residues in contact with SER 234 (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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195A VAL* 3.2 26.0 - - - +
196A SER* 4.2 26.2 - - - -
199A VAL* 4.1 14.2 - - - +
230A ALA 2.9 19.0 + - - -
231A ILE* 2.9 12.8 + - - -
233A LYS* 1.3 74.6 - - - +
235A GLY* 1.3 62.8 + - - +
236A GLY* 4.5 0.2 - - - -
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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