Contacts of the helix formed by residues 213 - 224 (chain A) in PDB entry 1P4K
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 VAL 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ILE 5.4 0.4 - - - +
188A GLY 3.2 22.8 - - - +
189A ALA* 4.6 2.5 - - + +
209A VAL 2.8 8.0 + - - -
210A ILE* 3.2 12.4 + - - +
212A THR* 1.3 82.4 - - - +
214A GLY* 1.3 64.2 + - - +
216A HIS* 3.8 2.0 - - + -
217A LEU* 3.2 15.2 + - - +
487C ILE* 4.3 4.7 - - + +
488C GLY* 3.9 12.1 - - - -
492C PHE* 3.5 32.8 - - + -
513C VAL* 3.5 29.6 - - + -
516C HIS* 3.6 18.6 - - + +
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Residues in contact with GLY 214 (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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188A GLY 3.7 1.2 + - - -
209A VAL* 3.1 15.9 + - - +
212A THR* 3.1 9.1 - - - -
213A VAL* 1.3 74.8 - - - +
215A THR* 1.3 57.7 + - - +
217A LEU* 3.3 9.8 + - - +
218A VAL* 3.0 28.2 + - - +
235A ALA* 4.6 0.5 - - - +
239A ILE* 5.5 0.2 - - - -
257A PHE* 3.5 28.3 - - - -
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Residues in contact with THR 215 (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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188A GLY 3.1 14.4 + - - -
189A ALA 2.7 25.5 + - - +
190A GLY 3.6 2.9 - - - +
191A LEU 3.2 11.6 - - - -
192A PHE* 3.6 5.8 - - - +
200A ALA* 3.3 37.2 - - + +
201A THR* 3.5 19.3 - - - +
202A ALA* 3.7 6.1 - - + +
214A GLY* 1.3 70.8 - - - +
216A HIS* 1.3 64.6 + - - +
218A VAL* 3.3 5.9 + - - +
219A VAL* 3.0 27.7 + - - +
257A PHE* 4.1 3.4 - - + -
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Residues in contact with HIS 216 (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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188A GLY* 3.0 25.5 + - - +
192A PHE* 3.7 26.7 - + - -
213A VAL* 3.8 11.2 - - + +
215A THR* 1.3 77.0 + - - +
217A LEU* 1.3 58.1 + - - +
219A VAL* 3.4 1.2 + - - +
220A GLU* 2.9 51.5 + - + +
512C THR 3.8 18.6 - - - -
513C VAL* 3.6 18.9 - - + +
516C HIS* 2.8 32.1 - + + -
517C LEU* 3.9 21.3 + - + +
520C GLU* 5.9 0.2 - - + -
538C ARG* 3.9 11.2 - - - -
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Residues in contact with LEU 217 (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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212A THR 4.4 4.9 - - - +
213A VAL 3.2 10.4 + - - +
214A GLY* 3.3 10.5 - - - +
215A THR 3.2 0.2 - - - -
216A HIS* 1.3 77.4 - - - +
218A VAL* 1.3 66.9 + - - +
220A GLU* 3.3 4.2 + - + +
221A LEU* 2.9 50.2 + - + +
234A GLU 5.2 0.2 - - - +
235A ALA* 3.8 24.7 - - + +
238A ARG* 3.3 52.5 - - + +
239A ILE* 5.3 2.7 - - + -
516C HIS* 4.0 10.7 + - - +
520C GLU* 4.0 17.9 - - + +
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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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200A ALA* 3.7 20.9 - - + -
214A GLY 3.0 20.8 + - - +
215A THR* 3.3 6.7 + - - +
217A LEU* 1.3 77.0 - - - +
219A VAL* 1.3 63.1 + - - +
221A LEU* 3.3 2.0 + - - -
222A MET* 3.1 21.2 + - + +
231A ALA* 3.5 30.3 - - + +
232A CYS* 4.2 6.1 - - - -
235A ALA* 3.5 22.4 - - + -
257A PHE* 3.9 24.5 - - + -
259A ALA* 3.9 16.4 - - + -
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Residues in contact with VAL 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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192A PHE* 3.7 49.8 - - + +
194A ASP* 4.0 11.4 - - + -
197A ILE* 3.5 16.3 - - + +
198A GLY 3.9 20.2 - - - +
199A ALA 4.0 3.1 - - - -
200A ALA* 3.9 12.6 - - + +
215A THR 3.0 19.3 + - - +
216A HIS* 3.9 1.1 - - + +
218A VAL* 1.3 75.3 - - - +
220A GLU* 1.3 59.1 + - - +
222A MET* 3.1 14.2 + - + +
223A ASN* 2.9 23.7 + - - +
538C ARG* 6.4 0.2 - - - +
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Residues in contact with GLU 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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197A ILE* 5.5 0.7 - - - +
216A HIS* 2.9 29.1 + - + +
217A LEU* 3.7 7.0 - - + +
219A VAL* 1.3 78.5 - - - +
221A LEU* 1.3 57.9 + - - +
223A ASN* 3.0 34.3 + - - +
224A GLN* 2.9 46.7 + - - +
517C LEU* 3.8 11.4 - - + +
520C GLU* 4.2 19.5 - - + -
521C LEU* 5.4 2.1 - - - +
524C GLN* 4.5 6.9 + - - +
538C ARG* 2.5 37.4 + - - -
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Residues in contact with LEU 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 LEU* 2.9 41.9 + - + +
218A VAL 3.6 4.5 - - - +
219A VAL 3.2 0.2 - - - -
220A GLU* 1.3 73.7 - - - +
222A MET* 1.3 67.3 + - - +
224A GLN* 2.9 27.1 + - - +
225A GLY 3.4 0.5 + - - -
226A ARG* 3.1 37.0 + - + +
231A ALA* 3.6 30.5 - - + +
234A GLU* 3.6 36.1 - - + +
235A ALA 4.0 5.6 - - - +
520C GLU* 5.5 3.1 - - - +
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Residues in contact with MET 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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197A ILE* 3.8 12.9 - - + +
198A GLY* 4.0 4.9 - - - -
199A ALA 3.7 20.9 - - - +
218A VAL* 3.1 9.1 + - + +
219A VAL* 3.1 27.0 + - + +
221A LEU* 1.3 76.1 - - - +
223A ASN* 1.3 61.3 + - - +
225A GLY* 3.1 13.0 + - - -
226A ARG 3.4 19.4 - - - +
228A PRO* 3.9 30.1 - - + -
231A ALA* 3.6 19.1 - - + -
259A ALA* 4.1 8.7 - - + -
260A LEU 3.7 25.6 - - - +
261A ASN* 4.1 9.9 - - + -
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Residues in contact with ASN 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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197A ILE* 3.4 38.4 - - + +
219A VAL 2.9 8.3 + - - +
220A GLU* 3.0 35.5 + - - +
222A MET* 1.3 76.2 - - - +
224A GLN* 1.3 59.1 + - - +
225A GLY 3.2 3.7 + - - -
538C ARG* 4.1 10.9 - - - +
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Residues in contact with GLN 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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217A LEU* 6.1 0.2 - - - +
220A GLU* 2.9 32.4 + - - +
221A LEU* 2.9 22.3 + - - +
223A ASN* 1.3 80.7 - - + +
225A GLY* 1.3 55.6 + - - -
226A ARG* 3.3 38.1 + - - +
520C GLU* 4.5 6.8 + - - +
524C GLN* 3.2 46.6 + - - +
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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