Contacts of the helix formed by residues 216 - 227 (chain A) in PDB entry 1K7E
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 SER 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A SER* 1.3 86.3 - - - +
217A PRO* 1.3 69.1 - - - +
218A GLU* 3.7 28.0 + - - +
219A GLN* 2.8 46.3 + - - +
220A VAL 3.6 2.8 + - - -
262A MET* 3.4 9.1 - - - +
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Residues in contact with PRO 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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215A SER 4.5 0.7 - - - +
216A SER* 1.3 90.8 - - - +
218A GLU* 1.3 67.5 + - + +
219A GLN 2.9 0.9 + - - -
220A VAL* 3.0 14.1 + - + +
221A SER* 3.1 10.0 + - - -
258A PHE* 5.3 2.5 - - + -
261A ALA* 4.0 26.2 - - + +
262A MET* 3.2 19.6 - - - -
265A ALA* 3.5 25.3 - - + +
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Residues in contact with GLU 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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216A SER* 3.7 21.3 + - - +
217A PRO* 1.3 79.0 - - + +
219A GLN* 1.3 58.7 + - + +
221A SER* 2.8 11.4 + - - -
222A ALA* 2.8 30.3 + - - +
225A ARG* 4.9 0.9 + - - -
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Residues in contact with GLN 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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210A GLN* 4.9 1.9 + - - +
213A GLY 2.8 22.4 + - - -
214A ILE* 3.6 25.2 - - + +
215A SER* 2.4 35.1 + - - -
216A SER* 2.8 25.8 + - - +
218A GLU* 1.3 80.1 - - + +
220A VAL* 1.3 57.6 + - - +
222A ALA* 3.6 7.1 - - + +
223A ALA* 2.6 36.0 + - - +
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Residues in contact with VAL 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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18A ALA 5.1 2.5 - - - +
19A PHE* 4.5 12.8 - - + -
214A ILE* 4.3 7.2 - - + -
216A SER 4.0 0.2 - - - +
217A PRO 3.4 9.2 - - - +
219A GLN* 1.3 78.1 - - - +
221A SER* 1.3 62.5 + - - +
223A ALA* 3.0 3.8 + - - +
224A VAL* 2.7 31.6 + - + +
230A GLY* 6.1 0.4 - - - -
231A ALA* 4.4 16.1 - - + +
262A MET* 3.4 60.8 - - + +
265A ALA* 4.2 0.7 - - + -
266A SER* 3.9 24.9 - - - +
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Residues in contact with SER 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 PRO 3.1 5.2 + - - -
218A GLU* 2.8 24.9 + - - -
220A VAL* 1.3 82.1 - - - +
222A ALA* 1.3 60.7 + - - +
224A VAL* 3.3 5.7 + - - +
225A ARG* 3.1 44.3 + - - +
265A ALA* 3.7 21.3 + - - -
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Residues in contact with ALA 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 GLU 2.8 20.7 + - - +
219A GLN* 3.6 9.2 - - - +
221A SER* 1.3 72.9 + - - +
223A ALA* 1.3 67.1 + - - +
225A ARG* 3.2 22.9 + - - +
226A ALA* 2.8 23.6 + - - +
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Residues in contact with ALA 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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210A GLN* 3.4 29.6 + - + +
219A GLN 2.6 21.6 + - - +
220A VAL 3.0 5.1 + - - +
222A ALA* 1.3 74.4 - - - +
224A VAL* 1.3 64.9 + - - +
226A ALA* 3.0 14.3 + - - +
228A ALA* 3.1 20.7 + - + +
230A GLY 4.1 20.9 - - - +
231A ALA* 4.4 7.0 - - + -
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Residues in contact with VAL 224 (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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15A ARG 5.6 3.1 - - - +
16A GLU 4.9 1.8 - - - -
17A GLY* 4.0 34.3 - - - +
220A VAL* 2.7 32.3 + - + +
221A SER* 3.7 8.1 - - - +
223A ALA* 1.3 75.7 - - + +
225A ARG* 1.3 64.1 + - - +
227A GLY* 2.9 15.6 + - - -
228A ALA 3.5 13.7 - - - +
230A GLY* 5.3 4.0 - - - -
265A ALA 4.9 0.2 - - - +
266A SER* 4.4 14.4 - - - +
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Residues in contact with ARG 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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194A HIS* 5.0 1.5 + - - -
218A GLU 4.9 0.8 + - - -
221A SER* 3.1 43.6 + - - +
222A ALA* 3.4 26.7 - - - +
224A VAL* 1.3 81.2 - - - +
226A ALA* 1.3 64.1 + - - +
227A GLY* 2.9 1.6 + - - -
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Residues in contact with ALA 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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193A LEU* 5.8 2.2 - - + -
194A HIS* 3.6 43.8 - - + +
197A ILE* 3.6 27.0 - - + +
198A GLU* 4.6 6.8 - - - +
210A GLN* 5.9 0.9 - - - +
222A ALA 2.8 16.5 + - - +
223A ALA* 3.0 9.3 + - - +
225A ARG* 1.3 79.6 - - - +
227A GLY* 1.3 56.2 + - - +
228A ALA 3.6 0.2 - - - -
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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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197A ILE* 3.6 13.2 - - - +
198A GLU* 5.4 2.2 - - - -
201A LYS* 3.4 32.4 + - - -
224A VAL 2.9 12.2 + - - -
225A ARG 2.9 3.6 + - - -
226A ALA* 1.3 76.2 - - - +
228A ALA* 1.3 64.2 + - - +
229A ALA* 3.6 1.9 + - - +
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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