Contacts of the helix formed by residues 208 - 223 (chain A) in PDB entry 4KZK
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 ASP 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 4.2 14.6 - - - +
206A THR* 2.7 36.2 + - - +
207A ALA* 1.3 75.4 - - - +
209A THR* 1.3 65.2 + - - +
210A GLU* 3.6 11.5 + - - +
211A GLY 2.9 17.7 + - - -
212A ALA* 3.0 22.7 + - - +
237A ASP* 4.9 6.7 - - + -
238A THR* 3.6 10.6 - - - +
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Residues in contact with THR 209 (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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208A ASP* 1.3 76.0 - - - +
210A GLU* 1.3 57.6 + - - +
212A ALA* 3.3 2.1 + - - +
213A PHE* 2.8 31.8 + - + +
237A ASP* 2.9 39.5 + - - +
240A VAL* 4.4 11.2 - - + +
241A GLY* 3.7 17.9 - - - +
244A ARG* 5.6 3.4 - - + -
266A VAL* 5.9 0.5 - - - +
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Residues in contact with GLU 210 (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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206A THR* 5.1 3.4 + - - +
208A ASP* 3.3 12.3 + - - +
209A THR* 1.3 79.0 - - - +
211A GLY* 1.3 62.7 + - - +
213A PHE* 3.6 7.0 - - + +
214A ASN* 3.0 40.2 + - - +
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Residues in contact with GLY 211 (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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204A GLU* 4.0 7.0 - - - +
205A MET* 4.7 5.0 + - - -
206A THR* 3.4 33.1 + - - -
208A ASP* 2.9 11.1 + - - -
210A GLU* 1.3 77.7 - - - +
212A ALA* 1.3 57.1 + - - +
214A ASN* 3.5 6.1 + - - +
215A ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 212 (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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170A LEU* 3.8 9.1 - - + +
204A GLU* 3.3 25.8 + - - +
208A ASP 3.0 15.5 + - - +
209A THR 3.7 2.7 - - - +
211A GLY* 1.3 75.2 - - - +
213A PHE* 1.3 60.5 + - - +
215A ALA 4.5 0.2 - - - +
216A ALA* 2.8 34.0 + - - +
238A THR* 3.0 31.2 - - - +
241A GLY* 4.0 3.8 - - - -
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Residues in contact with PHE 213 (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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209A THR* 2.8 23.7 + - + +
210A GLU* 3.6 8.1 - - + +
212A ALA* 1.3 71.7 - - - +
214A ASN* 1.3 76.6 + - - +
217A ASN* 3.1 47.9 + - - -
241A GLY* 3.5 24.2 - - - +
244A ARG* 3.9 17.3 - - + -
245A ALA* 3.6 26.0 - - - +
248A GLY* 6.4 0.9 - - - -
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Residues in contact with ASN 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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210A GLU* 3.0 36.5 + - - +
211A GLY* 3.9 5.6 - - - +
213A PHE* 1.3 93.6 - - - +
215A ALA* 1.3 62.5 + - - +
217A ASN* 3.5 5.6 + - - +
218A ILE* 3.3 30.6 + - + +
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Residues in contact with ALA 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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170A LEU* 4.6 0.7 - - + -
202A ALA* 3.7 25.0 - - + +
203A PRO* 3.4 27.1 - - + +
204A GLU* 4.2 4.7 - - + -
211A GLY 3.0 18.3 + - - +
212A ALA* 3.9 2.7 - - - +
214A ASN* 1.3 77.5 - - - +
216A ALA* 1.3 63.7 + - - +
218A ILE* 3.3 12.5 + - - +
219A ALA* 3.2 20.6 + - - +
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Residues in contact with ALA 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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168A LEU* 3.8 21.1 - - + -
170A LEU* 4.4 3.5 - - + +
202A ALA* 4.7 0.7 - - - -
212A ALA 2.8 18.8 + - - +
215A ALA* 1.3 75.4 - - - +
217A ASN* 1.3 58.6 + - - +
219A ALA* 3.0 5.6 + - - +
220A PHE* 2.8 36.4 + - + -
242A ALA* 3.7 17.7 - - + -
245A ALA* 3.7 19.7 - - + -
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Residues in contact with ASN 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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213A PHE* 3.1 53.6 + - - +
214A ASN* 3.9 6.4 + - - +
215A ALA 3.3 0.2 - - - -
216A ALA* 1.3 75.5 - - - +
218A ILE* 1.3 61.7 + - + +
220A PHE* 4.3 1.6 - - - -
221A THR* 2.9 30.6 + - - -
245A ALA* 3.5 23.8 - - - +
249A ARG* 3.3 24.2 + - - +
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Residues in contact with ILE 218 (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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214A ASN* 3.3 19.3 + - + +
215A ALA* 3.6 11.9 - - - +
216A ALA 3.2 0.4 - - - -
217A ASN* 1.3 79.1 - - + +
219A ALA* 1.3 61.7 + - - +
221A THR* 3.5 6.2 + - - -
222A LYS* 3.4 45.1 + - + +
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Residues in contact with ALA 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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168A LEU* 3.5 29.2 - - + -
200A VAL* 3.8 17.5 - - + -
201A ASP 4.9 2.2 - - - +
202A ALA* 4.3 5.6 - - + -
215A ALA 3.2 10.7 + - - +
216A ALA 3.0 8.8 + - - +
218A ILE* 1.3 76.3 - - - +
220A PHE* 1.3 67.1 + - + +
222A LYS* 3.2 4.7 + - - -
223A HIS* 3.1 30.5 + - - +
229A TRP* 5.2 0.9 - - + -
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Residues in contact with PHE 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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168A LEU* 3.7 23.6 - - + -
216A ALA* 2.8 35.8 + - + +
217A ASN 4.0 1.8 - - - +
219A ALA* 1.3 72.4 - - + +
221A THR* 1.3 62.6 + - - +
223A HIS 3.2 18.8 + - - +
224A ARG* 3.6 6.6 + - - +
229A TRP* 3.7 37.2 - + - -
242A ALA 3.8 7.2 - - - -
245A ALA* 3.9 2.9 - - + -
246A GLY* 3.4 28.9 - - - -
249A ARG* 3.1 36.7 + - - -
251A ILE* 3.6 20.9 - - + -
256A MET* 3.9 17.5 - - + -
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Residues in contact with THR 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 ASN 2.9 17.7 + - - -
218A ILE* 3.7 7.4 - - - -
220A PHE* 1.3 78.8 - - - +
222A LYS* 1.3 62.6 + - + +
224A ARG* 4.3 8.8 + - - +
249A ARG* 2.9 30.8 + - - +
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Residues in contact with LYS 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 ILE* 3.4 31.2 + - + +
219A ALA* 3.2 5.1 + - - +
221A THR* 1.3 79.1 - - + +
223A HIS* 1.3 82.3 + - + +
224A ARG 3.7 1.8 + - - -
225A ASN* 4.7 1.0 - - - +
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Residues in contact with HIS 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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200A VAL* 3.5 41.1 - - + +
219A ALA* 3.1 25.2 + - - +
220A PHE 3.2 6.0 + - - +
222A LYS* 1.3 95.4 + - + +
224A ARG* 1.3 56.8 + - - +
225A ASN* 3.1 25.6 + - - +
226A PHE* 3.6 14.1 + + + +
229A TRP* 3.5 32.2 + - + -
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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