Contacts of the helix formed by residues 208 - 224 (chain A) in PDB entry 1K89
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 ALA 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A VAL* 2.9 18.6 + - - +
205A ARG 3.6 9.4 - - - +
206A PRO 3.3 2.2 - - - -
207A GLU* 1.3 73.9 - - - +
209A THR* 1.3 58.4 + - - +
211A TYR* 4.1 0.2 - - - +
212A GLY* 2.9 27.2 + - - -
375A GLY* 3.5 17.5 - - - +
376A GLY* 4.1 4.7 - - - -
379A VAL* 3.3 32.1 - - + -
402A LEU* 4.1 10.5 - - + +
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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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205A ARG 4.8 1.1 + - - -
206A PRO 4.7 1.6 + - - -
207A GLU 3.4 0.8 - - - -
208A ALA* 1.3 77.1 - - - +
210A GLY* 1.3 63.2 + - - +
212A GLY* 3.8 0.5 - - - -
213A SER* 3.1 22.5 + - - -
240A ASN* 5.0 6.2 + - - -
241A VAL* 3.9 33.1 - - + +
345A VAL* 4.6 2.0 - - + -
372A VAL 4.8 1.4 - - - +
373A ASN* 3.9 32.6 + - + +
375A GLY* 4.5 1.0 - - - -
376A GLY* 3.5 21.6 - - - +
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PRO 5.4 0.4 + - - -
207A GLU 3.3 4.4 + - - -
209A THR* 1.3 77.7 - - - +
211A TYR* 1.3 61.6 + - - +
213A SER* 2.8 24.1 + - - -
214A VAL* 3.4 10.9 + - - +
240A ASN 5.1 0.6 + - - -
241A VAL* 3.6 30.9 + - - +
244A GLY* 3.8 3.3 - - - -
245A ALA* 3.6 12.8 - - - -
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Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.3 11.4 - - + -
207A GLU* 2.9 48.2 + - + +
208A ALA 4.1 1.8 - - - +
210A GLY* 1.3 77.0 - - - +
212A GLY* 1.3 63.9 + - - +
214A VAL* 3.3 3.8 + - - +
215A TYR* 3.1 33.7 + - + -
244A GLY* 3.5 20.0 - - - -
247A LYS* 3.6 35.4 + - + +
248A LYS* 3.6 43.5 + - + +
251A GLU* 4.8 3.5 + - - -
399A ASP* 3.6 20.9 - - - -
402A LEU* 4.3 4.5 - - + -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 2.9 19.4 + - - -
209A THR 3.8 0.9 - - - -
211A TYR* 1.3 77.9 - - - +
213A SER* 1.3 62.1 + - - +
215A TYR* 3.3 6.6 + - - -
216A TYR 3.1 17.2 + - - -
372A VAL 4.3 0.7 - - - -
375A GLY* 4.6 2.0 - - - -
402A LEU* 4.3 5.6 - - - +
406A MET* 3.6 37.3 - - - +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR 3.1 13.1 + - - -
210A GLY* 2.8 21.5 + - - -
212A GLY* 1.3 76.5 - - - +
214A VAL* 1.3 56.9 + - - +
216A TYR* 3.4 4.7 + - - +
217A VAL* 3.1 29.6 + - - +
245A ALA* 4.3 4.0 - - - +
318A MET* 3.4 17.8 - - - +
345A VAL* 4.0 15.5 - - - +
372A VAL* 3.4 35.0 + - - +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLY 3.6 13.9 - - - +
211A TYR 3.3 6.4 + - - +
212A GLY 3.2 0.4 - - - -
213A SER* 1.3 77.7 + - - +
215A TYR* 1.3 58.9 + - - +
216A TYR 3.1 1.8 - - - -
217A VAL* 3.3 7.5 + - + +
218A GLU* 2.9 27.2 + - - +
228A LEU* 3.9 13.6 - - + +
245A ALA* 3.7 28.5 - - + +
248A LYS* 3.9 11.9 - - + -
249A LEU* 4.0 20.6 - - + +
252A LEU* 3.6 27.6 - - + -
318A MET* 4.7 3.8 - - + -
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Residues in contact with TYR 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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211A TYR* 3.1 20.1 + - + -
212A GLY* 3.3 6.7 + - - +
214A VAL* 1.3 76.0 - - - +
216A TYR* 1.3 62.2 + - - +
218A GLU* 3.5 14.6 + - - +
219A ALA* 3.2 19.1 + - - +
248A LYS* 2.9 41.2 + - + -
252A LEU* 4.7 6.5 - - + -
399A ASP* 2.7 33.8 + - - -
402A LEU* 4.0 20.9 - - + -
403A HIS* 3.3 62.4 + + + -
406A MET* 3.8 13.2 - - + -
407A THR* 4.4 6.4 + - - -
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Residues in contact with TYR 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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212A GLY 3.1 12.7 + - - +
213A SER* 3.4 11.7 - - - +
214A VAL 3.1 0.2 - - - -
215A TYR* 1.3 73.9 - - - +
217A VAL* 1.3 65.7 + - + +
219A ALA* 2.9 23.6 + - - +
220A VAL* 3.0 31.7 + - + +
343A ILE* 5.0 0.2 - - + -
367A ALA* 3.7 22.3 - - + +
368A PRO* 4.2 5.4 - - - +
371A ALA* 4.0 34.1 - - + +
372A VAL* 3.9 17.7 - - + -
406A MET* 4.2 21.0 - - + +
409A ILE* 4.1 1.6 - - + -
410A HIS* 3.7 30.7 - + + -
413A SER* 5.1 2.1 + - - -
426A LEU* 3.6 29.5 + - + +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A SER 3.1 14.4 + - - +
214A VAL* 3.7 9.4 - - + +
216A TYR* 1.3 75.7 - - + +
218A GLU* 1.3 58.6 + - - +
220A VAL* 2.9 11.4 + - + +
221A MET* 2.8 48.4 + - + +
228A LEU* 4.2 18.8 - - + -
249A LEU* 6.0 1.6 - - + -
316A ILE* 4.3 10.5 - - + -
318A MET* 3.9 16.4 - - + -
343A ILE* 3.9 36.8 - - + -
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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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214A VAL 2.9 17.1 + - - +
215A TYR* 3.5 6.5 - - - +
216A TYR 3.1 0.2 - - - -
217A VAL* 1.3 79.6 - - - +
219A ALA* 1.3 64.1 + - - +
221A MET* 3.3 10.3 + - - +
222A LYS* 3.1 22.9 + - + +
228A LEU* 4.4 12.2 - - + +
252A LEU* 3.9 23.7 - - - +
403A HIS* 2.9 35.2 + - - -
407A THR* 4.9 3.7 + - - +
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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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215A TYR 3.2 10.2 + - - +
216A TYR 2.9 11.9 + - - +
218A GLU* 1.3 80.7 - - - +
220A VAL* 1.3 55.0 + - - +
222A LYS* 3.5 8.1 + - - +
223A HIS* 3.0 21.8 + - - +
407A THR* 4.1 25.6 - - + +
410A HIS* 3.6 37.8 - - + +
411A ASP* 4.4 2.6 - - - +
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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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216A TYR* 3.0 31.5 + - + +
217A VAL* 2.9 12.9 + - + +
219A ALA* 1.3 73.2 - - - +
221A MET* 1.3 69.5 + - + +
223A HIS* 3.0 13.2 + - - +
224A GLU* 3.0 14.1 + - + +
341A TYR* 3.8 29.8 - - + -
343A ILE* 4.7 8.7 - - + -
365A VAL* 4.0 12.3 - - + -
410A HIS* 3.4 28.9 - - + +
424A TYR* 3.7 11.0 - - - +
426A LEU* 4.2 5.8 - - + -
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Residues in contact with MET 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 VAL* 2.8 39.1 + - + +
218A GLU* 3.3 6.9 + - - +
220A VAL* 1.3 72.3 - - + +
222A LYS* 1.3 63.9 - - - +
224A GLU* 2.9 4.2 + - - -
225A ASN 2.9 19.2 + - - -
226A ASP* 3.0 32.2 + - - +
227A THR* 3.9 6.3 - - - +
228A LEU* 3.8 26.0 - - + +
231A LYS* 3.5 25.4 - - - -
316A ILE* 4.0 10.1 - - + -
341A TYR* 3.6 42.4 - - + -
343A ILE* 6.4 0.2 - - + -
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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 GLU* 3.1 11.3 + - + +
219A ALA* 3.6 11.9 - - - +
221A MET* 1.3 80.9 - - - +
223A HIS* 1.3 61.4 + - - +
225A ASN* 3.2 20.3 + - - +
226A ASP 4.5 3.3 + - - +
411A ASP* 5.8 2.4 + - - -
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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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219A ALA 3.0 14.3 + - - +
220A VAL 3.0 10.3 + - - +
222A LYS* 1.3 77.0 - - - +
224A GLU* 1.3 87.5 + - - +
225A ASN* 3.3 7.4 + - - +
410A HIS* 3.9 9.2 - + + -
414A ALA* 4.6 8.3 - - + +
424A TYR* 3.3 51.9 - + + +
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Residues in contact with GLU 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 VAL* 3.5 20.9 - - + +
221A MET 2.9 4.5 + - - +
223A HIS* 1.3 109.9 + - - +
225A ASN* 1.3 72.0 + - - +
226A ASP* 3.2 5.3 + - + +
340A LYS* 2.7 35.4 + - - +
341A TYR* 3.9 20.0 - - + +
365A VAL* 4.2 1.6 - - + +
424A TYR* 3.5 19.2 - - + -
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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
------------------------------------------------------------
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