Contacts of the helix formed by residues 240 - 252 (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 ASN 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG 5.2 0.9 - - - +
206A PRO* 2.9 39.1 + - - +
209A THR* 5.0 5.9 + - - -
210A GLY 5.1 0.7 + - - -
239A GLY* 1.3 69.1 - - - -
241A VAL* 1.3 72.6 + - + +
243A TRP* 3.7 16.8 - - - -
244A GLY* 2.9 25.3 + - - -
282A LEU* 6.3 0.9 - - - -
285A ARG* 5.0 13.0 - - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR* 3.9 30.5 - - + +
210A GLY* 3.6 12.4 - - - +
213A SER* 5.3 0.4 - - - +
239A GLY 3.4 0.4 - - - -
240A ASN* 1.3 84.4 - - + +
242A ALA* 1.3 59.0 + - - +
244A GLY 3.1 1.2 + - - -
245A ALA* 2.8 29.5 + - - +
320A CYS* 4.2 21.8 - - + +
345A VAL* 3.5 32.1 - - + -
346A ALA* 5.5 1.8 - - - +
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.0 6.5 - - + +
236A ALA 3.5 24.5 - - - +
237A GLY 3.8 6.1 - - - +
239A GLY* 3.4 16.2 + - - +
240A ASN 3.4 0.2 - - - -
241A VAL* 1.3 77.5 - - - +
243A TRP* 1.3 64.5 + - - +
245A ALA* 3.1 3.5 + - - +
246A ALA* 2.9 26.2 + - - +
259A LEU* 4.6 4.5 - - + -
281A MET* 3.6 17.5 - - + -
320A CYS* 4.1 15.1 + - + +
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Residues in contact with TRP 243 (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 PRO* 4.0 28.7 - - + -
207A GLU* 3.8 26.0 - - + -
239A GLY 2.6 24.4 + - - +
240A ASN* 3.7 19.5 - - - -
242A ALA* 1.3 72.9 - - - +
244A GLY* 1.3 71.7 + - - +
246A ALA* 3.5 1.2 + - - +
247A LYS* 3.1 54.7 + - + +
278A ILE* 3.4 42.1 + - + +
279A ASN* 4.9 3.8 + - - -
281A MET* 3.3 20.3 - - + +
282A LEU* 4.0 41.5 - - + +
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Residues in contact with GLY 244 (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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207A GLU* 4.6 4.7 - - - -
210A GLY* 3.8 13.7 - - - -
211A TYR* 3.5 21.0 - - - -
240A ASN 2.9 18.5 + - - -
241A VAL 3.6 2.5 - - - -
243A TRP* 1.3 84.1 - - - +
245A ALA* 1.3 64.5 + - - +
247A LYS* 3.5 3.6 + - - +
248A LYS* 3.1 17.3 + - - +
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Residues in contact with ALA 245 (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 GLY* 3.6 17.6 - - - +
213A SER* 4.3 9.6 - - - +
214A VAL* 3.7 8.5 - - + +
235A LEU* 4.1 20.6 - - + -
241A VAL* 2.8 17.4 + - + +
242A ALA* 3.6 3.6 - - - +
244A GLY* 1.3 74.0 - - - +
246A ALA* 1.3 58.7 + - - +
248A LYS* 3.0 2.3 + - - -
249A LEU* 2.7 41.6 + - + +
318A MET* 5.0 2.9 - - + -
320A CYS* 4.8 4.0 - - - -
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Residues in contact with ALA 246 (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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235A LEU* 4.2 16.7 - - + +
242A ALA 2.9 19.6 + - - +
243A TRP 3.8 3.4 - - - +
245A ALA* 1.3 71.8 - - - +
247A LYS* 1.3 59.4 + - - +
249A LEU* 3.2 7.6 + - - +
250A ALA* 2.8 34.5 + - - +
256A ALA* 4.6 6.6 + - + -
272A ILE* 4.2 18.4 - - + +
273A THR* 5.4 0.3 - - - +
278A ILE* 4.6 6.3 - - + -
281A MET* 4.4 15.9 - - - -
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Residues in contact with LYS 247 (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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207A GLU* 4.2 8.3 + - - +
211A TYR* 3.6 27.6 + - + +
243A TRP* 3.1 55.9 + - + +
244A GLY 3.5 5.6 - - - +
246A ALA* 1.3 82.4 - - - +
248A LYS* 1.3 57.9 + - - +
250A ALA* 3.5 2.6 + - - +
251A GLU* 3.1 30.2 + - - +
278A ILE* 4.1 21.7 - - + +
279A ASN* 5.9 2.7 - - - +
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Residues in contact with LYS 248 (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* 3.6 44.3 + - + +
214A VAL* 3.9 17.9 - - + -
215A TYR* 2.9 36.3 + - + -
244A GLY 3.1 4.5 + - - +
245A ALA 3.0 3.9 + - - +
247A LYS* 1.3 76.8 - - - +
249A LEU* 1.4 60.6 + - - +
251A GLU* 3.2 35.9 + - - +
252A LEU* 2.9 53.9 + - + +
399A ASP* 4.3 4.4 + - - -
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Residues in contact with LEU 249 (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* 4.0 25.0 - - + +
217A VAL* 6.0 1.8 - - + -
228A LEU* 4.2 10.5 - - + -
233A VAL* 3.8 40.8 - - + -
235A LEU* 4.3 9.2 - - + -
245A ALA* 2.7 31.5 + - + +
246A ALA* 3.4 9.4 - - - +
248A LYS* 1.4 67.7 - - - +
250A ALA* 1.3 71.5 + - - +
252A LEU* 2.7 12.8 + - - +
253A GLY 3.1 0.2 + - - -
254A ALA* 3.0 44.6 + - + +
255A LYS* 4.6 3.1 - - - +
256A ALA* 4.6 6.1 - - + +
318A MET* 4.5 7.4 - - - -
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Residues in contact with ALA 250 (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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246A ALA 2.8 21.4 + - - +
247A LYS 3.5 4.3 - - - +
249A LEU* 1.3 78.2 - - - +
251A GLU* 1.3 55.4 + - - +
252A LEU 2.7 8.5 + - - -
253A GLY* 2.8 12.5 + - - -
254A ALA 3.4 12.1 + - - +
273A THR* 3.7 35.8 - - + +
278A ILE* 4.2 9.4 - - + -
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Residues in contact with GLU 251 (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* 4.8 5.2 + - - -
247A LYS* 3.1 17.0 + - + +
248A LYS* 3.2 42.8 + - + +
250A ALA* 1.3 78.2 - - - +
252A LEU* 1.3 67.1 + - + +
253A GLY 3.5 0.6 + - - -
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Residues in contact with LEU 252 (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* 3.6 28.7 - - + -
215A TYR* 4.7 7.9 - - + -
218A GLU* 3.9 22.9 - - - +
228A LEU* 4.1 18.4 - - + +
229A VAL* 3.6 20.5 + - - +
248A LYS* 2.9 32.7 + - + +
249A LEU 2.7 9.0 + - - +
250A ALA 2.7 5.3 + - - -
251A GLU* 1.3 81.4 - - + +
253A GLY* 1.3 57.0 + - - -
254A ALA* 3.4 2.2 - - - -
403A HIS* 6.1 1.6 - - + -
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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