Contacts of the helix formed by residues 243 - 255 (chain C) in PDB entry 1KKQ
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 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C ILE 3.9 0.4 - - - -
242C HIS* 1.3 111.5 - - - +
244C MET* 1.3 58.6 + - - +
245C GLU* 2.8 26.6 + - - +
246C THR* 2.7 34.8 + - - +
247C LEU* 2.8 16.5 + - - +
343C PHE* 4.0 7.8 - - - -
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Residues in contact with MET 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ASP* 1.3 71.2 - - - +
245C GLU* 1.3 64.0 + - - +
247C LEU* 3.7 8.1 - - + -
248C CYS* 3.1 24.9 + - - -
265C ASN* 5.2 5.6 - - - +
268C ALA* 3.1 39.0 - - + +
269C GLU* 4.1 10.8 - - - +
271C ARG* 3.4 7.8 + - - +
343C PHE* 3.7 15.3 - - + -
347C LEU* 3.9 23.6 - - + -
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ASP* 2.8 22.6 + - - +
244C MET* 1.3 69.7 - - - +
246C THR* 1.3 58.1 + - - +
248C CYS* 2.6 36.4 + - - +
249C MET* 3.0 32.7 + - + +
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Residues in contact with THR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 3.5 23.2 - - + -
240C VAL 3.8 18.8 - - - +
241C ILE* 4.3 2.5 - - - -
242C HIS* 3.3 14.3 + - + +
243C ASP* 2.7 47.1 + - - +
245C GLU* 1.3 79.3 - - - +
247C LEU* 1.3 60.3 + - - +
248C CYS 3.0 1.0 + - - -
249C MET* 3.2 26.8 + - + -
250C ALA* 3.0 19.3 + - - +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ILE* 3.7 17.7 - - + +
243C ASP 2.8 17.8 + - - +
244C MET* 3.7 8.1 - - + +
246C THR* 1.3 76.5 + - - +
248C CYS* 1.3 50.2 + - - +
250C ALA* 3.6 4.5 - - - +
251C GLU* 2.7 31.2 - - + +
268C ALA* 3.3 30.3 - - + -
271C ARG* 3.6 11.7 - - - +
272C ILE* 3.2 45.1 - - + -
343C PHE* 3.5 13.5 - - + -
777C 471 3.9 16.6 - - + -
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Residues in contact with CYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C MET 3.1 12.2 + - - -
245C GLU* 2.6 17.5 + - - +
247C LEU* 1.3 69.1 - - - +
249C MET* 1.3 55.7 + - + +
250C ALA 2.6 13.3 + - - -
251C GLU* 2.5 21.1 - - - +
252C LYS* 2.9 22.1 - - + +
264C GLN 3.7 15.7 - - - +
265C ASN* 3.6 14.8 - - - -
271C ARG* 2.6 38.4 - - - +
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Residues in contact with MET 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 4.1 18.8 - - + -
245C GLU* 3.8 31.2 - - + +
246C THR* 3.5 42.6 - - + +
248C CYS* 1.3 78.3 - - + +
250C ALA* 1.3 62.2 + - - +
252C LYS* 4.0 12.0 - - - +
253C THR* 3.3 19.9 + - - +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 4.2 9.8 - - + -
241C ILE* 3.5 33.0 - - + -
246C THR 3.0 12.6 + - - +
247C LEU 3.6 5.8 - - - +
248C CYS 2.6 5.9 + - - -
249C MET* 1.3 69.3 - - - +
251C GLU* 1.3 55.3 + - - +
252C LYS 2.5 15.6 + - - -
253C THR* 2.7 26.7 + - - -
254C LEU* 3.2 10.0 + - + +
777C 471 4.5 4.3 - - + -
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Residues in contact with GLU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LEU* 2.7 24.2 - - + +
248C CYS* 2.5 32.2 - - - +
250C ALA* 1.3 76.0 - - - +
252C LYS* 1.3 65.8 + - - +
253C THR 3.4 0.2 - - - -
254C LEU* 3.2 20.3 - - + +
255C VAL* 3.1 25.8 + - - +
258C LEU* 5.1 5.1 - - + +
271C ARG* 3.1 47.1 + - + +
275C CYS* 3.4 28.5 - - + -
777C 471 4.2 13.0 - - + -
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C CYS* 2.9 28.3 - - + +
249C MET* 4.0 10.1 - - - +
250C ALA 2.5 5.4 + - - +
251C GLU* 1.3 79.6 + - - +
253C THR* 1.3 60.6 + - + +
255C VAL 2.9 23.7 - - - +
256C ALA* 4.8 0.5 - - - -
258C LEU* 5.1 8.2 + - + +
259C VAL* 2.9 47.2 + - + +
263C ILE 5.6 5.8 - - - +
264C GLN* 5.6 11.6 - - + +
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C MET 3.3 13.1 + - - +
250C ALA* 2.7 19.9 + - - -
252C LYS* 1.3 76.8 - - + +
254C LEU* 1.3 72.7 + - - +
255C VAL 4.3 0.4 - - - -
256C ALA* 4.1 9.3 + - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA* 3.2 12.5 + - + +
251C GLU* 3.2 30.1 - - + +
252C LYS 3.1 0.4 - - - -
253C THR* 1.3 86.1 - - - +
255C VAL* 1.3 63.5 + - + +
256C ALA* 2.8 9.4 + - - +
275C CYS* 4.3 11.9 - - + +
278C CYS* 5.9 6.1 - - + -
333C ALA* 4.9 18.2 - - + -
777C 471 3.7 26.7 - - + -
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU 3.1 11.9 + - - +
252C LYS 2.9 18.2 - - - +
254C LEU* 1.3 78.1 - - + +
256C ALA* 1.3 53.6 + - - +
257C LYS* 2.7 35.7 + - + +
258C LEU* 3.5 43.9 + - + +
274C HIS* 5.6 6.7 - - + +
275C CYS* 4.3 18.8 - - - -
278C CYS* 5.2 8.7 - - - -
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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