Contacts of the helix formed by residues 276 - 288 (chain B) in PDB entry 1KB6
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 CYS 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B CYS* 3.7 7.9 - - - -
261B PRO* 4.0 12.1 - - + -
262B PHE* 5.1 4.3 - - + -
266B CYS* 4.0 12.3 - - + -
268B ILE* 5.1 1.5 - - + +
272B ASN 4.0 1.4 + - - -
273B ARG 3.6 6.9 + - - +
275B HIS* 1.3 76.4 - - + +
277B GLN* 1.3 61.9 + - - +
278B ALA* 3.0 9.0 - - - -
279B CYS* 3.2 26.7 - - + -
280B ARG* 2.9 33.8 + - - +
351B ZN 2.4 36.3 - - - -
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 3.7 24.7 - - + -
258B PHE* 3.2 48.2 - - + -
273B ARG 5.6 0.2 - - - -
274B ARG 4.6 13.0 - - - +
275B HIS 3.8 2.8 + - - +
276B CYS* 1.3 73.3 - - - +
278B ALA* 1.3 65.1 + - - +
280B ARG* 4.4 1.8 - - - +
281B LEU* 3.1 24.3 + - - +
419D T 5.4 3.4 - - - -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B PHE* 3.3 20.7 - - + +
259B THR* 3.5 11.4 + - - +
260B CYS* 3.4 37.5 - - + +
261B PRO* 6.0 0.2 - - - +
276B CYS* 3.0 2.4 - - - -
277B GLN* 1.3 81.0 - - - +
279B CYS* 1.3 64.6 + - - +
281B LEU* 3.6 2.1 - - - +
282B LYS* 3.0 24.1 + - - +
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Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B CYS* 3.8 7.4 - - - -
264B GLY* 3.8 17.0 - - - -
265B ASP 4.5 0.2 - - - -
266B CYS* 3.6 33.0 - - + +
268B ILE* 3.6 8.2 - - + +
276B CYS* 3.2 6.9 - - + -
278B ALA* 1.3 80.4 - - - +
280B ARG* 1.3 53.2 + - - +
282B LYS* 3.2 10.4 + - - +
283B ARG* 2.7 36.6 + - - +
351B ZN 2.4 34.3 - - - -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B VAL* 3.9 15.5 - - + +
243B GLY 3.5 8.5 + - - -
244B CYS* 3.3 23.4 - - - -
247B PHE* 3.2 51.7 - - + +
268B ILE* 3.1 20.7 - - + +
273B ARG* 3.2 45.3 - - - +
274B ARG* 4.5 10.3 - - - +
276B CYS 2.9 23.0 + - - +
277B GLN* 4.1 1.6 - - - +
279B CYS* 1.3 72.4 - - - +
281B LEU* 1.3 58.4 + - - +
283B ARG* 3.1 2.9 + - - +
284B CYS* 2.9 29.2 + - - -
419D T 4.7 5.3 - - - -
420D G 3.1 28.5 + - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 3.7 18.5 - - + -
248B PHE* 4.1 13.0 - - + -
251B SER* 3.8 17.7 - - - -
252B MET* 3.6 32.5 - - + -
256B ALA 4.2 9.9 - - - +
258B PHE* 3.7 28.0 - - + +
277B GLN 3.1 18.9 + - - +
278B ALA 3.6 2.5 - - - +
280B ARG* 1.3 77.2 - - - +
282B LYS* 1.3 62.7 + - - +
284B CYS* 3.1 19.1 + - + +
285B VAL* 3.3 9.3 + - + +
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Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B GLY* 5.0 14.6 - - - +
278B ALA 3.0 16.5 + - - +
279B CYS* 3.6 10.3 - - - +
281B LEU* 1.3 76.1 - - - +
283B ARG* 1.3 63.0 + - - +
284B CYS 3.4 0.2 + - - -
285B VAL* 3.4 7.3 + - - +
286B ASP* 3.1 47.9 + - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLY* 2.5 29.5 + - - -
226B VAL* 3.7 29.8 + - + +
268B ILE* 3.8 12.9 - - + +
279B CYS 2.7 21.0 + - - +
280B ARG 3.6 3.6 - - - +
282B LYS* 1.3 73.5 - - - +
284B CYS* 1.3 64.4 + - - +
286B ASP* 3.1 16.7 + - - +
287B ILE* 3.0 36.0 + - - +
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Residues in contact with CYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B VAL* 3.5 23.3 - - - -
244B CYS* 4.6 4.9 - - - -
247B PHE* 4.4 13.7 - - - -
248B PHE* 3.8 32.5 - - + -
280B ARG 2.9 16.7 + - - -
281B LEU* 3.1 11.4 - - - +
283B ARG* 1.3 76.4 - - - +
285B VAL* 1.3 60.6 + - - +
287B ILE* 2.6 25.4 - - - +
289B MET* 3.2 30.1 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 4.7 3.6 - - + -
252B MET* 4.0 24.2 - - + -
281B LEU* 3.3 13.4 + - + +
282B LYS* 3.8 9.0 - - - +
283B ARG 3.3 0.6 - - - -
284B CYS* 1.3 75.7 - - + +
286B ASP* 1.3 68.6 + - - +
288B GLY* 3.2 13.0 + - - -
289B MET 4.1 13.7 + - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B LYS* 3.1 43.7 + - - +
283B ARG* 3.1 18.4 + - - +
285B VAL* 1.3 78.4 - - - +
287B ILE* 1.3 62.4 + - - +
288B GLY* 3.0 6.4 + - - -
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLY* 3.6 38.6 - - - +
226B VAL* 3.8 16.6 - - + -
237B ASN 5.2 0.3 - - - +
238B ALA* 3.9 27.7 - - + +
239B MET 5.3 1.3 - - - +
240B THR* 5.1 1.1 - - + -
283B ARG* 3.0 23.5 + - - +
284B CYS* 2.6 26.9 - - - +
286B ASP* 1.3 75.3 - - - +
288B GLY* 1.3 56.6 + - - +
289B MET* 3.9 5.6 - - + -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ASN* 3.8 17.0 + - - +
238B ALA* 4.2 3.4 - - - -
285B VAL 3.2 8.3 + - - -
286B ASP 3.0 6.1 - - - -
287B ILE* 1.3 81.1 - - - +
289B MET* 1.3 63.8 + - - +
290B MET* 2.9 28.8 - - - +
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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