Contacts of the helix formed by residues 267 - 286 (chain C) in PDB entry 2BP1
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 LYS 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TYR* 4.0 4.5 - - - -
262C ARG 4.9 0.9 - - - +
263C ASN 3.3 22.6 + - - -
264C ARG* 2.8 26.4 + - - +
265C PHE* 2.9 10.6 + - - +
266C TRP* 1.3 78.8 - - - +
268C GLU* 1.3 61.2 + - - +
269C HIS 3.2 0.2 - - - -
270C HIS* 2.9 30.0 + - + +
271C PHE* 3.2 10.0 + - - -
351C VAL* 6.4 0.7 - - + -
354C GLU* 2.7 62.3 + - + +
356C PRO* 3.7 10.1 - - - +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TYR* 3.5 44.5 + - + +
267C LYS* 1.3 71.8 - - - +
269C HIS* 1.3 63.5 + - + +
271C PHE* 3.1 6.4 + - + +
272C GLU* 3.0 41.9 + - + +
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Residues in contact with HIS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LYS 3.2 1.0 - - - -
268C GLU* 1.3 83.8 - - + +
270C HIS* 1.3 57.2 + - - +
272C GLU* 3.4 31.4 + - - +
273C ALA* 2.9 28.1 + - - +
350C LEU* 3.7 36.3 + - + +
351C VAL* 3.6 4.8 - - + +
353C HIS* 4.4 12.9 + + - -
354C GLU* 3.3 20.8 + - - +
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Residues in contact with HIS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 2.8 43.6 + - + +
205C THR* 4.9 1.8 - - - -
230C ALA* 4.0 9.0 - - + -
233C LEU* 3.4 19.1 - - + +
234C LEU* 4.0 6.7 - - - +
265C PHE* 2.9 48.3 + + - +
267C LYS* 2.9 20.7 + - + +
269C HIS* 1.3 78.9 - - - +
271C PHE* 1.3 55.4 + - - +
273C ALA* 3.3 1.9 + - + +
274C ILE* 3.0 31.7 + - + +
351C VAL* 3.5 19.1 - - + +
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Residues in contact with PHE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LEU* 3.8 25.8 - - + -
238C TYR* 3.7 22.4 - - + -
239C LYS* 3.5 7.2 - - - -
240C TYR* 3.5 40.4 - + + -
266C TRP* 3.6 51.1 - + - -
267C LYS 3.2 23.5 + - - -
268C GLU* 3.1 8.6 + - + +
270C HIS* 1.3 74.4 - - - +
272C GLU* 1.3 64.5 + - - +
274C ILE* 3.3 14.7 + - + +
275C ALA* 3.0 23.2 + - - +
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Residues in contact with GLU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLU* 3.0 29.7 + - + +
269C HIS* 3.4 38.9 + - - +
271C PHE* 1.3 75.4 - - - +
273C ALA* 1.3 57.6 + - - +
275C ALA* 3.4 7.2 + - - +
276C LEU* 3.1 27.2 + - - +
350C LEU* 4.0 16.3 - - + +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 4.6 3.4 - - + -
269C HIS 2.9 13.8 + - - +
270C HIS* 3.3 19.3 - - + +
272C GLU* 1.3 73.6 - - - +
274C ILE* 1.3 63.2 + - - +
276C LEU* 3.3 6.8 - - - +
277C VAL* 3.2 25.6 + - - +
347C ALA* 3.6 35.6 - - + +
350C LEU* 3.7 12.3 - - + +
351C VAL* 4.3 4.0 - - + -
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 5.6 0.9 - - + -
233C LEU* 3.3 48.7 - - + +
234C LEU* 3.9 22.2 - - + -
236C GLY* 4.3 14.1 - - - -
270C HIS* 3.0 19.5 + - + +
271C PHE* 3.7 15.9 - - + +
273C ALA* 1.3 72.8 - - - +
275C ALA* 1.3 59.5 + - - +
277C VAL* 3.1 9.0 + - - +
278C GLU* 2.9 47.9 + - + +
292C VAL* 4.7 9.2 - - + -
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C PHE 3.0 16.9 + - - +
272C GLU* 3.7 7.9 - - - +
274C ILE* 1.3 72.9 - - - +
276C LEU* 1.3 60.4 + - - +
278C GLU* 3.5 16.2 - - - +
279C LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLU 3.1 12.7 + - - +
273C ALA 3.3 9.2 - - - +
275C ALA* 1.3 76.7 - - - +
277C VAL* 1.3 58.0 + - + +
279C LYS* 3.3 11.8 + - - +
280C ALA* 3.0 24.9 + - + +
343C ALA* 3.8 28.5 - - + +
346C GLN* 4.1 23.6 - - + +
347C ALA* 4.3 6.7 - - - +
350C LEU* 4.1 23.1 - - + -
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Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 5.8 1.1 - - + -
273C ALA 3.2 13.9 + - - +
274C ILE* 3.1 10.8 + - - +
276C LEU* 1.3 73.9 - - - +
278C GLU* 1.3 65.0 + - - +
280C ALA* 3.1 8.2 + - - +
281C LEU* 2.9 39.4 + - + +
292C VAL* 4.3 9.0 - - + -
340C VAL* 4.9 4.3 - - + +
343C ALA* 4.0 11.4 - - - +
344C PHE* 3.6 54.7 - - + -
347C ALA* 3.8 14.6 - - + -
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLY* 3.9 24.8 - - - +
274C ILE* 2.9 25.4 + - + +
275C ALA* 3.5 20.6 + - - +
277C VAL* 1.3 77.3 - - - +
279C LYS* 1.3 60.4 + - - +
281C LEU* 3.4 10.1 + - + +
282C GLN* 3.1 33.5 + - - +
292C VAL* 4.0 21.9 - - + +
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA 3.0 18.6 + - - +
276C LEU* 3.5 9.0 - - - +
278C GLU* 1.3 76.2 - - - +
280C ALA* 1.3 56.9 + - - +
282C GLN* 3.4 15.7 + - - +
283C ALA* 3.0 29.5 + - + +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.0 10.3 + - + +
277C VAL 3.1 6.0 + - - +
279C LYS* 1.3 74.0 - - - +
281C LEU* 1.3 57.3 + - - +
283C ALA* 3.9 5.5 - - - +
284C ALA* 2.8 37.8 + - - +
339C ALA* 4.4 9.6 - - + +
340C VAL* 4.1 8.7 - - + -
343C ALA* 3.5 33.0 - - + -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 2.9 26.2 + - + +
278C GLU* 3.6 11.4 - - + +
279C LYS 3.4 0.2 - - - -
280C ALA* 1.3 74.8 - - - +
282C GLN* 1.3 64.0 + - + +
285C TYR* 3.0 41.1 + - + +
289C ALA* 3.5 12.0 - - + +
290C PRO* 3.9 28.0 - - + +
292C VAL* 3.9 32.3 - - + +
295C ALA* 3.8 17.7 - - + -
336C LEU* 5.0 0.7 - - + -
340C VAL* 3.8 24.5 - - + -
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Residues in contact with GLN 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C GLU* 3.1 21.2 + - - +
279C LYS* 3.6 17.2 + - - +
281C LEU* 1.3 78.2 - - + +
283C ALA* 1.3 55.6 + - - +
286C GLY* 2.7 36.6 + - - +
289C ALA* 4.4 8.7 - - + +
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LYS* 3.0 20.0 + - + +
280C ALA* 3.9 7.0 - - - +
282C GLN* 1.3 78.0 - - - +
284C ALA* 1.3 61.6 + - - +
286C GLY* 4.2 1.9 + - - -
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA 2.8 22.0 + - - +
283C ALA* 1.3 76.4 - - - +
285C TYR* 1.3 68.6 + - + +
337C GLU* 4.3 16.8 - - + +
339C ALA* 4.9 11.4 - - + -
340C VAL* 3.8 20.6 - - + -
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Residues in contact with TYR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU* 3.0 25.4 + - + +
284C ALA* 1.3 82.3 - - + +
286C GLY* 1.3 64.7 + - - +
287C ALA 3.3 0.5 + - - -
288C SER* 3.2 24.3 + - - -
289C ALA* 3.3 21.1 - - - +
290C PRO* 3.5 30.1 - - + -
298C ARG* 4.4 7.2 + - - -
335C PRO 4.5 0.7 + - - -
336C LEU* 3.4 15.9 - - + +
337C GLU* 2.9 49.2 + - + +
340C VAL* 3.9 20.6 - - + -
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Residues in contact with GLY 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLN* 2.7 28.6 + - - +
283C ALA 4.2 2.0 + - - -
284C ALA 3.8 0.6 - - - -
285C TYR* 1.3 71.4 - - - +
287C ALA* 1.3 62.7 + - - -
289C ALA* 3.0 21.7 + - - +
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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
------------------------------------------------------------
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