Contacts of the helix formed by residues 337 - 352 (chain D) 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 GLU 337 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D ALA* 4.3 14.8 - - + +
285D TYR* 2.9 41.3 + - + +
336D LEU* 1.3 74.9 - - - +
338D PRO* 1.4 81.2 - - + +
339D ALA* 4.5 3.8 - - + +
340D VAL* 2.9 24.8 + - + +
341D VAL* 3.2 8.5 + - - +
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Residues in contact with PRO 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU 3.5 4.5 - - - +
337D GLU* 1.4 95.5 - - + +
339D ALA* 1.3 56.3 + - - +
341D VAL* 3.1 10.8 + - + +
342D ASP* 2.9 40.4 + - - +
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ALA* 4.4 6.1 - - + +
284D ALA* 4.9 13.9 - - + -
337D GLU* 3.1 3.4 + - + +
338D PRO* 1.3 80.2 - - - +
340D VAL* 1.3 58.2 + - - +
342D ASP* 3.6 12.1 + - - +
343D ALA* 3.0 24.8 + - - +
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Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL* 4.9 3.4 - - + -
280D ALA* 3.9 11.0 - - + +
281D LEU* 3.5 27.8 - - + +
284D ALA* 3.7 29.2 - - + -
285D TYR* 3.9 16.2 - - + -
336D LEU* 4.2 15.0 - - + -
337D GLU* 2.9 11.4 + - + +
339D ALA* 1.3 73.2 - - - +
341D VAL* 1.3 66.0 + - - +
343D ALA* 3.1 7.5 + - - +
344D PHE* 2.9 48.3 + - + -
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Residues in contact with VAL 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D TRP* 4.7 4.5 - - + +
303D HIS* 3.6 56.1 - - + +
336D LEU* 4.0 7.9 - - + +
337D GLU 3.6 13.2 - - - +
338D PRO* 3.1 11.3 + - + +
340D VAL* 1.3 77.5 - - - +
342D ASP* 1.3 63.8 + - - +
344D PHE* 3.2 10.2 + - - +
345D ASN* 3.2 35.5 + - - +
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Residues in contact with ASP 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D PRO* 2.9 25.0 + - - +
339D ALA* 3.7 9.6 - - - +
341D VAL* 1.3 78.0 - - - +
343D ALA* 1.3 65.2 + - - +
345D ASN* 3.2 11.7 + - - +
346D GLN* 2.9 38.6 + - - +
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D LEU* 3.3 25.1 - - + +
277D VAL* 4.1 8.7 - - + -
280D ALA* 3.5 31.9 - - + -
339D ALA 3.0 11.0 + - - +
340D VAL* 3.1 9.8 + - + +
342D ASP* 1.3 76.5 - - - +
344D PHE* 1.3 58.2 + - - +
346D GLN* 3.3 6.5 + - - +
347D ALA* 2.8 29.3 + - - +
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Residues in contact with PHE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ALA* 3.4 30.9 - - + +
204D THR* 5.3 2.0 - - + -
206D ARG* 3.1 14.0 + - - +
234D LEU* 5.4 7.2 - - + -
277D VAL* 3.5 32.1 - - + -
292D VAL* 5.1 3.8 - - + -
295D ALA* 4.0 24.7 - - + -
296D ALA* 4.0 10.3 - - + -
299D TRP* 3.9 25.4 - + + -
336D LEU* 3.9 15.9 - - + -
340D VAL* 2.9 43.9 + - + -
341D VAL* 3.4 8.1 - - - +
342D ASP 3.2 0.4 - - - -
343D ALA* 1.3 77.1 - - - +
345D ASN* 1.3 56.4 + - - +
347D ALA* 3.4 6.7 - - + +
348D TRP* 3.0 22.7 + - - +
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Residues in contact with ASN 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ARG* 3.1 32.2 + - - +
299D TRP* 4.2 5.0 + - - -
341D VAL* 3.2 19.3 + - - +
342D ASP* 3.5 14.3 + - - +
343D ALA 3.2 0.2 - - - -
344D PHE* 1.3 76.4 - - - +
346D GLN* 1.3 65.0 + - + +
348D TRP* 3.3 3.9 + - + +
349D HIS* 3.0 40.4 + - + +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D LEU* 4.0 26.8 - - + +
342D ASP* 2.9 33.7 + - - +
343D ALA* 3.5 11.2 - - - +
345D ASN* 1.3 74.9 - - + +
347D ALA* 1.3 63.4 + - - +
349D HIS* 3.3 15.3 + - + +
350D LEU* 3.0 23.2 + - - +
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D THR* 4.3 10.5 - - + -
273D ALA* 3.6 42.9 - - + +
276D LEU* 4.6 4.4 - - + +
277D VAL* 3.9 9.2 - - + -
343D ALA 2.8 17.3 + - - +
344D PHE* 3.4 7.4 - - - +
346D GLN* 1.3 77.5 - - - +
348D TRP* 1.3 61.7 + - - +
350D LEU* 3.2 19.9 + - - +
351D VAL* 3.4 6.8 + - - +
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Residues in contact with TRP 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C HIS 5.9 0.4 + - - -
203D ALA 3.7 5.2 - - - +
204D THR* 3.3 30.2 - - - +
206D ARG* 3.4 75.5 - - + +
207D GLN* 3.9 6.3 - - - -
209D GLU* 5.4 1.0 + - - -
344D PHE 3.0 13.9 + - - +
345D ASN* 3.5 7.0 - - + +
347D ALA* 1.3 75.3 - - - +
349D HIS* 1.3 70.3 + + - +
351D VAL* 3.0 6.9 + - + -
352D ALA* 2.8 62.4 + - + +
355D CYS* 3.7 23.1 - - + -
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Residues in contact with HIS 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C HIS* 3.6 61.8 + + + +
345D ASN* 3.0 32.4 + - + +
346D GLN* 3.3 14.6 + - + +
348D TRP* 1.3 91.9 - + - +
350D LEU* 1.3 62.8 + - - +
351D VAL 3.4 0.5 + - - -
352D ALA* 3.7 3.9 + - - -
353D HIS* 4.9 2.8 + - - -
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Residues in contact with LEU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D HIS* 3.6 40.1 + - + +
272D GLU* 4.0 18.2 - - + +
273D ALA* 4.0 26.5 - - - +
276D LEU* 4.5 17.9 - - + -
346D GLN 3.0 10.0 + - - +
347D ALA 3.3 12.6 - - - +
348D TRP 3.2 0.2 - - - -
349D HIS* 1.3 78.1 - - - +
351D VAL* 1.3 56.3 + - - +
353D HIS* 3.1 23.6 + - - -
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Residues in contact with VAL 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D THR* 3.2 34.1 - - - +
269D HIS 3.5 12.6 - - - +
270D HIS* 3.5 40.8 - - + +
273D ALA* 4.2 2.5 - - + -
347D ALA 3.7 11.4 - - - +
348D TRP* 3.0 16.5 + - + +
350D LEU* 1.3 75.5 - - - +
352D ALA* 1.3 66.9 + - - +
353D HIS* 3.2 3.4 - - - -
354D GLU* 2.9 30.0 + - + +
355D CYS* 3.2 10.5 + - + -
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ALA* 5.1 3.1 - - - +
353C HIS* 4.0 30.1 - - + -
348D TRP* 2.8 51.7 + - + +
349D HIS* 3.7 1.3 + - + -
350D LEU 3.7 1.0 - - - -
351D VAL* 1.3 73.2 - - - +
353D HIS* 1.3 61.6 + - - +
354D GLU 3.0 1.4 + - - -
355D CYS* 3.2 14.7 + - - +
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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