Contacts of the helix formed by residues 337 - 352 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B ALA* 4.3 15.3 - - + +
285B TYR* 2.9 41.1 + - + +
336B LEU* 1.3 75.8 - - - +
338B PRO* 1.3 74.7 - - + +
339B ALA* 4.4 4.3 - - + +
340B VAL* 2.9 31.7 + - + +
341B VAL* 3.2 7.8 + - - +
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Residues in contact with PRO 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU 3.4 4.0 - - - +
337B GLU* 1.3 94.6 - - + +
339B ALA* 1.3 56.0 + - - +
341B VAL* 3.2 10.6 + - + +
342B ASP* 2.9 40.9 + - - +
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 4.4 5.4 - - + +
284B ALA* 4.9 15.0 - - + -
337B GLU* 3.1 2.6 + - + -
338B PRO* 1.3 79.6 - - - +
340B VAL* 1.3 57.6 + - - +
342B ASP* 3.7 10.1 + - - +
343B ALA* 3.0 25.5 + - - +
346B GLN* 5.4 0.3 + - - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 4.9 3.6 - - + -
280B ALA* 3.9 13.0 - - + +
281B LEU* 3.8 25.4 - - + +
284B ALA* 3.7 28.7 - - + -
285B TYR* 4.0 15.9 - - + -
336B LEU* 4.3 15.5 - - + -
337B GLU* 2.9 12.2 + - + +
339B ALA* 1.3 75.7 - - - +
341B VAL* 1.3 58.1 + - - +
343B ALA* 3.2 6.9 + - - +
344B PHE* 2.9 49.8 + - + -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TRP* 4.7 6.7 - - + +
303B HIS* 3.7 55.6 - - + +
336B LEU* 4.0 8.7 - - + +
337B GLU 3.2 14.1 + - - +
338B PRO* 3.2 10.1 + - + +
340B VAL* 1.3 77.0 - - - +
342B ASP* 1.3 62.8 + - - +
344B PHE* 3.3 11.0 + - - +
345B ASN* 3.2 30.9 + - - +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 2.9 26.7 + - - +
339B ALA* 3.8 9.2 - - - +
340B VAL 3.3 0.2 - - - -
341B VAL* 1.3 78.0 - - - +
343B ALA* 1.3 59.0 + - - +
345B ASN* 3.1 15.9 + - - +
346B GLN* 2.9 42.3 + - - +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.0 28.5 - - + +
277B VAL* 4.1 7.0 - - + -
280B ALA* 3.5 26.2 - - + -
339B ALA 3.0 16.6 + - - +
340B VAL* 3.2 9.4 + - + +
342B ASP* 1.3 75.9 - - - +
344B PHE* 1.3 56.9 + - - +
346B GLN* 3.3 9.4 + - - +
347B ALA* 2.9 24.3 + - - +
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Residues in contact with PHE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA* 3.4 32.3 - - + +
204B THR* 5.2 2.2 - - + -
206B ARG* 3.1 13.4 + - - +
234B LEU* 5.2 8.7 - - + -
277B VAL* 3.7 33.8 - - + +
292B VAL* 5.0 2.7 - - + -
295B ALA* 3.9 15.3 - - + -
296B ALA* 3.8 30.7 - - + -
299B TRP* 4.0 24.0 - + + -
336B LEU* 4.1 7.6 - - + -
340B VAL* 2.9 40.9 + - + -
341B VAL* 3.5 9.4 - - - +
342B ASP 3.2 0.2 - - - -
343B ALA* 1.3 74.8 - - - +
345B ASN* 1.3 57.2 + - - +
347B ALA* 3.3 5.4 - - + +
348B TRP 3.0 23.2 + - - -
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Residues in contact with ASN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.1 29.5 + - - +
299B TRP* 4.5 5.0 + - - -
341B VAL* 3.2 22.2 + - - +
342B ASP* 3.1 18.9 + - - +
344B PHE* 1.3 74.6 - - - +
346B GLN* 1.3 65.1 + - - +
348B TRP* 3.3 4.8 + - + +
349B HIS* 3.0 39.9 + - + -
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.7 28.4 - - + +
339B ALA 5.4 0.6 + - - -
342B ASP* 2.9 32.7 + - - +
343B ALA* 3.5 12.0 - - - +
345B ASN* 1.3 75.2 - - - +
347B ALA* 1.3 61.4 + - - +
349B HIS* 3.4 12.3 + - - +
350B LEU* 3.2 24.4 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 4.1 10.3 - - + -
273B ALA* 3.7 39.5 - - + +
276B LEU* 4.4 3.5 - - + +
277B VAL* 4.0 8.3 - - + -
343B ALA 2.9 14.1 + - - +
344B PHE* 3.3 11.4 - - - +
346B GLN* 1.3 73.9 - - - +
348B TRP* 1.3 66.4 + - - +
350B LEU* 3.2 20.3 + - - +
351B VAL* 3.4 10.5 + - - +
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Residues in contact with TRP 348 (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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203B ALA 3.8 3.1 - - - +
204B THR* 3.3 31.1 - - - +
206B ARG* 3.4 76.1 - - + +
207B GLN* 3.8 9.6 - - - -
209B GLU* 5.4 1.4 + - - -
344B PHE 3.0 13.8 + - - +
345B ASN* 3.5 7.0 - - - +
347B ALA* 1.3 76.9 - - - +
349B HIS* 1.3 78.2 + + - +
351B VAL* 3.0 6.8 + - + -
352B ALA* 2.8 59.6 + - + +
355B CYS* 3.8 18.2 - - + -
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Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A HIS* 3.6 61.2 + - + +
345B ASN* 3.0 32.1 + - + -
346B GLN* 3.6 12.0 - - - +
347B ALA 3.3 0.2 - - - -
348B TRP* 1.3 95.4 + + - +
350B LEU* 1.3 60.9 + - - +
351B VAL 3.5 0.2 + - - -
352B ALA* 3.8 4.8 + - + +
353B HIS* 5.0 2.9 + - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B HIS* 3.6 37.8 + - + +
272B GLU* 4.1 17.9 - - + +
273B ALA* 3.9 28.3 - - - +
276B LEU* 4.7 14.8 - - + -
346B GLN 3.2 14.2 + - - +
347B ALA 3.2 10.9 + - - +
348B TRP 3.1 0.2 - - - -
349B HIS* 1.3 76.4 - - - +
351B VAL* 1.3 59.8 + - - +
353B HIS* 3.3 22.2 + - - -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 3.2 33.4 - - - +
269B HIS* 3.5 31.6 - - + +
270B HIS* 3.6 24.2 - - + +
273B ALA* 4.1 3.1 - - + -
347B ALA 3.5 12.1 - - - +
348B TRP* 3.3 15.9 - - + +
350B LEU* 1.3 78.3 - - - +
352B ALA* 1.3 63.9 + - - +
353B HIS 3.2 2.9 - - - -
354B GLU* 2.9 27.8 + - + +
355B CYS* 3.2 10.0 + - - -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ALA* 5.2 2.4 - - - +
353A HIS* 4.0 29.2 - - + +
348B TRP* 2.8 51.7 + - + +
349B HIS* 3.8 1.5 + - + -
350B LEU 3.7 1.4 - - - -
351B VAL* 1.3 72.2 - - - +
353B HIS* 1.3 61.9 + - - +
354B GLU 3.2 1.0 + - - -
355B CYS* 3.3 14.0 + - - +
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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
------------------------------------------------------------
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