Contacts of the helix formed by residues 337 - 352 (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 GLU 337 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284C ALA* 4.3 22.7 - - + +
285C TYR* 2.9 41.9 + - + +
335C PRO 5.6 0.7 - - - +
336C LEU* 1.3 74.9 - - - +
338C PRO* 1.4 70.3 - - + +
339C ALA* 3.2 3.8 - - + +
340C VAL* 2.9 26.3 + - + +
341C VAL* 3.3 7.7 + - - +
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Residues in contact with PRO 338 (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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336C LEU 3.5 4.2 - - - +
337C GLU* 1.4 92.9 - - + +
339C ALA* 1.3 56.5 - - - +
341C VAL* 3.1 12.2 + - + +
342C ASP* 2.9 38.9 + - - +
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Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 4.4 5.2 - - + +
284C ALA* 4.9 14.6 - - + -
337C GLU* 3.2 2.5 - - + +
338C PRO* 1.3 80.9 - - - +
340C VAL* 1.3 58.3 + - - +
342C ASP* 3.6 10.4 + - - +
343C ALA* 3.0 25.8 + - - +
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 4.9 4.3 - - + -
280C ALA* 3.8 14.1 - - + +
281C LEU* 3.8 24.2 - - + -
284C ALA* 3.8 27.8 - - + -
285C TYR* 3.9 16.6 - - + -
336C LEU* 4.1 16.2 - - + -
337C GLU* 2.9 11.6 + - + +
339C ALA* 1.3 74.2 - - - +
341C VAL* 1.3 61.0 + - - +
343C ALA* 3.2 7.9 + - - +
344C PHE* 2.9 46.9 + - + -
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ARG* 5.1 0.2 + - - -
299C TRP* 4.6 7.9 + - - +
303C HIS* 3.8 56.3 - - + +
336C LEU* 4.0 9.0 - - + +
337C GLU 3.6 13.7 - - - +
338C PRO* 3.1 11.6 + - + +
340C VAL* 1.3 76.1 - - - +
342C ASP* 1.3 63.8 + - - +
344C PHE* 3.2 11.1 + - - +
345C ASN* 3.0 21.0 + - + +
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Residues in contact with ASP 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C PRO* 2.9 30.2 + - - +
339C ALA* 3.8 9.2 - - - +
341C VAL* 1.3 75.0 - - - +
343C ALA* 1.3 60.2 + - - +
345C ASN* 3.2 9.6 + - - +
346C GLN* 2.9 35.9 + - + +
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.8 20.1 - - + +
277C VAL* 4.0 9.7 - - + +
280C ALA* 3.5 26.7 - - + -
339C ALA 3.0 18.5 + - - +
340C VAL* 3.2 6.0 + - + +
342C ASP* 1.3 74.7 - - - +
344C PHE* 1.3 59.0 + - - +
346C GLN* 3.3 4.6 + - - +
347C ALA* 2.8 29.1 + - - +
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Residues in contact with PHE 344 (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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203C ALA* 3.4 28.4 - - + +
204C THR* 5.0 6.3 - - + -
206C ARG* 3.3 11.1 + - - +
234C LEU* 5.4 6.1 - - + -
277C VAL* 3.6 37.7 - - + -
292C VAL* 4.9 3.6 - - + -
295C ALA* 3.8 19.3 - - + -
296C ALA* 3.7 29.4 - - + -
299C TRP* 3.8 28.3 - + + -
336C LEU* 4.0 11.9 - - + -
340C VAL* 2.9 30.1 + - + -
341C VAL* 3.2 7.8 + - - +
343C ALA* 1.3 75.9 - - - +
345C ASN* 1.3 58.3 + - - +
347C ALA* 3.3 3.6 + - - +
348C TRP* 3.0 23.2 + - - +
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Residues in contact with ASN 345 (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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206C ARG* 3.0 28.2 + - - +
341C VAL 3.0 13.0 + - - +
342C ASP* 3.3 13.7 - - - +
344C PHE* 1.3 74.3 - - - +
346C GLN* 1.3 72.3 + - - +
348C TRP* 3.3 4.2 + - - +
349C HIS* 3.0 58.1 + - - -
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Residues in contact with GLN 346 (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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276C LEU* 4.1 18.6 - - + +
342C ASP* 2.9 23.0 + - + +
343C ALA* 3.8 6.7 - - - +
345C ASN* 1.3 84.0 + - - +
347C ALA* 1.3 61.5 + - - +
349C HIS* 3.3 26.8 + - - +
350C LEU* 3.1 24.9 + - - +
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Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 4.2 10.3 - - + -
273C ALA* 3.6 43.7 - - + +
276C LEU* 4.3 4.4 - - + +
277C VAL* 3.8 10.3 - - + -
343C ALA 2.8 14.7 + - - +
344C PHE* 3.3 9.9 - - - +
345C ASN 3.1 0.2 - - - -
346C GLN* 1.3 73.6 - - - +
348C TRP* 1.3 65.2 + - - +
350C LEU* 3.1 19.1 + - - +
351C VAL* 3.4 6.9 + - - +
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Residues in contact with TRP 348 (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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203C ALA 3.7 4.0 - - - +
204C THR* 3.4 29.3 - - - +
206C ARG* 3.4 72.5 - - + +
207C GLN* 3.9 10.8 - - + -
209C GLU* 5.3 2.2 + - - -
344C PHE 3.0 12.6 + - - +
345C ASN* 3.6 7.0 - - - +
347C ALA* 1.3 74.5 - - - +
349C HIS* 1.3 79.1 + + - +
351C VAL* 3.0 7.6 + - + -
352C ALA* 2.7 63.8 + - + +
355C CYS* 3.8 18.4 - - + -
353D HIS 5.5 1.8 + - - -
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Residues in contact with HIS 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C ASN* 3.0 42.3 + - - -
346C GLN* 3.5 29.0 + - - +
347C ALA 3.3 0.2 - - - -
348C TRP* 1.3 95.3 + + - +
350C LEU* 1.3 62.3 + - - +
351C VAL 3.4 0.3 + - - -
352C ALA* 3.7 3.7 + - - -
353C HIS* 4.8 4.0 + - - -
353D HIS* 3.5 60.3 + + + +
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Residues in contact with LEU 350 (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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269C HIS* 3.7 30.3 + - + +
272C GLU* 4.0 15.9 - - + +
273C ALA* 3.7 33.0 - - + +
276C LEU* 4.1 21.3 - - + -
346C GLN 3.1 9.7 + - - +
347C ALA* 3.1 12.5 + - - +
349C HIS* 1.3 77.6 - - + +
351C VAL* 1.3 55.9 + - - +
353C HIS* 3.3 20.6 + - - -
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 3.3 33.7 - - - +
267C LYS* 6.1 0.9 - - + -
269C HIS* 3.6 11.4 - - + +
270C HIS* 3.5 46.2 - - + +
273C ALA* 4.3 0.9 - - + -
347C ALA 3.7 11.4 - - - +
348C TRP* 3.0 17.1 + - + +
350C LEU* 1.3 76.4 - - - +
352C ALA* 1.3 59.8 + - - +
353C HIS* 3.2 5.8 - - - -
354C GLU* 2.8 32.6 + - + +
355C CYS* 3.2 10.7 + - - -
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Residues in contact with ALA 352 (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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348C TRP* 2.7 55.6 + - + +
349C HIS 3.7 0.6 + - - -
350C LEU 3.7 1.0 - - - -
351C VAL* 1.3 71.8 - - - +
353C HIS* 1.3 63.0 + - - +
354C GLU 3.2 0.9 + - - -
355C CYS* 3.4 14.2 + - - +
352D ALA* 5.1 3.0 - - - +
353D HIS* 3.9 29.8 - - + -
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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