Contacts of the helix formed by residues 342 - 361 (chain B) in PDB entry 2BXE
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 SER 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B TYR* 1.3 76.8 - - - +
343B VAL* 1.3 63.1 + - - +
344B VAL* 3.2 8.7 - - - +
345B LEU* 3.1 26.0 + - - +
346B LEU* 3.1 19.3 + - - +
446B MET* 4.7 5.3 - - - +
447B PRO* 3.7 26.0 - - - +
450B GLU* 4.1 10.7 + - - +
451B ASP* 3.2 25.6 - - - -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 3.1 48.7 - - + +
217B ALA* 4.3 11.4 - - + -
218B ARG* 3.5 41.1 - - - +
221B GLN* 3.8 5.6 - - - +
341B TYR 3.8 0.4 + - - -
342B SER* 1.3 71.9 - - - +
344B VAL* 1.3 63.0 + - + +
346B LEU* 3.5 9.2 + - - +
347B LEU* 3.0 33.4 + - + +
451B ASP* 3.0 17.1 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 6.5 0.2 - - + -
342B SER* 3.2 14.6 - - - +
343B VAL* 1.3 72.8 - - + +
345B LEU* 1.3 52.4 + - - +
347B LEU* 2.9 11.5 + - + +
348B ARG* 2.7 55.8 + - - +
450B GLU* 3.8 19.3 - - - +
451B ASP* 2.9 19.3 + - - +
454B SER* 3.7 17.7 - - - +
481B LEU 5.4 1.6 - - - +
482B VAL* 3.9 26.9 - - + +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B TYR* 3.8 30.7 - - + -
342B SER* 3.1 23.5 + - - +
344B VAL* 1.3 76.7 - - - +
346B LEU* 1.3 58.0 + - - +
348B ARG* 3.0 24.1 + - + +
349B LEU* 2.8 44.5 + - + +
380B LEU* 3.6 30.7 - - + +
381B VAL* 3.9 16.6 - - + -
446B MET* 3.0 31.6 - - + -
450B GLU* 4.9 0.4 - - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA* 4.4 9.2 - - + -
221B GLN* 3.7 30.5 - - + +
330B PHE* 5.5 0.3 - - - -
331B LEU* 4.1 12.3 - - + +
334B TYR* 3.6 33.7 - - + +
335B ALA* 3.9 32.3 - - + +
338B HIS* 4.4 2.5 - - + +
341B TYR* 4.0 18.6 - - + -
342B SER 3.1 12.2 + - - +
343B VAL* 3.5 10.1 - - - +
344B VAL 3.1 0.2 - - - -
345B LEU* 1.3 78.1 - - - +
347B LEU* 1.3 52.7 + - - +
348B ARG 3.1 0.2 + - - -
349B LEU* 3.1 6.9 + - + +
350B ALA* 2.6 37.0 + - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA 5.7 0.4 - - - +
213B ALA* 3.7 26.5 - - + +
214B TRP* 3.9 27.4 - - + +
217B ALA* 4.7 1.3 - - + -
331B LEU* 3.8 12.1 - - + -
343B VAL* 3.0 24.4 + - + +
344B VAL* 2.9 12.6 + - + +
346B LEU* 1.3 76.9 - - + +
348B ARG* 1.3 57.3 + - - +
350B ALA* 3.6 4.1 - - - +
351B LYS* 3.0 28.4 + - - +
482B VAL* 3.7 16.2 - - + +
2002B 1FL 3.3 38.1 - - + -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 2.7 29.0 + - - +
345B LEU* 3.0 25.7 + - + +
347B LEU* 1.3 70.2 - - - +
349B LEU* 1.3 67.4 + - - +
351B LYS* 2.9 7.8 + - - +
352B THR* 2.9 24.8 + - - +
380B LEU* 4.7 22.3 + - + -
383B GLU* 4.7 1.6 + - - -
384B PRO* 3.8 15.2 - - - +
450B GLU* 2.3 41.0 + - - -
482B VAL* 3.3 33.4 + - + +
483B ASN* 3.6 23.8 - - - +
485B ARG* 3.9 5.9 - - - +
486B PRO* 4.0 16.9 - - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PHE* 4.6 2.9 - - + -
334B TYR* 3.9 23.1 - - + +
341B TYR* 3.7 34.1 - - + -
345B LEU* 2.8 23.6 + - + +
346B LEU* 3.5 7.6 - - + +
348B ARG* 1.3 73.8 - - - +
350B ALA* 1.3 65.6 + - - +
352B THR* 3.0 7.3 + - - -
353B TYR* 3.0 19.4 + - - +
377B PHE* 3.5 53.9 - - + +
380B LEU* 3.9 22.9 - - + -
381B VAL* 4.2 5.4 - - + -
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.4 3.8 - - - +
330B PHE* 3.7 19.9 - - + -
331B LEU* 3.6 21.1 - - + -
346B LEU 2.6 21.5 + - - +
347B LEU 3.6 4.9 - - - +
349B LEU* 1.3 73.0 - - - +
351B LYS* 1.3 61.2 + - - +
353B TYR* 3.4 4.9 - - - +
354B GLU* 3.1 20.6 + - - +
2002B 1FL 3.1 28.4 - - + -
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Residues in contact with LYS 351 (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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347B LEU 3.0 16.2 + - - +
348B ARG* 2.9 8.0 + - - +
350B ALA* 1.3 75.0 - - - +
352B THR* 1.3 64.7 + - - +
354B GLU* 3.2 20.0 + - - +
355B THR* 3.0 29.7 + - - +
479B GLU 5.6 0.2 + - - -
480B SER* 4.1 14.1 + - - -
482B VAL* 5.2 5.2 - - + -
483B ASN* 5.1 6.1 + - - +
2002B 1FL 3.6 59.9 + - + +
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Residues in contact with THR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 2.9 11.0 + - - +
349B LEU 3.0 7.6 + - - -
351B LYS* 1.3 76.4 - - - +
353B TYR* 1.3 65.3 + - - +
355B THR* 3.1 8.8 + - - -
356B THR* 2.9 27.0 + - - +
373B VAL* 4.9 0.7 - - + -
376B GLU* 3.8 30.7 - - + +
377B PHE* 4.1 17.5 - - + -
380B LEU* 3.2 26.6 - - + +
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PHE* 2.6 43.3 + + + +
310B VAL* 5.1 0.9 - - + -
315B VAL* 3.8 6.1 - - - +
326B PHE* 3.7 21.0 - + - -
327B LEU* 3.9 17.9 - - + -
330B PHE* 4.0 31.9 - + + -
349B LEU 3.0 11.0 + - - +
350B ALA 3.4 9.4 - - - +
351B LYS 3.2 0.2 - - - -
352B THR* 1.3 76.0 - - - +
354B GLU* 1.3 62.2 + - - +
356B THR* 3.1 3.8 + - - -
357B LEU* 2.8 55.9 + - + +
370B TYR* 6.0 1.3 - + + -
373B VAL* 4.0 37.5 - - + -
374B PHE* 5.2 1.3 - + - -
377B PHE* 4.1 10.0 - + + -
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Residues in contact with GLU 354 (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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209B ARG* 3.1 34.0 + - - -
319B TYR* 3.9 14.2 + - - +
327B LEU* 3.7 30.9 - - + +
350B ALA 3.1 8.7 + - - +
351B LYS* 3.2 16.8 + - - +
353B TYR* 1.3 78.2 - - - +
355B THR* 1.3 54.4 + - - +
357B LEU* 3.1 7.8 + - - +
358B GLU* 2.7 37.3 + - + +
2002B 1FL 3.6 15.0 - - + -
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Residues in contact with THR 355 (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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351B LYS* 3.0 17.1 + - - +
352B THR* 3.4 10.2 - - - -
354B GLU* 1.3 79.2 - - - +
356B THR* 1.3 64.3 + - - +
358B GLU* 2.9 19.3 + - + +
359B LYS* 3.1 20.5 + - + +
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Residues in contact with THR 356 (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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352B THR* 2.9 14.3 + - - +
353B TYR* 3.4 7.6 - - - -
355B THR* 1.3 77.0 - - - +
357B LEU* 1.3 59.3 + - + +
359B LYS* 3.3 10.3 - - + +
360B CYS* 2.8 51.0 + - - +
369B CYS 4.9 1.1 - - - +
370B TYR* 3.9 14.8 - - + -
373B VAL* 3.4 31.9 - - + +
376B GLU* 3.8 19.5 + - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.8 22.0 - - + -
319B TYR* 3.6 42.1 - - + -
326B PHE* 3.8 13.0 - - + -
327B LEU* 5.0 2.0 - - + -
353B TYR* 2.8 56.8 + - + +
354B GLU 3.4 7.9 - - - +
356B THR* 1.3 72.3 - - + +
358B GLU* 1.3 63.4 + - - +
360B CYS* 4.5 1.1 - - - -
361B CYS* 3.1 36.0 + - - +
370B TYR* 4.4 20.6 - - + -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 2.5 37.7 + - - -
323B LYS* 4.3 9.7 + - - +
354B GLU* 2.7 20.7 + - + +
355B THR* 2.9 14.8 + - + +
357B LEU* 1.3 74.5 - - - +
359B LYS* 1.3 58.5 + - - +
361B CYS* 5.0 1.3 - - - +
362B ALA* 4.3 13.2 + - - +
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B THR* 3.1 17.5 + - + +
356B THR* 3.3 15.3 - - + +
358B GLU* 1.3 76.0 - - - +
360B CYS* 1.3 76.9 + - - +
361B CYS 3.3 0.4 - - - -
362B ALA* 3.3 16.0 + - - +
363B ALA* 3.4 11.4 + - - +
369B CYS* 4.8 4.3 - - - -
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Residues in contact with CYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 2.8 26.3 + - - +
357B LEU* 4.2 1.6 - - - +
359B LYS* 1.3 81.9 - - - +
361B CYS* 1.3 60.9 + - - +
362B ALA 3.3 0.2 - - - -
363B ALA* 3.6 10.4 + - - +
366B PRO* 3.4 22.2 - - - +
369B CYS* 2.0 49.6 - - + -
370B TYR* 3.0 42.8 - - + +
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Residues in contact with CYS 361 (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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316B CYS* 2.0 58.7 - - + +
319B TYR* 4.3 14.8 - - + -
357B LEU* 3.1 34.2 + - - +
358B GLU 5.0 2.0 - - - +
360B CYS* 1.3 76.9 - - - +
362B ALA* 1.3 63.4 + - - +
363B ALA 3.2 5.3 - - - +
366B PRO* 4.5 6.5 - - - +
370B TYR* 5.1 0.2 - - - -
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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