Contacts of the helix formed by residues 402 - 420 (chain T) in PDB entry 1BGX
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 ALA 402 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308T GLY* 3.5 26.6 - - - +
309T PHE* 4.0 2.7 - - - -
310T VAL* 3.6 24.0 - - + +
323T ALA* 4.0 17.7 - - + +
324T LEU* 4.2 2.9 - - - +
325T ALA* 3.6 5.8 - - + +
401T GLU* 1.3 74.9 + - - +
403T GLY* 1.3 64.5 + - - +
405T ARG* 3.9 7.7 - - - +
406T ALA* 3.1 27.0 + - - +
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Residues in contact with GLY 403 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325T ALA* 4.0 6.4 - - - +
332T VAL* 3.6 37.2 - - - +
334T ARG* 3.8 15.2 - - - +
401T GLU* 3.1 21.1 + - - -
402T ALA* 1.3 79.3 - - - +
404T GLU* 1.3 61.1 + - - +
406T ALA* 4.3 0.7 - - - +
407T ALA* 3.8 9.0 + - - +
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Residues in contact with GLU 404 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292T LYS* 3.8 33.7 - - + +
334T ARG* 5.1 4.5 - - - +
399T THR* 3.4 38.4 + - - +
401T GLU* 3.7 20.5 + - + +
403T GLY* 1.3 76.8 - - - +
405T ARG* 1.3 63.9 + - - +
406T ALA 3.4 0.7 - - - -
407T ALA* 3.7 6.7 + - - +
408T LEU* 3.3 20.6 + - - +
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Residues in contact with ARG 405 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 5.6 1.6 + - - -
63H LYS* 4.5 8.7 - - - +
292T LYS* 5.7 0.4 - - - +
307T VAL 4.4 0.9 - - - +
308T GLY* 4.6 8.9 - - - -
309T PHE 2.9 28.3 + - - +
310T VAL* 3.3 19.0 - - - +
351T LEU* 4.6 2.3 - - - +
398T TRP* 3.6 53.6 - - + +
399T THR* 3.3 32.8 + - - +
400T GLU* 2.8 29.0 + - - +
401T GLU 3.4 15.6 + - - +
402T ALA* 3.4 6.7 + - - +
404T GLU* 1.3 76.9 - - - +
406T ALA* 1.3 59.5 + - - +
408T LEU* 3.5 15.2 + - + +
409T SER* 3.2 20.8 + - - -
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Residues in contact with ALA 406 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306T PHE* 3.3 30.7 - - - +
307T VAL 3.9 7.9 - - - -
308T GLY* 3.7 12.1 - - - +
325T ALA* 3.9 15.3 - - + -
326T ALA 3.9 10.3 - - - +
327T ALA* 3.4 7.8 - - - +
402T ALA 3.1 17.6 + - - +
403T GLY 4.3 3.4 - - - +
404T GLU 3.4 0.2 - - - -
405T ARG* 1.3 76.7 - - - +
407T ALA* 1.3 62.7 + - - +
408T LEU 3.1 1.1 + - - -
409T SER* 3.5 12.8 + - - -
410T GLU 3.9 0.5 + - - -
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Residues in contact with ALA 407 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292T LYS* 5.7 1.3 - - + +
294T LEU* 3.7 35.0 - - + +
327T ALA* 4.1 11.4 - - + +
332T VAL* 4.2 13.9 - - + +
403T GLY 3.8 14.6 + - - +
404T GLU* 3.7 7.4 + - - +
405T ARG 3.3 0.2 - - - -
406T ALA* 1.3 78.6 - - - +
408T LEU* 1.3 59.2 + - - +
409T SER 3.5 0.2 - - - -
410T GLU* 3.8 8.4 + - - +
411T ARG* 3.5 24.2 + - - +
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Residues in contact with LEU 408 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292T LYS* 4.9 0.4 - - - -
351T LEU* 3.9 10.5 - - + -
387T PRO 4.8 0.2 - - - +
391T ALA* 4.0 22.2 - - + -
395T GLY 5.1 0.2 - - - +
396T GLY* 4.3 3.4 - - - -
397T GLU 3.3 30.3 - - - +
398T TRP* 3.8 27.8 - - + -
404T GLU 3.3 13.5 + - - +
405T ARG* 3.6 10.5 - - - +
406T ALA 3.1 0.4 - - - -
407T ALA* 1.3 75.8 - - - +
409T SER* 1.3 59.8 + - - +
410T GLU 3.1 2.2 - - - -
411T ARG* 3.2 35.6 + - - +
412T LEU* 3.0 41.8 + - + +
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Residues in contact with SER 409 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306T PHE* 3.6 19.7 - - - -
307T VAL 3.8 5.9 + - - -
350T GLY* 4.1 5.4 - - - -
351T LEU* 3.3 43.1 + - - +
373T PRO* 3.9 9.2 - - - +
405T ARG 3.2 13.9 + - - -
406T ALA 3.5 9.1 + - - -
408T LEU* 1.3 76.9 - - - +
410T GLU* 1.3 60.4 + - - +
411T ARG 3.4 0.2 - - - -
412T LEU* 4.0 1.3 - - - +
413T PHE* 3.5 21.7 + - - +
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Residues in contact with GLU 410 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294T LEU* 4.6 5.6 - - - +
306T PHE* 3.8 29.2 - - + -
327T ALA* 3.3 29.6 - - + +
329T GLY 3.2 13.8 + - - -
330T GLY* 3.2 37.4 + - - -
406T ALA 3.9 1.6 + - - -
407T ALA 3.8 10.0 + - - +
408T LEU 3.1 0.2 - - - -
409T SER* 1.3 78.5 - - - +
411T ARG* 1.3 66.3 + - + +
413T PHE* 3.6 5.5 + - - +
414T ALA* 3.4 19.6 + - - +
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Residues in contact with ARG 411 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T SER* 3.5 34.1 + - - +
291T PRO* 3.3 37.9 + - - -
292T LYS* 3.3 25.8 - - - +
294T LEU* 4.1 13.3 - - + +
395T GLY 3.5 16.9 + - - -
396T GLY* 4.3 5.1 - - - -
407T ALA 3.5 17.3 + - - +
408T LEU* 3.2 37.8 + - - +
410T GLU* 1.3 79.8 - - + +
412T LEU* 1.3 62.4 + - + +
413T PHE 3.0 6.2 + - - -
414T ALA* 3.3 7.1 + - - +
415T ASN* 3.0 32.6 + - - +
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Residues in contact with LEU 412 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351T LEU* 3.8 27.4 - - + -
373T PRO* 4.0 20.1 - - + +
376T LEU* 4.2 0.7 - - - +
387T PRO 5.1 1.1 - - - +
390T VAL* 3.5 43.3 - - + +
391T ALA* 4.0 16.8 - - + +
394T TYR* 4.4 12.6 - - + -
395T GLY 4.9 7.4 - - - +
408T LEU* 3.0 34.3 + - + +
409T SER 4.2 0.7 - - - -
410T GLU 3.5 0.2 - - - -
411T ARG* 1.3 77.0 - - + +
413T PHE* 1.3 58.7 + - - +
415T ASN* 4.3 4.0 - - - +
416T LEU* 3.4 33.7 - - + +
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Residues in contact with PHE 413 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306T PHE* 3.9 24.2 - + + -
349T ARG* 3.8 23.3 - - - -
371T ASP* 3.8 29.4 - - + -
373T PRO* 4.8 6.1 - - + -
376T LEU* 3.8 19.5 - - + -
409T SER 3.5 18.7 + - - +
410T GLU 3.7 5.8 - - - +
411T ARG 3.0 0.6 - - - -
412T LEU* 1.3 78.4 - - - +
414T ALA* 1.3 60.6 + - - +
415T ASN 3.3 0.2 - - - -
417T TRP* 2.9 79.7 + + + +
430T TYR* 4.7 1.1 - - - -
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Residues in contact with ALA 414 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288T LEU* 4.3 12.6 - - + +
410T GLU 3.4 10.5 + - - +
411T ARG* 3.3 11.8 + - - +
413T PHE* 1.3 84.9 - - - +
415T ASN* 1.3 66.2 + - - +
417T TRP* 4.9 1.6 - - - +
418T GLY* 4.1 11.4 + - - -
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Residues in contact with ASN 415 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288T LEU* 3.4 42.6 - - + +
289T GLU 5.3 0.9 + - - +
290T SER* 3.6 25.3 + - - -
394T TYR* 4.6 17.9 + - + +
395T GLY 5.3 2.0 + - - -
411T ARG* 3.0 23.0 + - - +
412T LEU* 4.7 6.1 - - - +
413T PHE 3.3 0.4 - - - -
414T ALA* 1.3 83.5 - - - +
416T LEU* 1.3 73.4 + - + +
417T TRP 3.5 0.4 + - - -
418T GLY* 3.9 1.9 + - - -
419T ARG* 3.5 23.4 + - - +
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Residues in contact with LEU 416 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373T PRO 3.6 23.8 - - - +
376T LEU* 3.9 14.8 - - + +
377T ALA* 3.7 25.8 - - + +
380T LEU* 4.2 15.3 - - + +
390T VAL* 3.9 9.4 - - + -
394T TYR* 4.0 36.8 - - + -
412T LEU* 3.4 28.4 + - + +
413T PHE 3.5 1.4 + - - -
415T ASN* 1.3 83.1 - - + +
417T TRP* 1.3 60.3 + - - +
418T GLY 3.3 1.8 - - - -
419T ARG* 3.5 8.4 + - - +
420T LEU* 3.1 26.9 + - - +
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Residues in contact with TRP 417 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371T ASP* 4.7 2.7 - - - -
376T LEU* 4.0 15.8 - - + +
413T PHE* 2.9 55.3 + + + +
414T ALA* 4.9 2.5 - - - +
416T LEU* 1.3 74.5 - - - +
418T GLY* 1.3 61.2 + - - +
420T LEU* 3.1 13.0 + - + +
421T GLU* 2.9 65.2 + - + +
427T LEU* 3.8 14.8 - - + -
430T TYR* 3.8 31.0 - + - -
431T ARG* 5.0 11.2 - - - -
435T ARG* 5.5 6.3 - - - -
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Residues in contact with GLY 418 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T GLU* 3.0 33.4 - - - +
288T LEU* 6.5 0.9 - - - -
414T ALA 4.1 9.2 + - - -
415T ASN 3.9 5.9 + - - -
416T LEU 3.3 0.8 - - - -
417T TRP* 1.3 82.0 - - - +
419T ARG* 1.3 63.9 + - - +
420T LEU 3.6 0.2 + - - -
421T GLU* 3.8 9.8 + - - +
422T GLY 4.1 2.1 + - - -
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Residues in contact with ARG 419 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T LEU* 5.8 4.9 - - - +
53T LYS* 5.9 1.8 - - - +
56T LYS* 4.1 25.6 - - - +
284T GLU* 2.9 52.5 + - - +
288T LEU* 5.8 6.1 - - + +
380T LEU* 3.9 23.3 - - + +
394T TYR* 6.0 6.5 - - + -
415T ASN 3.5 16.3 + - - +
416T LEU* 3.5 8.6 + - - +
417T TRP 3.2 0.4 - - - -
418T GLY* 1.3 77.8 + - - +
420T LEU* 1.3 60.2 + - - +
422T GLY* 4.1 4.3 + - - -
423T GLU* 3.6 19.2 - - - +
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Residues in contact with LEU 420 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376T LEU* 3.7 45.3 - - + +
379T LEU* 4.5 7.6 - - + -
380T LEU* 4.2 13.7 - - + -
416T LEU 3.1 14.1 + - - +
417T TRP* 3.1 14.8 + - + +
419T ARG* 1.3 76.9 - - - +
421T GLU* 1.3 58.9 + - - +
422T GLY 3.2 2.7 - - - -
423T GLU* 2.9 31.7 + - - +
426T LEU* 4.1 26.0 - - + +
427T LEU* 3.5 29.7 - - + +
430T TYR* 4.3 16.6 - - + -
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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