Contacts of the helix formed by residues 402 - 420 (chain B) in PDB entry 6BFN
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ILE* 3.4 19.1 - - - +
365B SER* 5.8 0.9 - - - -
400B ARG* 3.5 38.7 + - - +
401B LEU* 1.3 74.8 - - - +
403B VAL* 1.3 65.6 + - + +
404B ASP* 3.1 10.8 - - + +
405B THR* 3.2 24.4 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B HIS* 3.6 40.6 - - + +
335B SER* 3.8 24.5 - - - +
337B ILE* 4.0 13.4 - - + +
365B SER* 5.2 3.1 - - - -
402B ALA* 1.3 70.3 - - + +
404B ASP* 1.3 78.0 + - - +
405B THR 3.1 0.2 - - - -
406B ASP* 3.0 7.5 + - - +
407B THR* 3.0 24.3 + - - +
510B PRO* 6.3 2.5 - - + -
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Residues in contact with ASP 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLU* 5.1 0.4 - - - +
400B ARG* 3.2 24.4 + - - +
402B ALA* 3.1 5.3 - - + +
403B VAL* 1.3 89.6 - - - +
405B THR* 1.3 55.9 + - - +
407B THR* 3.3 11.4 + - - -
408B PHE 2.9 23.2 + - - -
505B ALA* 3.4 39.6 - - + +
506B LYS* 4.7 3.8 + - - +
508B ARG* 3.3 22.9 + - + +
509B PRO 5.6 0.9 - - - +
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Residues in contact with THR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE* 5.0 4.7 - - + -
339B GLY* 5.5 6.7 - - - -
391B LEU* 3.9 19.1 - - + -
392B PRO* 3.9 21.3 - - + -
394B GLU* 4.5 5.0 + - - -
395B TYR* 4.2 25.7 - - + +
400B ARG* 4.5 4.3 + - - -
402B ALA* 3.2 24.0 + - - +
403B VAL 3.1 0.2 - - - -
404B ASP* 1.3 76.0 - - - +
406B ASP* 1.3 68.2 + - - +
408B PHE* 3.1 7.9 + - - +
409B SER* 2.9 25.9 + - - +
508B ARG* 4.3 3.3 - - - +
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Residues in contact with ASP 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 4.3 1.7 - - + +
329B LEU* 5.6 0.3 - - - +
330B HIS* 3.0 28.9 + - + +
337B ILE* 3.5 10.3 - - - +
338B HIS* 2.7 28.0 + - - +
339B GLY* 2.8 28.8 + - - -
341B ILE* 3.7 24.6 - - + +
402B ALA 4.1 0.2 + - - -
403B VAL 3.0 9.7 + - - +
405B THR* 1.3 77.2 - - - +
407B THR* 1.3 58.1 + - - +
409B SER* 3.3 6.1 + - - -
410B PHE* 2.9 29.9 + - - +
511B MET* 5.2 1.1 - - - -
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Residues in contact with THR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B HIS* 4.5 0.7 - - - -
403B VAL* 3.0 14.9 + - - +
404B ASP* 3.5 14.6 + - - -
405B THR 3.2 0.2 - - - -
406B ASP* 1.3 76.3 - - - +
408B PHE* 1.3 57.1 + - - +
410B PHE* 3.3 3.6 + - - +
411B GLY 2.9 22.9 + - - -
500B CYS* 3.6 28.4 - - + +
508B ARG* 4.1 16.2 - - + -
509B PRO* 3.5 27.6 + - + +
510B PRO* 5.2 0.3 - - - +
511B MET* 3.7 29.2 + - - +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B TYR 3.6 9.0 - - - -
391B LEU 3.6 8.5 - - - -
392B PRO* 3.5 39.5 - - + -
404B ASP 2.9 14.8 + - - +
405B THR 3.1 7.4 + - - +
407B THR* 1.3 76.8 - - - +
409B SER* 1.3 61.8 + - - +
411B GLY* 2.9 12.1 + - - -
412B VAL* 3.0 28.1 + - + +
435B LYS* 4.0 23.3 - - + -
500B CYS 3.6 7.8 + - - -
501B LEU* 3.4 50.4 - - + +
502B HIS 5.3 0.2 - - - -
503B ARG* 6.0 0.9 - - - -
508B ARG* 3.7 26.7 - - - +
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLY* 5.2 2.1 + - - -
341B ILE* 3.6 32.9 + - - +
390B TYR* 2.7 29.4 + - - +
391B LEU* 4.0 11.3 - - - +
405B THR* 2.9 14.2 + - - +
406B ASP* 3.3 10.3 + - - -
408B PHE* 1.3 75.1 - - - +
410B PHE* 1.3 58.6 + - - +
412B VAL* 3.2 6.8 + - - +
413B VAL* 3.0 31.4 + - - +
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Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.5 36.3 - - + -
322B THR* 3.9 12.8 - - + -
323B ALA* 3.8 18.4 - - + -
326B ILE* 3.5 26.2 - - + -
341B ILE* 4.3 3.3 - - + +
406B ASP 2.9 17.4 + - - +
407B THR* 3.6 6.5 - - - +
409B SER* 1.3 73.4 - - - +
411B GLY* 1.3 62.1 + - - +
413B VAL* 3.1 12.5 + - + +
414B VAL* 2.9 48.2 + - + +
496B LEU* 4.8 2.0 - - + -
500B CYS* 4.4 7.2 - - - -
511B MET* 3.9 13.5 - - + -
514B VAL* 3.6 24.7 - - + -
518B LEU* 3.8 8.7 - - + -
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Residues in contact with GLY 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR 2.9 7.7 + - - -
408B PHE 2.9 9.1 + - - -
410B PHE* 1.3 77.1 - - - +
412B VAL* 1.3 55.8 + - - +
414B VAL* 3.2 8.7 + - - +
415B LEU* 3.0 30.5 + - - +
497B ALA* 4.3 4.1 - - - +
500B CYS* 3.6 26.0 - - - -
501B LEU* 3.8 10.8 - - - +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA 3.9 14.4 - - - +
390B TYR* 3.6 28.7 - - + -
408B PHE* 3.0 32.4 + - + +
409B SER 3.2 6.9 + - - +
411B GLY* 1.3 75.0 - - - +
413B VAL* 1.3 57.2 - - - +
415B LEU* 3.2 8.1 + - + +
416B GLU* 2.9 27.6 + - - +
423B ALA* 4.3 12.6 - - + -
434B LEU* 4.4 5.1 - - + +
435B LYS* 3.9 18.8 - - + +
501B LEU* 3.6 14.6 - - + +
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.3 16.2 - - + -
319B LEU* 4.2 17.0 - - + -
322B THR* 5.5 3.1 - - + +
341B ILE* 4.1 15.0 - - + -
342B LYS 4.0 17.7 - - - +
343B SER* 4.2 4.7 - - - +
346B VAL* 5.1 7.6 - - + -
390B TYR* 4.0 16.4 - - + -
409B SER 3.0 18.3 + - - +
410B PHE* 3.4 17.0 - - + +
412B VAL* 1.3 76.1 - - - +
414B VAL* 1.3 57.3 + - - +
416B GLU* 3.3 10.5 + - - +
417B THR* 2.8 36.0 + - - +
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Residues in contact with VAL 414 (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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319B LEU* 4.1 28.0 - - + +
410B PHE* 2.9 49.7 + - + +
411B GLY* 3.2 8.7 + - - +
413B VAL* 1.3 75.7 - - - +
415B LEU* 1.3 62.4 + - - +
417B THR* 3.1 4.3 + - - -
418B LEU* 2.9 24.3 + - + +
493B LEU* 3.7 33.9 - - + +
496B LEU* 5.3 7.6 - - + -
497B ALA* 3.9 11.7 - - + +
500B CYS* 5.9 0.4 - - - -
518B LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 415 (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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411B GLY 3.0 9.1 + - - +
412B VAL* 3.2 9.2 + - - +
414B VAL* 1.3 76.2 - - - +
416B GLU* 1.3 57.8 + - - +
418B LEU* 3.2 13.3 + - + +
419B ALA* 2.9 35.5 + - + +
434B LEU* 3.7 35.2 - - + +
435B LYS* 4.9 0.4 - - - -
437B LEU* 4.4 13.2 - - + -
438B VAL* 4.3 11.0 - - + -
473B ILE* 4.2 27.4 - - + -
497B ALA* 3.9 16.8 - - + -
501B LEU* 3.6 30.3 - - + -
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Residues in contact with GLU 416 (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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297B GLU* 4.5 1.2 - - - +
300B LEU* 3.8 7.8 - - + +
301B HIS* 2.7 29.5 + - + +
343B SER* 2.8 31.1 + - - -
390B TYR* 2.6 31.5 + - - -
412B VAL* 2.9 12.3 + - + +
413B VAL* 3.4 8.9 - - - +
414B VAL 3.2 0.2 - - - -
415B LEU* 1.3 76.6 - - - +
417B THR* 1.3 57.5 + - - +
420B GLY* 2.8 30.3 + - - -
421B GLN 3.5 16.4 - - - +
422B ARG* 4.4 3.3 + - - -
423B ALA* 4.4 8.2 + - - +
434B LEU* 3.6 13.4 - - + +
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Residues in contact with THR 417 (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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296B LEU* 3.9 20.5 - - + +
300B LEU* 3.8 15.0 - - + +
315B ARG* 2.4 73.7 + - + +
318B ILE* 6.1 1.1 - - + -
319B LEU* 3.7 28.3 - - + +
413B VAL 2.8 15.1 + - - -
414B VAL 3.5 8.5 - - - -
416B GLU* 1.3 76.3 - - - +
418B LEU* 1.3 59.8 + - - +
493B LEU* 6.1 1.6 - - + -
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Residues in contact with LEU 418 (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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312B TRP* 3.7 22.6 - - + -
414B VAL* 2.9 17.3 + - + +
415B LEU* 3.2 19.7 + - + +
417B THR* 1.3 77.2 - - - +
419B ALA* 1.3 62.5 + - + +
473B ILE* 4.7 12.1 - - + -
478B LEU* 3.7 25.3 - - + -
479B ASP* 3.0 27.1 + - - +
490B GLY* 4.4 10.1 - - - +
493B LEU* 3.8 30.7 - - + +
494B GLY* 3.7 33.2 - - - +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 2.9 18.1 + - + +
418B LEU* 1.3 75.8 - - - +
420B GLY* 1.3 62.4 + - - +
421B GLN* 3.2 32.0 + - + +
434B LEU* 4.6 9.2 - - + -
437B LEU* 5.7 2.5 - - + -
473B ILE* 5.9 2.2 - - + +
477B HIS* 3.1 28.9 - - + +
478B LEU 4.2 0.7 - - - +
479B ASP* 3.2 18.0 + - - +
480B PRO* 4.9 0.9 - - - +
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Residues in contact with GLY 420 (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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300B LEU* 5.1 4.0 - - - -
301B HIS* 3.3 18.6 + - - -
315B ARG* 4.8 2.0 - - - -
416B GLU 2.8 17.3 + - - -
417B THR 4.6 2.2 - - - -
418B LEU 3.2 2.6 - - - -
419B ALA* 1.3 78.3 - - - +
421B GLN* 1.3 59.0 + - - +
479B ASP* 3.9 17.9 - - - -
481B ARG* 3.7 21.1 + - - -
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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