Contacts of the helix formed by residues 423 - 440 (chain B) in PDB entry 3A8X
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 PHE 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B HIS* 3.0 73.1 - + + +
365B ILE 3.7 16.6 - - - -
366B ILE* 3.9 17.9 - - + -
395B LEU* 4.2 31.0 - - + -
397B PRO* 5.8 7.4 - - + -
422B GLY* 1.3 69.9 - - - -
424B SER* 1.3 66.8 + - - +
425B VAL* 2.8 2.4 + - - -
426B ASP* 2.9 20.0 + - - +
427B TRP* 3.8 9.8 + - + +
497B GLY 6.1 0.2 - - - +
498B CYS* 6.5 0.4 - - - -
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU* 2.7 24.2 + - - +
421B TYR* 4.5 0.9 - - - +
422B GLY 2.9 10.6 + - - -
423B PHE* 1.3 76.9 - - - +
425B VAL* 1.3 61.9 + - - +
427B TRP* 2.9 23.0 + - - +
428B TRP 3.3 2.3 + - - -
492B PRO* 3.6 15.0 - - - +
495B ARG* 3.0 25.5 + - - -
498B CYS* 3.5 27.2 - - - +
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ILE* 3.8 18.2 - - + -
368B ARG* 4.3 12.6 - - + -
410B TYR 4.9 1.6 - - - +
412B ALA* 3.6 31.1 + - + +
414B GLU* 3.7 7.9 - - - +
415B ILE* 3.7 27.6 - - + -
421B TYR* 3.9 21.5 - - + -
422B GLY 3.6 11.7 - - - +
423B PHE 2.8 3.2 + - - -
424B SER* 1.3 80.7 + - - +
426B ASP* 1.3 65.4 + - - +
427B TRP 3.3 0.2 - - - -
428B TRP* 3.7 3.6 + - - +
429B ALA* 3.2 21.8 + - - +
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Residues in contact with ASP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.8 18.1 - - + +
361B HIS* 2.6 39.0 + - + +
366B ILE* 3.9 7.3 - - - +
367B TYR* 3.0 29.8 + - - +
368B ARG* 2.9 29.8 + - - -
369B ASP 4.8 0.2 + - - -
370B LEU* 4.2 3.3 + - - +
423B PHE 2.9 4.2 + - - +
425B VAL* 1.3 78.0 - - - +
427B TRP* 1.3 60.3 + - - +
429B ALA* 3.4 6.3 + - - +
430B LEU* 3.1 26.5 + - - +
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Residues in contact with TRP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B SER* 3.7 32.5 - - - -
357B LEU* 3.8 17.5 - - + -
358B ASN* 4.3 14.8 - - + -
361B HIS* 3.4 31.8 + + - -
423B PHE* 3.9 17.7 - - + +
424B SER 2.9 6.2 + - - +
426B ASP* 1.3 74.3 - - - +
428B TRP* 1.3 65.0 + - - +
430B LEU* 3.5 30.9 + - + +
431B GLY 3.1 15.8 + - - -
487B PHE* 3.5 18.9 - + + -
495B ARG* 4.2 2.0 - - - -
496B LEU 3.7 19.1 - - - +
497B GLY 3.3 25.9 + - - -
498B CYS* 4.2 9.2 - - - -
504B PHE* 4.4 4.9 - + - -
507B ILE* 3.7 28.3 - - + -
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B TYR 3.5 15.9 + - - -
411B ILE 3.6 11.5 + - - -
412B ALA* 3.4 31.6 - - + -
413B PRO* 3.4 34.8 - - + -
424B SER 3.3 5.1 + - - -
425B VAL 3.9 2.2 - - - +
427B TRP* 1.3 77.8 - - - +
429B ALA* 1.3 62.1 + - - +
431B GLY* 2.9 12.5 + - - -
432B VAL* 3.0 27.1 + - + +
444B PHE* 3.8 24.6 - + - -
465B ILE* 3.9 11.4 - - + -
470B ILE* 4.4 13.2 - - + -
487B PHE 3.7 11.9 - - - -
488B LEU* 3.1 46.4 - - + +
489B ASN 3.7 12.8 - - - -
490B LYS* 4.1 9.2 - - + -
495B ARG* 3.8 12.4 - - - +
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ARG 6.4 0.7 - - - -
370B LEU* 3.8 32.1 - - + +
410B TYR* 4.0 23.7 - - + +
425B VAL 3.2 16.0 + - - +
426B ASP* 3.6 8.1 - - - +
427B TRP 3.3 0.2 - - - -
428B TRP* 1.3 80.1 - - - +
430B LEU* 1.3 58.4 + - - +
432B VAL* 3.1 8.0 + - - +
433B LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B SER* 4.0 16.4 - - - +
353B ILE* 4.2 25.1 - - + -
354B SER* 3.6 22.2 - - - +
357B LEU* 4.2 4.9 - - + -
370B LEU* 3.4 16.2 - - + +
426B ASP 3.1 15.3 + - - +
427B TRP* 3.7 15.0 - - + +
429B ALA* 1.3 75.9 - - - +
431B GLY* 1.3 57.5 + - - +
433B LEU* 3.2 5.1 + - + +
434B MET* 2.8 54.7 + - + +
487B PHE* 3.7 29.2 - - + -
513B PHE* 5.6 0.2 - - + -
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Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B TRP 3.1 6.9 + - - -
428B TRP 2.9 8.6 + - - -
430B LEU* 1.3 75.9 - - - +
432B VAL* 1.3 56.7 + - - +
434B MET* 3.2 5.1 + - - +
435B PHE* 2.9 29.5 + - - +
484B LEU* 3.7 6.1 - - - +
487B PHE* 3.6 28.7 - - - +
488B LEU* 3.7 10.9 - - - +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASN* 3.6 34.1 - - - +
410B TYR* 3.7 14.4 - - + -
428B TRP* 3.0 41.2 + - + +
429B ALA* 3.4 8.1 - - - +
431B GLY* 1.3 73.9 - - - +
433B LEU* 1.3 58.7 + - - +
435B PHE* 3.3 8.8 + - - +
436B GLU* 2.9 31.1 + - - +
443B PRO* 4.1 13.0 - - + -
444B PHE* 4.0 14.4 - - + -
488B LEU* 3.6 12.1 - - + +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 4.4 4.0 - - + -
350B SER* 6.3 0.2 - - - -
353B ILE* 4.1 20.2 - - + -
370B LEU* 3.8 23.8 - - + -
371B LYS* 3.6 35.4 - - - +
372B LEU* 3.6 20.0 - - + +
375B VAL* 4.2 3.1 - - + -
410B TYR* 4.4 2.5 - - + -
429B ALA 2.9 11.9 + - - +
430B LEU* 3.2 13.2 + - + +
432B VAL* 1.3 78.7 - - - +
434B MET* 1.3 57.6 + - + +
436B GLU* 3.3 11.2 + - - +
437B MET* 3.0 54.4 + - + +
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Residues in contact with MET 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA* 4.9 3.1 - - + +
350B SER* 3.6 33.0 - - - +
430B LEU* 2.8 42.3 + - + +
431B GLY 3.7 3.6 - - - +
433B LEU* 1.3 76.9 - - + +
435B PHE* 1.3 64.9 + - - +
437B MET* 3.2 8.0 + - - +
438B MET* 3.0 37.8 + - + +
483B VAL* 3.8 20.2 - - + -
484B LEU* 3.8 10.8 - - + -
487B PHE* 3.9 22.2 - - - -
512B PHE* 3.8 23.3 - - + -
513B PHE* 4.0 7.2 - - + -
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLY 2.9 13.3 + - - +
432B VAL 3.3 10.1 - - - +
434B MET* 1.3 74.6 - - - +
436B GLU* 1.3 54.1 + - - +
438B MET* 5.1 0.4 - - - -
439B ALA* 2.8 51.4 + - + +
441B ARG* 3.1 38.6 - - + -
442B SER 3.8 2.2 - - - -
443B PRO* 3.5 43.7 - - + -
470B ILE* 4.0 8.1 - - + -
471B ARG 3.6 24.5 - - - -
472B ILE* 4.4 3.6 - - + -
473B PRO* 3.8 20.9 - - + -
484B LEU* 3.3 27.2 - - + +
488B LEU* 4.3 11.2 - - + -
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 3.7 7.1 - - - +
372B LEU* 3.5 25.6 - - + +
409B ASN* 2.8 28.6 + - - -
410B TYR* 2.5 31.5 + - - -
432B VAL* 2.9 17.2 + - - +
433B LEU* 3.5 9.0 - - - +
434B MET 3.1 0.2 - - - -
435B PHE* 1.3 78.1 - - - +
437B MET* 1.3 57.7 + - - +
440B GLY* 2.8 29.3 + - - -
441B ARG* 3.5 21.1 - - - +
442B SER* 3.8 17.3 - - - -
443B PRO* 4.4 0.7 - - + -
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Residues in contact with MET 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 3.5 25.4 - - + -
335B MET* 3.8 15.1 - - - +
340B LYS* 3.8 0.9 - - - -
341B LEU* 2.8 62.3 + - + +
346B ALA* 4.0 21.8 - - + +
349B TYR* 3.3 32.5 - - + -
350B SER* 5.3 3.1 - - - -
353B ILE* 5.6 0.4 - - - -
372B LEU* 4.4 7.2 - - + -
433B LEU* 3.0 40.0 + - + +
434B MET* 3.2 7.4 + - - +
436B GLU* 1.3 77.7 - - - +
438B MET* 1.3 62.0 + - - +
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Residues in contact with MET 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LYS* 3.1 24.5 - - - +
341B LEU 4.1 6.9 - - - +
343B GLU* 4.4 14.8 - - + -
346B ALA* 3.4 22.9 - - + -
434B MET* 3.0 49.6 + - + +
435B PHE* 4.3 1.3 - - - +
437B MET* 1.3 79.4 - - - +
439B ALA* 1.3 57.4 + - - +
476B LEU* 3.9 28.5 - - + +
480B ALA* 3.9 16.2 - - + -
483B VAL* 4.5 1.1 - - + -
484B LEU* 4.0 19.7 - - + -
512B PHE* 3.8 28.0 - - + -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LYS* 3.7 17.5 - - - +
435B PHE* 2.8 44.4 + - + +
438B MET* 1.3 74.9 - - - +
440B GLY* 1.3 61.7 + - - +
441B ARG* 3.3 22.3 + - + -
473B PRO* 3.7 24.9 - - + -
476B LEU* 5.1 1.6 - - + -
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 4.4 4.9 - - - -
339B ARG 3.3 27.0 - - - +
340B LYS* 4.4 1.1 - - - +
436B GLU* 2.8 19.0 + - - -
437B MET 4.2 1.0 + - - -
438B MET 3.6 1.4 - - - -
439B ALA* 1.3 76.8 - - - +
441B ARG* 1.3 60.1 + - - +
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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
------------------------------------------------------------
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