Contacts of the helix formed by residues 422 - 444 (chain B) in PDB entry 5FWP
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 ASP 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU 3.3 6.3 + - - +
419B LEU* 2.9 16.2 + - - +
420B ALA 3.7 0.2 - - - -
421B GLU* 1.3 74.3 - - - +
423B LYS* 1.3 50.9 + - - +
424B GLU* 3.4 8.0 + - - +
425B ASN* 2.9 25.6 + - + +
426B TYR 2.8 27.9 + - - -
129E VAL* 3.7 10.1 - - + +
131E THR* 2.5 33.9 + - - +
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Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ALA 3.7 10.1 - - - +
421B GLU 2.9 11.5 + - - +
422B ASP* 1.3 70.4 + - - +
424B GLU* 1.3 57.7 + - - +
426B TYR* 3.3 4.2 + - - +
427B LYS* 2.9 57.8 + - + +
465B GLU* 2.7 30.0 + - - -
466B MET 6.0 0.7 - - - -
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 3.0 7.6 + - - +
423B LYS* 1.3 80.2 - - - +
425B ASN* 1.3 63.9 + - - +
427B LYS* 2.8 35.5 + - - +
428B LYS* 3.3 44.3 + - - +
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Residues in contact with ASN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.0 23.8 - - + +
337B ARG* 4.6 2.9 + - - -
419B LEU* 4.1 10.8 - - + -
422B ASP* 2.9 18.3 + - - +
424B GLU* 1.3 79.0 - - - +
426B TYR* 1.3 59.6 - - - +
428B LYS* 3.3 33.2 + - - +
429B PHE* 2.9 26.9 + - - +
129E VAL* 4.1 2.3 - - + +
130E ASN 5.2 0.9 - - - -
131E THR* 2.4 48.0 + - - +
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Residues in contact with TYR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B PHE 4.2 3.1 - - - -
419B LEU* 3.3 27.0 + - + +
420B ALA* 3.6 32.3 - - + +
422B ASP 2.8 9.6 + - - +
423B LYS* 3.6 7.4 - - - +
425B ASN* 1.3 74.9 - - - +
427B LYS* 1.3 59.8 + - + +
429B PHE* 3.0 25.6 + + - +
430B TYR* 2.7 59.4 + + + +
437B LEU* 4.1 1.7 - - - +
454B LEU* 2.6 53.1 + - + +
456B ARG* 4.0 24.5 - - + -
466B MET* 4.8 3.4 - - + -
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Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS* 2.9 46.1 + - + +
424B GLU* 2.8 38.3 + - - +
426B TYR* 1.3 78.4 - - + +
428B LYS* 1.3 56.9 + - + +
430B TYR* 3.3 0.5 + - - +
431B GLU* 2.9 45.6 + - - +
465B GLU* 5.5 10.2 + - + +
466B MET* 3.7 28.7 - - + -
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 5.1 9.0 - - + -
337B ARG* 4.8 13.7 - - - +
424B GLU* 3.5 30.7 - - - +
425B ASN* 3.3 32.8 + - + +
426B TYR 3.2 0.2 - - - -
427B LYS* 1.3 79.0 - - + +
429B PHE* 1.3 61.9 + - - +
431B GLU* 3.5 12.1 + - - +
432B ALA* 3.2 22.0 + - - +
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.7 8.9 - - + +
335B ILE* 3.6 34.1 - - + -
337B ARG 5.6 0.7 - - - -
376B PHE* 3.8 15.7 - + - -
416B PHE* 3.6 33.4 - + - -
419B LEU* 3.5 17.9 - - + -
425B ASN 2.9 14.7 + - - +
426B TYR* 3.3 32.8 - + - +
428B LYS* 1.3 74.3 - - - +
430B TYR* 1.3 60.6 + + - +
432B ALA* 3.1 3.6 + - - -
433B PHE* 2.7 66.3 + + + -
437B LEU* 6.0 6.1 - - + -
454B LEU* 5.9 2.5 - - + -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B TYR* 2.7 47.9 + + + +
427B LYS 3.7 2.7 - - - +
429B PHE* 1.3 76.9 - + - +
431B GLU* 1.3 66.2 + - + +
434B SER* 2.7 55.4 + - - +
437B LEU* 3.6 17.5 - - + -
438B LYS* 4.0 18.0 + - - -
454B LEU 3.3 17.9 - - - -
455B LEU* 3.9 3.5 - - - +
456B ARG* 2.6 35.1 + - + -
457B TYR* 5.0 0.5 - - - -
466B MET* 3.3 33.9 - - + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS* 2.9 35.3 + - - +
428B LYS* 3.7 11.5 - - - +
430B TYR* 1.3 83.7 - - + +
432B ALA* 1.3 60.4 + - - +
434B SER* 4.5 5.3 + - - -
435B LYS* 6.2 0.3 - - - +
466B MET* 5.2 5.7 - - + +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG 4.1 12.3 - - - +
338B ARG* 4.7 0.7 - - - -
339B ALA* 3.8 21.9 - - + +
343B LEU* 5.1 3.1 - - - +
428B LYS 3.2 9.9 + - - +
429B PHE* 3.1 8.5 + - - +
431B GLU* 1.3 81.5 - - - +
433B PHE* 1.3 85.8 + - + +
434B SER 3.8 0.4 - - - -
435B LYS* 5.2 7.3 + - - +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PRO* 3.4 44.0 - - + -
337B ARG 4.7 0.2 - - - -
338B ARG 4.3 0.4 - - - -
339B ALA* 3.6 36.3 - - + -
340B PRO* 4.5 2.7 - - + -
343B LEU* 4.6 3.4 - - + -
376B PHE* 3.6 28.5 - + + -
429B PHE* 2.7 57.2 + + + +
430B TYR* 4.6 1.3 - - - -
432B ALA* 1.3 88.5 - - + +
434B SER* 1.3 58.0 + - - +
435B LYS* 3.1 3.4 - - - +
436B ASN* 2.9 42.6 + - + +
437B LEU* 3.1 10.0 + - - +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B PHE* 6.2 0.2 - - - -
430B TYR* 2.7 62.5 + - - -
431B GLU* 4.5 4.9 + - - -
432B ALA 3.8 0.6 - - - -
433B PHE* 1.3 71.6 - - - +
435B LYS* 1.3 62.6 + - - +
437B LEU* 3.3 9.8 - - - +
438B LYS* 2.8 38.4 + - - +
515B GLU* 4.3 11.1 + - - -
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU 3.3 28.5 + - - +
612A ARG* 4.6 0.6 - - - +
613A ASP* 3.8 32.9 - - - +
343B LEU* 6.0 1.6 - - + -
344B PHE* 3.7 26.8 - - + -
431B GLU 6.2 0.4 - - - +
432B ALA 5.5 5.8 - - - +
433B PHE* 3.1 2.2 - - - -
434B SER* 1.3 82.3 + - - +
436B ASN* 1.3 59.6 + - - +
438B LYS* 3.5 2.4 + - - +
439B LEU* 2.8 26.7 + - - +
515B GLU* 2.7 34.5 + - - +
516B PRO* 6.2 1.0 - - - +
517B ILE* 4.0 21.1 - - + +
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Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.8 26.5 - - - +
344B PHE* 4.5 9.5 - - - -
372B GLU 5.1 2.0 + - - +
373B TYR* 3.2 31.4 + - - +
375B ASN 5.2 1.2 + - - -
376B PHE* 3.5 29.3 - - + -
433B PHE* 2.9 25.2 + - - +
435B LYS* 1.3 76.0 - - - +
437B LEU* 1.3 60.0 + - - +
439B LEU* 3.2 17.7 + - - +
440B GLY* 2.8 24.1 + - - -
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Residues in contact with LEU 437 (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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373B TYR* 5.4 1.6 - - - -
416B PHE* 6.2 0.7 - - + -
426B TYR* 4.1 1.1 - - - +
429B PHE* 6.0 6.1 - - + -
430B TYR* 3.6 20.9 - - + -
433B PHE 3.1 7.6 + - - +
434B SER* 3.2 12.8 + - - +
436B ASN* 1.3 76.9 - - - +
438B LYS* 1.3 57.6 + - - +
440B GLY* 3.0 4.7 + - - -
441B ILE* 3.0 25.5 + - - +
451B LEU* 3.4 42.9 - - + +
454B LEU* 3.5 46.4 - - + +
455B LEU* 3.7 15.0 - - + -
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Residues in contact with LYS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B TYR* 4.0 20.9 + - - -
434B SER* 2.8 21.3 + - - +
435B LYS 3.8 3.8 - - - +
437B LEU* 1.3 72.7 - - - +
439B LEU* 1.3 66.3 + - - +
441B ILE* 3.1 12.5 + - - +
442B HIS* 3.0 21.7 + - - +
455B LEU* 4.1 14.1 - - + -
456B ARG 5.5 0.2 + - - -
457B TYR* 4.2 19.6 - - - -
515B GLU* 2.8 23.9 + - - +
517B ILE* 3.7 23.6 - - + +
518B ASP* 2.8 32.8 + - - +
521B CYS* 4.1 18.7 - - + +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 6.0 6.3 - - + -
344B PHE* 5.8 7.0 - - + -
372B GLU* 4.5 13.0 - - + +
373B TYR* 3.8 27.6 - - + +
435B LYS 2.8 19.7 + - - +
436B ASN* 3.3 16.6 - - - +
437B LEU 3.2 0.2 - - - -
438B LYS* 1.3 76.3 - - - +
440B GLY* 1.3 51.7 + - - +
442B HIS* 3.0 12.9 + - + +
443B GLU* 2.7 63.9 + - + +
517B ILE* 5.5 0.2 - - - +
92K VAL* 5.5 7.2 - - + -
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 3.4 33.3 - - - +
436B ASN 2.8 10.7 + - - -
437B LEU 3.0 4.9 + - - -
439B LEU* 1.3 76.7 - - - +
441B ILE* 1.3 57.5 + - - +
443B GLU 4.3 0.2 - - - -
444B ASP* 2.7 34.0 + - - +
451B LEU* 3.6 11.2 - - - -
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU 3.0 19.7 + - - +
438B LYS* 3.1 13.9 + - - +
440B GLY* 1.3 75.4 - - - +
442B HIS* 1.3 61.3 + - - +
448B ARG* 2.7 68.1 + - + +
451B LEU* 3.6 16.8 - - + -
452B SER* 3.6 15.7 - - - +
455B LEU* 4.2 9.2 - - + -
521B CYS* 3.7 39.3 - - - +
524B GLN* 3.5 12.0 - - + +
525B LEU* 4.2 6.1 - - + -
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 5.4 1.4 + - - -
438B LYS 3.0 11.2 + - - +
439B LEU* 3.0 15.3 + - + +
441B ILE* 1.3 81.0 - - - +
443B GLU* 1.3 83.7 + - + +
448B ARG* 4.2 5.4 + - - -
520B TYR* 3.5 44.0 + + + +
523B GLN* 4.3 2.2 - - - -
524B GLN* 4.2 5.8 - - - +
92K VAL* 4.3 15.0 - - + +
93K PHE 2.7 30.1 + - - -
95K HIS* 3.0 60.2 + + - -
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 2.7 36.3 + - - +
372B GLU* 6.1 3.4 - - + -
373B TYR* 4.6 10.3 - - + +
439B LEU* 2.7 46.1 + - + +
440B GLY* 4.3 2.5 - - - +
442B HIS* 1.3 94.3 - - - +
444B ASP* 1.3 61.8 + - + +
445B SER* 3.6 3.8 + - - -
448B ARG* 5.0 0.8 + - - -
92K VAL* 5.7 0.9 - - - +
93K PHE 5.8 0.3 + - - -
95K HIS* 5.7 2.3 - - - -
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PRO* 5.6 1.4 - - - +
373B TYR* 2.7 38.3 + - + +
440B GLY 2.7 20.5 + - - +
443B GLU* 1.3 70.6 - - - +
445B SER* 1.3 60.3 + - - +
446B THR* 2.7 27.6 + - - +
447B ASN* 2.9 25.8 + - - +
448B ARG* 3.4 26.0 + - - +
451B LEU* 4.5 2.2 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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