Contacts of the helix formed by residues 413 - 439 (chain I) in PDB entry 6MZL
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 413 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410I PRO* 4.7 8.4 - - - +
412I LEU* 1.3 79.3 + - - +
414I ASN* 1.3 52.8 + - - +
415I ILE* 3.3 3.4 - - - -
416I ASP* 3.2 23.6 + - - +
417I ARG* 2.7 45.1 + - - +
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Residues in contact with ASN 414 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412I LEU* 4.0 21.3 - - - +
413I SER* 1.3 69.8 - - - +
415I ILE* 1.3 62.8 + - - +
417I ARG* 3.3 33.9 + - - +
418I ILE* 2.9 46.6 + - + +
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Residues in contact with ILE 415 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I ARG* 3.8 59.0 - - + +
323I VAL* 5.7 4.7 - - + -
413I SER* 3.3 0.6 - - - -
414I ASN* 1.3 77.7 - - - +
416I ASP* 1.3 69.4 + - - +
418I ILE* 4.1 2.3 - - - +
419I GLY* 2.9 27.5 + - - -
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Residues in contact with ASP 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I TRP* 4.7 17.2 - - + +
406I VAL* 5.7 0.2 - - - -
413I SER* 3.2 23.3 + - - +
415I ILE* 1.3 84.4 - - - +
417I ARG* 1.3 59.7 + - - +
419I GLY* 4.9 0.7 - - - -
420I ALA* 2.9 35.0 + - - +
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Residues in contact with ARG 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I VAL* 4.7 14.6 + - + +
407I LEU* 5.7 0.3 - - - +
409I GLY 5.3 1.6 - - - +
410I PRO* 2.4 57.2 + - + +
411I VAL 2.5 26.3 + - - -
412I LEU* 3.6 12.6 - - - +
413I SER 2.7 24.5 + - - +
414I ASN* 3.3 28.4 + - + +
415I ILE 3.3 0.2 - - - -
416I ASP* 1.3 73.0 - - - +
418I ILE* 1.3 61.6 + - + +
420I ALA* 4.3 0.3 - - - +
421I ASP* 2.8 33.6 + - - +
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Residues in contact with ILE 418 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I ASN* 2.9 36.2 + - + +
415I ILE* 4.2 1.3 - - - +
417I ARG* 1.3 71.3 - - + +
419I GLY* 1.3 65.2 + - - +
421I ASP* 3.7 4.9 - - - +
422I HIS* 2.9 32.0 + - + +
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Residues in contact with GLY 419 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 4.5 11.4 - - - -
370I TRP* 5.4 0.7 - - - -
415I ILE 2.9 18.1 + - - -
416I ASP* 3.9 1.1 - - - -
418I ILE* 1.3 76.0 - - - +
420I ALA* 1.3 61.3 + - - +
422I HIS* 2.6 36.0 + - - -
423I VAL* 3.0 12.7 + - - +
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Residues in contact with ALA 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I TRP* 3.7 40.7 - - + +
406I VAL* 4.0 21.1 - - + -
416I ASP* 2.9 21.4 + - - +
419I GLY* 1.3 72.3 - - - -
421I ASP* 1.3 55.3 + - - +
423I VAL* 3.5 8.0 - - - +
424I GLN* 2.8 38.4 + - - +
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Residues in contact with ASP 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I VAL* 4.8 2.2 - - + +
407I LEU* 3.7 37.8 - - + +
417I ARG 2.8 22.1 + - - +
418I ILE* 3.7 5.8 - - - +
420I ALA* 1.3 76.8 - - - +
422I HIS* 1.3 59.8 + - - +
424I GLN* 3.3 9.5 + - - +
425I SER* 2.8 38.3 + - - -
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Residues in contact with HIS 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I ASP* 5.8 1.1 - - - -
327I TRP* 3.2 57.8 + + + +
418I ILE* 2.9 22.8 + - + +
419I GLY* 2.6 28.4 + - - -
421I ASP* 1.3 76.7 - - - +
423I VAL* 1.3 61.4 + - + +
425I SER* 3.3 8.6 + - - -
426I LEU* 2.9 53.0 + - + +
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Residues in contact with VAL 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 3.6 26.9 - - + -
370I TRP* 4.6 10.5 - - + +
373I ARG* 5.3 2.9 - - + -
374I TYR* 3.5 43.7 - - + +
419I GLY 3.0 21.8 + - - +
420I ALA* 3.5 9.4 - - - +
422I HIS* 1.3 85.5 - - + +
424I GLN* 1.3 62.3 + - + +
426I LEU* 3.3 2.7 + - - +
427I LEU* 2.9 44.3 + - + +
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Residues in contact with GLN 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I TRP* 4.3 13.5 - - + -
399I GLU 5.5 0.4 - - - +
402I ARG* 3.5 5.5 + - - +
403I ILE* 3.4 57.8 - - + +
406I VAL* 3.4 34.0 - - - +
407I LEU* 4.4 5.2 - - - +
420I ALA* 2.8 23.2 + - - +
421I ASP* 3.7 8.5 - - - +
423I VAL* 1.3 80.2 - - + +
425I SER* 1.3 58.8 + - - +
427I LEU* 4.3 3.8 - - - +
428I LEU* 2.8 32.6 + - - +
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Residues in contact with SER 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421I ASP* 2.8 30.0 + - - -
422I HIS* 3.6 8.5 - - - -
423I VAL 3.2 0.2 - - - -
424I GLN* 1.3 77.2 - - - +
426I LEU* 1.3 62.0 + - - +
428I LEU* 3.3 11.3 + - - +
429I LYS* 3.0 27.4 + - - +
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Residues in contact with LEU 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I TRP* 4.9 4.7 - - + -
331I ASP* 5.4 2.2 - - - +
374I TYR* 3.6 35.0 - - + +
422I HIS* 2.9 46.8 + - + +
423I VAL 3.6 3.6 - - - +
425I SER* 1.3 77.0 - - - +
427I LEU* 1.3 59.5 + - + +
429I LYS* 3.8 1.3 - - - +
430I HIS* 2.9 32.8 + - - +
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Residues in contact with LEU 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I TYR* 3.7 40.4 - - + -
377I ILE* 3.8 44.4 - - + +
378I ALA* 4.2 17.9 - - + +
381I ALA* 5.4 0.7 - - + -
423I VAL* 2.9 24.1 + - + +
424I GLN* 4.3 3.8 - - - +
426I LEU* 1.3 75.3 - - + +
428I LEU* 1.3 59.4 + - - +
430I HIS* 4.1 13.2 - - + +
431I CYS* 2.8 33.4 + - - +
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Residues in contact with LEU 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I LEU* 6.0 3.8 - - + -
403I ILE* 5.6 11.9 - - + -
424I GLN 2.8 21.4 + - - +
425I SER* 3.3 10.5 - - - +
426I LEU 3.2 0.4 - - - -
427I LEU* 1.3 76.6 - - - +
429I LYS* 1.3 65.5 + - + +
431I CYS* 3.1 6.5 + - - +
432I ALA* 2.9 26.8 + - + +
454I SER 4.5 4.7 - - - +
455I LEU* 3.7 35.0 - - + +
458I LEU* 3.7 29.4 - - + -
459I LEU* 4.6 9.6 - - + +
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Residues in contact with LYS 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425I SER 3.0 12.9 + - - +
426I LEU* 3.8 1.8 - - - +
428I LEU* 1.3 87.0 - - + +
430I HIS* 1.3 59.2 + - - +
432I ALA* 3.7 15.9 - - - +
433I PRO* 3.8 6.1 - - - +
458I LEU* 2.3 46.3 + - - +
459I LEU* 5.8 0.2 - - - -
461I SER* 3.4 12.5 - - - -
462I GLN* 3.0 30.1 - - + +
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Residues in contact with HIS 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378I ALA* 6.0 0.4 - - - -
381I ALA* 3.5 38.9 + - + +
382I GLU* 4.7 14.5 + - - +
426I LEU 2.9 20.7 + - - +
427I LEU* 4.1 11.9 - - + +
429I LYS* 1.3 76.5 - - - +
431I CYS* 1.3 61.6 + - - +
432I ALA 3.3 0.4 - - - -
433I PRO* 3.3 20.2 - - + +
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Residues in contact with CYS 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ILE* 6.5 0.7 - - + -
381I ALA* 6.3 1.1 - - - -
388I ILE* 3.7 24.0 - - + -
392I ILE* 3.7 32.8 - - + -
396I LEU* 5.9 5.2 - - - -
427I LEU 2.8 21.1 + - - +
428I LEU* 3.6 5.2 - - - +
430I HIS* 1.3 78.4 - - - +
432I ALA* 1.3 64.6 + - - +
433I PRO* 3.4 0.4 - - - -
434I VAL* 3.2 20.5 + - - +
435I LEU* 4.1 2.4 + - - +
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Residues in contact with ALA 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I LEU* 2.9 16.2 + - + +
429I LYS* 3.7 10.3 - - - +
431I CYS* 1.3 76.7 - - - +
433I PRO* 1.4 62.6 - - + +
434I VAL 3.2 0.5 + - - -
435I LEU* 3.5 5.7 + - - +
436I ALA* 2.9 28.3 + - + +
459I LEU* 5.3 8.5 - - + +
462I GLN* 3.7 28.7 - - + +
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Residues in contact with PRO 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 4.2 2.0 - - - -
429I LYS 3.8 5.8 - - - +
430I HIS* 3.3 21.3 - - + +
431I CYS 3.5 0.2 - - - -
432I ALA* 1.4 91.8 - - + +
434I VAL* 1.3 57.0 + - - +
436I ALA* 3.7 10.2 - - + +
437I LYS* 2.9 28.9 + - - +
466I ALA* 5.8 3.8 - - + -
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Residues in contact with VAL 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 3.5 32.1 - - + +
388I ILE* 4.0 23.1 - - + -
389I LYS* 5.0 7.0 - - + +
431I CYS* 3.2 13.7 + - - +
432I ALA 3.2 0.8 - - - -
433I PRO* 1.3 79.0 - - - +
435I LEU* 1.3 52.7 + - - +
437I LYS* 3.1 4.2 + - - -
438I LEU* 2.6 34.0 + - - +
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Residues in contact with LEU 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I LEU* 6.3 5.4 - - + -
431I CYS 4.1 2.8 + - - +
432I ALA* 3.5 6.3 + - - +
434I VAL* 1.3 76.2 - - - +
436I ALA* 1.3 59.0 + - - +
438I LEU* 3.4 11.0 - - + -
439I ARG* 2.4 39.0 + - + +
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Residues in contact with ALA 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I ALA* 2.9 18.9 + - + +
433I PRO* 3.7 10.8 - - + +
434I VAL 3.2 0.2 - - - -
435I LEU* 1.3 76.9 - - - +
437I LYS* 1.3 58.8 + - - +
439I ARG 2.9 19.2 - - - +
462I GLN 5.7 0.2 - - - +
463I VAL* 5.3 10.1 - - + -
466I ALA* 4.1 25.4 - - + -
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Residues in contact with LYS 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 3.5 24.2 - - + +
433I PRO 2.9 18.4 + - - +
436I ALA* 1.3 75.7 - - - +
438I LEU* 1.3 62.5 + - - +
439I ARG 5.2 0.2 - - - -
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Residues in contact with LEU 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I HIS* 5.7 0.7 - - - -
389I LYS* 5.3 14.4 - - + +
434I VAL 2.6 21.6 + - - +
435I LEU* 3.7 9.2 - - + -
437I LYS* 1.3 77.4 - - - +
439I ARG* 1.3 63.8 + - + +
440I PRO 3.9 0.7 - - - -
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Residues in contact with ARG 439 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I LEU* 2.4 30.8 + - + +
436I ALA* 2.9 22.2 - - - +
438I LEU* 1.3 77.2 - - + +
440I PRO* 1.3 71.1 - - - +
441I PRO* 3.9 1.4 - - - +
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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