Contacts of the helix formed by residues 381 - 402 (chain A) in PDB entry 3ZFW
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 LYS 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A GLU* 2.8 32.9 + - - -
348A ARG* 3.4 13.1 - - - +
376A TYR* 2.7 37.7 + - + +
379A GLN* 3.7 36.1 + - + +
380A GLY* 1.4 69.5 - - - +
382A TYR* 1.3 61.5 + - - +
383A GLN 3.5 2.5 - - - -
384A ASP* 3.2 26.2 + - + +
385A ALA* 3.1 18.5 + - - +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.5 46.4 + - + -
380A GLY* 3.0 25.9 + - - +
381A LYS* 1.3 73.6 - - - +
383A GLN* 1.4 56.6 + - - +
385A ALA* 3.2 6.0 + - - +
386A GLU* 2.9 30.0 + - - +
458A LEU* 3.7 20.6 - - + +
461A ARG* 3.9 38.3 + - + -
462A GLN* 5.5 3.1 - - - +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS 3.5 0.6 - - - -
382A TYR* 1.4 72.0 - - - +
384A ASP* 1.3 65.5 + - - +
386A GLU* 3.2 19.0 + - - +
387A THR* 2.9 39.3 + - - +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 5.4 2.3 + - - -
376A TYR* 3.6 29.4 - - + -
381A LYS* 3.2 37.8 + - + +
383A GLN* 1.3 82.2 - - - +
385A ALA* 1.4 62.6 + - - +
387A THR* 3.5 6.1 + - - -
388A LEU* 3.4 21.7 + - - +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA* 3.6 25.8 - - - +
376A TYR* 3.7 10.0 - - + -
377A LEU* 3.8 22.7 - - + -
381A LYS 3.1 11.9 + - - +
382A TYR 3.5 8.1 - - - +
384A ASP* 1.4 71.0 - - - +
386A GLU* 1.3 64.8 + - - +
388A LEU* 2.9 15.4 + - - +
389A TYR* 3.1 22.7 + - + -
458A LEU* 4.1 3.6 - - + -
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A TYR 2.9 13.9 + - - +
383A GLN* 3.4 23.0 + - - +
385A ALA* 1.3 76.6 - - - +
387A THR* 1.3 58.1 + - - +
389A TYR* 3.5 2.8 + - - +
390A LYS* 2.7 66.6 + - - +
455A LEU* 3.7 16.8 - - + -
458A LEU* 3.7 12.9 - - + +
459A TYR* 5.1 3.1 - - - -
462A GLN* 2.8 32.9 + - - +
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Residues in contact with THR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLN* 2.9 21.9 + - - +
384A ASP* 3.8 6.7 - - - -
385A ALA 3.2 0.2 - - - -
386A GLU* 1.3 76.3 + - - +
388A LEU* 1.3 59.9 + - + +
390A LYS* 3.4 7.3 + - + +
391A GLU* 3.0 54.0 + - + +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU* 4.7 5.4 - - + -
369A LYS* 3.7 40.7 - - + +
372A LEU* 3.7 16.4 - - + -
373A ALA* 3.7 14.4 - - + +
376A TYR* 3.4 36.1 - - + -
384A ASP 3.4 7.3 + - - +
385A ALA 2.9 8.6 + - - +
387A THR* 1.3 76.9 - - + +
389A TYR* 1.4 61.5 + - - +
391A GLU* 3.2 25.2 + - - +
392A ILE* 3.1 27.4 + - - +
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Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ASN* 3.5 28.6 + - - -
373A ALA* 3.3 30.2 - - + +
374A SER* 3.9 6.9 + - - -
377A LEU* 3.5 21.8 - - + +
385A ALA* 3.1 22.1 + - + -
386A GLU 3.8 4.3 - - - +
388A LEU* 1.4 72.5 - - - +
390A LYS* 1.4 57.1 + - - +
392A ILE* 3.1 6.4 + - + +
393A LEU* 2.9 34.1 + - - +
451A THR* 3.5 20.1 - - + +
454A SER* 3.4 30.3 + - - -
455A LEU* 3.9 24.7 - - + -
458A LEU* 4.0 22.4 - - + -
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU* 2.7 54.6 + - + +
387A THR* 3.8 7.2 - - - +
388A LEU 3.3 0.2 - - - -
389A TYR* 1.4 77.2 - - - +
391A GLU* 1.4 49.7 + - - +
393A LEU* 3.3 1.4 + - - -
394A THR* 2.8 42.2 + - - -
412A TRP* 3.4 47.3 + - + +
416A GLU* 2.8 33.7 + - - -
455A LEU* 3.9 7.0 - - + -
459A TYR* 3.3 13.9 + - - -
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 5.8 0.2 - - - +
369A LYS* 2.8 42.8 + - - +
387A THR* 3.0 42.4 + - + +
388A LEU* 3.4 19.0 - - - +
390A LYS* 1.4 72.4 - - - +
392A ILE* 1.4 63.9 + - - +
394A THR* 4.0 5.6 - - - -
395A ARG* 3.0 26.0 + - - +
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ALA* 4.0 27.6 - - + +
369A LYS* 3.7 34.1 - - + +
370A ASN* 3.2 28.3 - - - +
388A LEU 3.1 20.2 + - - +
389A TYR* 3.1 10.2 + - + +
391A GLU* 1.4 74.9 - - - +
393A LEU* 1.3 60.1 + - + +
395A ARG* 3.8 3.8 - - - +
396A ALA* 3.0 27.9 + - + +
447A THR 5.3 0.2 - - - +
448A VAL* 4.5 17.5 - - + -
451A THR* 3.7 20.2 - - + +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A TYR 2.9 16.3 + - - +
392A ILE* 1.3 77.2 - - + +
394A THR* 1.4 55.0 + - - +
396A ALA* 3.3 6.5 + - + +
397A HIS* 2.9 29.9 + - - +
410A PRO* 4.6 1.9 - - + +
411A ILE* 4.1 21.7 + - + +
412A TRP* 3.7 23.1 - - + -
443A VAL* 6.4 0.2 - - + -
448A VAL* 4.2 15.5 - - + -
451A THR* 3.8 20.9 - - + -
452A LEU* 3.8 30.7 - - + -
455A LEU* 3.6 32.1 - - + -
471A LEU* 4.6 2.2 - - + -
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Residues in contact with THR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LYS 2.8 28.0 + - - -
391A GLU* 4.0 6.0 - - - -
393A LEU* 1.4 67.7 - - - +
395A ARG* 1.4 60.6 + - - +
397A HIS* 3.3 2.6 + - - +
398A GLU* 2.9 43.8 + - - +
404A VAL* 4.1 11.9 - - + -
410A PRO* 3.9 19.7 - - + +
412A TRP* 3.0 24.1 + - + +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A PRO* 3.7 37.9 - - - +
361A ASP* 2.7 38.5 + - - +
391A GLU 3.0 19.1 + - - +
392A ILE* 3.9 4.0 - - - +
394A THR* 1.4 72.5 - - - +
396A ALA* 1.3 59.8 - - - +
398A GLU* 3.1 39.5 + - - +
399A LYS* 2.9 44.6 + - + +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ILE 3.0 17.5 + - - +
393A LEU* 3.3 9.4 + - + +
395A ARG* 1.3 76.7 - - - +
397A HIS* 1.4 63.4 + - - +
399A LYS* 2.9 41.3 + - - +
400A GLU* 3.4 6.4 + - - +
443A VAL* 4.6 11.7 - - + -
448A VAL* 4.2 25.8 - - + -
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LEU 2.9 17.6 + - - +
394A THR 3.5 4.3 - - - +
396A ALA* 1.4 77.1 - - - +
398A GLU* 1.3 52.8 + - - +
400A GLU 3.4 1.2 + - - -
401A PHE* 2.8 61.9 + + + +
402A GLY 4.3 3.8 - - - -
404A VAL* 4.5 11.0 - - + -
408A ASN* 2.8 40.9 + - - -
409A LYS 3.2 31.8 + - - -
410A PRO* 3.9 17.1 - - + +
411A ILE 4.8 3.1 + - - +
443A VAL* 6.5 0.7 - - - -
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A THR* 2.9 31.7 + - - +
395A ARG* 3.5 28.1 + - - +
397A HIS* 1.3 76.6 - - - +
399A LYS* 1.4 58.6 + - - +
402A GLY* 2.8 43.2 + - - +
403A SER* 3.3 27.8 + - - +
404A VAL* 3.6 23.4 + - + +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ASP* 3.4 32.8 - - + +
395A ARG* 2.9 30.0 + - + +
396A ALA* 2.9 39.0 + - - +
398A GLU* 1.4 73.9 - - - +
400A GLU* 1.3 76.9 + - + +
402A GLY 5.1 0.3 + - - -
443A VAL* 4.3 14.9 - - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ALA 3.4 10.2 + - - +
397A HIS 3.4 1.6 + - - -
399A LYS* 1.3 95.6 - - + +
401A PHE* 1.3 90.1 + - + +
443A VAL* 6.2 1.6 - - + -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A HIS* 2.8 46.7 + + - +
400A GLU* 1.3 102.1 - - + +
402A GLY* 1.3 57.5 + - - +
408A ASN* 3.4 27.0 + - - +
440A ALA 4.6 15.5 - - - -
441A CYS* 5.1 9.9 - - - -
443A VAL* 6.3 2.7 - - + -
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A HIS* 4.3 2.1 - - - -
398A GLU* 2.8 38.1 + - - +
399A LYS 4.8 0.2 - - - -
401A PHE* 1.3 72.7 - - - +
403A SER* 1.3 66.2 + - - -
404A VAL* 3.3 2.4 + - - -
408A ASN* 3.0 10.0 - - - +
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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