Contacts of the helix formed by residues 381 - 402 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLU* 2.9 28.1 + - - -
348B ARG* 4.0 5.9 - - - +
376B TYR* 2.9 40.7 + - + +
379B GLN* 3.9 30.3 + - + +
380B GLY* 1.4 73.6 - - - +
382B TYR* 1.3 63.8 + - - +
383B GLN 3.5 2.7 - - - -
384B ASP* 3.3 31.3 + - - +
385B ALA* 3.1 17.8 + - - +
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Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.5 46.2 + - + -
380B GLY* 3.0 25.0 + - - +
381B LYS* 1.3 73.6 - - - +
383B GLN* 1.4 51.0 + - - +
385B ALA* 3.2 5.5 + - - +
386B GLU* 2.9 34.8 + - - +
458B LEU* 3.8 20.3 - - + +
461B ARG* 3.9 37.1 + - + -
462B GLN* 5.6 4.3 - - - +
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LYS 3.5 0.4 - - - -
382B TYR* 1.4 73.1 - - - +
384B ASP* 1.3 63.3 + - - +
386B GLU* 3.1 18.9 + - - +
387B THR* 2.9 38.9 + - - +
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Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 5.0 3.6 + - - -
376B TYR* 3.5 28.6 - - + -
381B LYS* 3.3 38.3 + - + +
383B GLN* 1.3 77.8 + - - +
385B ALA* 1.4 61.4 + - - +
387B THR* 3.6 5.9 + - - -
388B LEU* 3.4 26.3 + - - +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 3.6 30.1 - - + +
376B TYR* 3.7 8.4 - - + -
377B LEU* 3.9 23.6 - - + -
381B LYS 3.1 13.5 + - - +
382B TYR 3.6 6.5 - - - +
384B ASP* 1.4 74.4 - - - +
386B GLU* 1.3 62.2 + - - +
388B LEU* 3.3 4.5 + - - +
389B TYR* 3.1 33.7 + - + -
458B LEU* 4.4 0.4 - - + -
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B TYR 2.9 13.0 + - - +
383B GLN* 3.3 22.1 + - - +
385B ALA* 1.3 71.9 - - - +
387B THR* 1.3 62.7 + - - +
389B TYR* 3.5 5.1 + - - +
390B LYS* 2.7 68.0 + - - +
416B GLU* 5.9 0.2 - - - -
455B LEU* 3.8 14.5 - - + +
458B LEU* 3.7 13.4 - - + +
459B TYR* 5.1 2.7 - - - -
462B GLN* 2.8 32.9 + - - +
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Residues in contact with THR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 2.9 21.6 + - - +
384B ASP* 3.9 7.0 - - - -
385B ALA 3.3 0.2 - - - -
386B GLU* 1.3 76.6 + - - +
388B LEU* 1.3 57.5 + - + +
390B LYS* 3.4 8.1 + - - +
391B GLU* 3.0 49.5 + - + +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 4.7 4.3 - - + -
369B LYS* 3.7 41.4 - - + +
372B LEU* 3.7 17.3 - - + -
373B ALA* 3.7 19.1 - - + +
376B TYR* 3.6 31.2 - - + -
384B ASP 3.4 7.8 + - - +
385B ALA 3.3 8.2 + - - +
386B GLU 3.3 0.4 - - - -
387B THR* 1.3 78.2 - - + +
389B TYR* 1.4 61.6 + - - +
391B GLU* 3.2 26.1 + - - +
392B ILE* 3.1 26.6 + - - +
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ASN* 3.5 29.4 + - - -
373B ALA* 3.5 24.7 - - + +
374B SER* 3.9 6.8 + - - -
377B LEU* 3.5 20.2 - - + +
385B ALA* 3.1 24.3 + - + -
386B GLU* 3.8 4.9 - - - +
387B THR 3.4 0.2 - - - -
388B LEU* 1.4 74.9 - - - +
390B LYS* 1.4 58.2 + - - +
392B ILE* 3.1 7.4 + - + +
393B LEU* 2.9 33.2 + - - +
451B THR* 3.5 20.1 - - + +
454B SER* 3.4 33.0 + - - -
455B LEU* 3.9 24.5 - - + -
458B LEU* 4.0 22.9 - - + -
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Residues in contact with LYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU* 2.7 55.4 + - - +
387B THR* 3.8 7.2 - - - +
389B TYR* 1.4 76.7 - - - +
391B GLU* 1.4 50.0 + - - +
393B LEU 3.3 0.5 + - - -
394B THR* 2.8 41.8 + - - -
412B TRP* 3.4 46.7 + - + +
416B GLU* 2.8 33.3 + - - -
455B LEU* 3.8 7.4 - - + -
459B TYR* 3.3 13.7 + - - -
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LYS* 2.8 41.6 + - - +
387B THR* 3.0 42.3 + - + +
388B LEU* 3.2 18.6 + - - +
390B LYS* 1.4 70.8 - - - +
392B ILE* 1.4 63.2 + - - +
394B THR* 4.0 5.5 - - - +
395B ARG* 3.1 26.0 + - - +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA* 4.0 26.9 - - + +
369B LYS* 3.7 34.5 - - + +
370B ASN* 3.2 27.4 - - - +
388B LEU 3.1 24.6 + - - +
389B TYR* 3.4 9.2 - - + +
391B GLU* 1.4 76.1 - - - +
393B LEU* 1.3 59.7 + - + +
395B ARG* 3.3 4.4 + - - +
396B ALA* 3.0 26.3 + - - +
447B THR 5.3 0.2 - - - +
448B VAL* 4.7 16.8 - - + -
451B THR* 3.6 21.1 - - + +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR 2.9 16.3 + - - +
392B ILE* 1.3 74.5 - - + +
394B THR* 1.4 54.1 + - - +
396B ALA* 3.3 6.6 + - + +
397B HIS* 2.9 30.2 + - - +
410B PRO* 4.6 2.3 - - + +
411B ILE* 4.1 14.2 + - + +
412B TRP* 3.7 23.3 - - + -
443B VAL* 6.3 1.1 - - + -
448B VAL* 4.3 14.6 - - + -
451B THR* 3.8 18.4 - - + -
452B LEU* 3.5 38.4 - - + -
455B LEU* 3.6 34.3 - - + -
471B LEU* 4.8 1.6 - - + -
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LYS 2.8 27.7 + - - -
391B GLU* 4.0 6.3 - - - -
393B LEU* 1.4 68.4 - - - +
395B ARG* 1.3 61.4 + - - +
397B HIS* 3.3 2.4 + - - +
398B GLU* 2.9 44.0 + - - +
404B VAL* 4.2 12.1 - - + -
410B PRO* 3.8 20.3 - - + +
412B TRP* 3.0 24.3 + - + +
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Residues in contact with ARG 395 (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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360B PRO* 3.7 37.4 - - - +
361B ASP* 2.7 39.4 + - - +
369B LYS* 6.3 0.2 - - - +
391B GLU 3.1 18.4 + - - +
392B ILE* 3.8 4.3 - - - +
394B THR* 1.3 72.9 - - - +
396B ALA* 1.3 60.4 + - - +
398B GLU* 3.1 40.3 + - - +
399B LYS* 2.9 44.2 + - + +
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Residues in contact with ALA 396 (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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392B ILE* 3.0 17.5 + - + +
393B LEU* 3.5 10.5 - - + +
395B ARG* 1.3 76.9 - - - +
397B HIS* 1.4 59.8 + - - +
399B LYS* 2.9 39.2 + - - +
400B GLU* 3.4 6.2 + - - +
443B VAL* 4.7 13.5 - - + -
448B VAL* 4.5 22.4 - - + -
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Residues in contact with HIS 397 (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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393B LEU 2.9 16.5 + - - +
394B THR 3.5 4.0 - - - +
395B ARG 3.2 0.2 - - - -
396B ALA* 1.4 75.3 - - - +
398B GLU* 1.3 54.0 + - - +
400B GLU* 3.4 1.4 + - - -
401B PHE* 2.8 66.7 + + - +
402B GLY 4.3 3.6 - - - -
404B VAL* 4.5 11.0 - - + -
408B ASN* 2.8 36.7 + - - -
409B LYS 3.1 32.0 + - - -
410B PRO* 3.9 16.8 - - + +
411B ILE 4.8 1.1 + - - +
440B ALA* 3.8 19.1 + - + -
443B VAL* 6.1 0.6 - - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 2.9 31.0 + - - +
395B ARG* 3.1 28.7 + - - +
397B HIS* 1.3 75.5 - - - +
399B LYS* 1.4 59.0 + - - +
402B GLY* 2.8 42.8 + - - +
403B SER* 3.4 26.9 + - - -
404B VAL* 3.6 22.7 + - + +
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Residues in contact with LYS 399 (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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361B ASP* 3.4 32.8 - - + +
395B ARG* 2.9 30.2 + - - +
396B ALA* 2.9 39.2 + - - +
398B GLU* 1.4 73.8 - - - +
400B GLU* 1.3 79.0 + - + +
402B GLY 5.1 0.2 + - - -
443B VAL* 4.3 14.9 - - - +
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Residues in contact with GLU 400 (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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396B ALA 3.4 12.8 + - - +
397B HIS 3.4 3.2 + - - +
398B GLU 3.4 0.2 - - - -
399B LYS* 1.3 96.3 - - + +
401B PHE* 1.3 90.6 + - + +
441B CYS 5.5 3.2 - - - +
443B VAL* 6.1 2.5 - - + -
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Residues in contact with PHE 401 (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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397B HIS* 2.8 55.0 + + - +
400B GLU* 1.3 103.1 - - + +
402B GLY* 1.3 57.1 + - - +
408B ASN* 3.4 25.4 + - - +
439B LYS 4.8 7.2 - - - -
440B ALA* 4.1 19.1 - - - -
441B CYS* 4.5 14.6 - - - -
443B VAL* 6.3 0.4 - - + -
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B HIS* 4.3 2.4 - - - -
398B GLU* 2.8 37.9 + - - +
399B LYS 5.1 0.2 + - - -
400B GLU 4.0 0.2 - - - -
401B PHE* 1.3 74.2 - - - +
403B SER* 1.3 66.8 + - - -
404B VAL 3.3 1.7 + - - -
408B ASN* 3.0 9.7 - - - +
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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