Contacts of the helix formed by residues 362 - 379 (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 ASP 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B TYR* 4.5 0.2 - - - -
358B LEU* 3.3 34.1 - - + +
359B GLY* 3.6 19.0 + - - +
360B PRO 3.4 2.7 - - - +
361B ASP* 1.4 75.5 - - - +
363B PRO* 1.4 82.0 - - - +
364B ASN* 3.2 32.3 + - - +
365B VAL* 3.0 24.1 + - + +
366B ALA* 4.0 2.4 + - - +
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Residues in contact with PRO 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP 3.4 8.0 - - - +
362B ASP* 1.4 92.8 - - - +
364B ASN* 1.4 64.3 + - - +
366B ALA* 3.2 10.2 + - + +
367B LYS* 3.1 42.8 + - - +
447B THR* 4.8 2.4 + - - +
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Residues in contact with ASN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B TYR* 3.5 42.5 + - + -
358B LEU* 4.7 2.8 - - - +
362B ASP* 3.1 20.7 + - - +
363B PRO* 1.4 76.7 - - - +
365B VAL* 1.3 59.7 + - - +
367B LYS* 4.1 19.0 + - - +
368B THR* 2.9 35.6 + - - -
206Y GLU* 5.6 1.4 - - - +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 3.9 21.0 - - + +
354B TYR* 3.8 28.0 - - + +
355B ALA* 4.1 7.6 - - + +
359B GLY 3.6 24.0 - - - +
360B PRO* 4.3 14.6 - - + +
362B ASP* 3.0 16.0 + - + +
364B ASN* 1.3 76.3 - - - +
366B ALA* 1.4 57.3 + - - +
368B THR* 3.7 1.4 - - - -
369B LYS* 2.9 50.9 + - + +
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ASP 4.0 2.7 + - - +
363B PRO* 3.2 10.0 + - + +
365B VAL* 1.4 75.0 - - - +
367B LYS* 1.4 53.6 + - - +
369B LYS* 3.2 2.8 + - - +
370B ASN* 2.7 38.1 + - - +
392B ILE* 4.0 31.4 - - + +
447B THR* 3.7 20.9 - - + -
448B VAL* 6.0 2.5 - - + -
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Residues in contact with LYS 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PRO* 3.1 30.6 + - - +
364B ASN* 4.1 17.8 + - - +
366B ALA* 1.4 73.9 - - - +
368B THR* 1.4 57.9 + - - +
370B ASN* 3.2 5.3 + - - +
371B ASN* 2.9 41.5 + - - +
447B THR* 3.6 28.2 - - + +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER* 4.3 5.0 + - - -
347B TYR* 3.4 34.8 - - + +
350B ALA* 4.2 6.5 - - + -
351B LEU* 3.7 24.5 - - + +
354B TYR* 3.4 21.2 - - - -
364B ASN 2.9 22.9 + - - -
365B VAL 3.8 2.7 - - - -
367B LYS* 1.4 74.2 - - - +
369B LYS* 1.4 52.5 + - - +
371B ASN* 3.2 11.5 + - - +
372B LEU* 2.8 34.3 + - + +
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Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 3.8 27.4 - - + -
355B ALA* 6.1 1.6 - - - -
365B VAL* 2.9 38.7 + - + +
366B ALA* 3.6 4.0 - - - +
368B THR* 1.4 73.2 - - - +
370B ASN* 1.3 56.6 + - - +
372B LEU* 4.5 4.9 - - - -
373B ALA* 2.8 31.9 + - - +
388B LEU* 3.7 20.0 - - + +
391B GLU* 2.8 44.3 + - - +
392B ILE* 3.7 28.0 - - + +
395B ARG* 6.3 0.2 - - - +
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Residues in contact with ASN 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA 2.7 19.5 + - - +
367B LYS* 3.5 6.7 - - - +
369B LYS* 1.3 73.0 - - - +
371B ASN* 1.3 57.7 + - - +
373B ALA* 3.3 6.6 + - - +
374B SER* 3.0 28.8 + - - -
389B TYR* 3.5 16.8 + - - -
392B ILE* 3.2 11.4 - - - +
447B THR* 2.9 38.3 + - - +
450B THR* 3.7 22.9 - - + +
451B THR* 2.7 18.1 + - - -
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Residues in contact with ASN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER* 5.9 1.4 - - - -
332B LEU* 6.3 0.2 - - - -
335B GLN* 4.9 5.3 + - - +
347B TYR* 3.5 46.5 + - + -
367B LYS* 2.9 28.5 + - - +
368B THR* 3.5 6.8 + - - +
370B ASN* 1.3 74.9 - - - +
372B LEU* 1.3 63.3 + - - +
374B SER* 3.4 8.4 + - - -
375B CYS* 3.3 19.9 + - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU* 4.0 13.5 - - + +
347B TYR* 4.0 28.0 - - + -
348B ARG* 4.0 25.6 - - + -
351B LEU* 4.5 20.2 - - + -
368B THR* 2.8 20.4 + - + +
369B LYS 3.8 3.4 - - - +
371B ASN* 1.3 68.9 - - - +
373B ALA* 1.4 66.1 + - - +
375B CYS* 3.2 7.7 + - + +
376B TYR* 3.1 51.3 + - + +
388B LEU* 3.7 21.1 - - + -
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Residues in contact with ALA 373 (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 18.3 + - - +
370B ASN 3.5 2.7 - - - +
372B LEU* 1.4 75.3 - - - +
374B SER* 1.3 56.5 + - - +
376B TYR* 2.8 25.2 + - - +
377B LEU* 3.0 10.7 + - - +
385B ALA* 3.6 15.7 - - - +
388B LEU* 3.7 16.6 - - + +
389B TYR* 3.5 33.9 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLN* 6.0 2.2 - - - -
370B ASN 3.0 14.3 + - - -
371B ASN* 3.6 11.9 - - - -
372B LEU 3.4 0.2 - - - -
373B ALA* 1.3 74.5 - - - +
375B CYS* 1.3 59.8 + - - +
377B LEU* 3.4 17.2 + - - +
378B LYS* 3.2 45.9 + - - +
389B TYR* 3.9 4.0 + - - -
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Residues in contact with CYS 375 (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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335B GLN* 5.6 2.6 - - - +
340B ALA* 3.6 18.2 - - - -
343B VAL* 3.6 31.9 - - + -
344B GLU* 4.0 9.6 - - - -
371B ASN 3.3 9.6 + - - +
372B LEU* 3.2 15.0 + - + +
373B ALA 3.1 0.2 - - - -
374B SER* 1.3 76.7 - - - +
376B TYR* 1.3 65.4 + - - +
378B LYS* 3.3 19.7 + - - +
379B GLN* 3.2 38.5 + - - +
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Residues in contact with TYR 376 (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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344B GLU* 3.7 23.6 - - + -
348B ARG* 2.6 44.6 + - - -
372B LEU* 3.1 30.5 + - + +
373B ALA 2.8 7.0 + - - +
375B CYS* 1.3 75.6 - - + +
377B LEU* 1.4 59.8 + - - +
379B GLN* 3.0 7.7 + - - +
380B GLY 3.0 4.5 + - - -
381B LYS* 2.9 57.1 + - + +
384B ASP* 3.5 35.4 - - + -
385B ALA* 3.7 4.3 - - + -
388B LEU* 3.6 25.1 - - + -
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Residues in contact with LEU 377 (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 ALA 3.0 12.2 + - - +
374B SER* 3.6 16.4 - - - +
375B CYS 3.3 0.2 - - - -
376B TYR* 1.4 73.8 - - - +
378B LYS* 1.4 56.8 + - + +
380B GLY* 2.8 24.1 + - - -
382B TYR* 3.5 40.9 + - + -
385B ALA* 3.9 15.5 - - + -
389B TYR* 3.5 26.5 - - + +
454B SER* 5.3 5.6 - - - +
458B LEU* 3.9 18.4 - - + -
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLN* 5.2 19.9 - - - +
340B ALA* 5.9 3.8 - - + -
374B SER* 3.2 39.4 + - - +
375B CYS* 3.3 14.1 + - - +
377B LEU* 1.4 78.6 - - + +
379B GLN* 1.3 60.8 + - + +
380B GLY 3.8 0.2 + - - -
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Residues in contact with GLN 379 (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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340B ALA* 3.9 26.6 + - + +
341B GLU* 4.9 7.4 + - - +
344B GLU* 2.7 30.1 + - - +
375B CYS* 3.2 36.8 + - - +
376B TYR* 3.0 12.3 + - - +
378B LYS* 1.3 77.2 - - - +
380B GLY* 1.3 60.7 + - - +
381B LYS* 3.3 22.4 + - + +
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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
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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