Contacts of the helix formed by residues 362 - 379 (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 ASP 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A TYR* 4.5 0.3 - - - -
358A LEU* 3.3 34.9 - - + +
359A GLY* 3.6 18.6 + - - +
360A PRO 3.4 2.1 - - - +
361A ASP* 1.4 77.1 - - - +
363A PRO* 1.4 80.5 - - - +
364A ASN* 3.2 32.4 + - - +
365A VAL* 3.0 23.8 + - + +
366A ALA* 4.0 2.8 + - - +
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Residues in contact with PRO 363 (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 8.0 - - - +
362A ASP* 1.4 93.4 - - - +
364A ASN* 1.4 62.0 + - - +
366A ALA* 3.2 10.9 + - + +
367A LYS* 3.1 46.2 + - - +
447A THR* 4.9 3.0 - - + +
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Residues in contact with ASN 364 (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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354A TYR* 3.5 41.6 + - + -
358A LEU* 4.7 2.8 - - - +
362A ASP* 3.1 20.9 + - - +
363A PRO* 1.4 77.5 - - - +
365A VAL* 1.3 58.5 + - - +
367A LYS* 4.1 18.4 + - - +
368A THR* 2.9 36.4 + - - -
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.9 21.6 - - + +
354A TYR* 3.8 28.5 - - + +
355A ALA* 4.1 8.5 - - + +
359A GLY 3.6 23.8 - - - +
360A PRO* 4.3 14.8 - - + +
362A ASP* 3.0 16.1 + - + +
364A ASN* 1.3 77.8 - - - +
366A ALA* 1.4 58.1 + - - +
368A THR* 3.3 2.1 + - - -
369A LYS* 2.9 49.2 + - + +
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Residues in contact with ALA 366 (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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362A ASP 4.0 2.3 + - - +
363A PRO* 3.2 9.9 + - + +
365A VAL* 1.4 75.4 - - - +
367A LYS* 1.4 55.7 + - - +
369A LYS* 3.2 2.1 + - - +
370A ASN* 2.7 38.5 + - - +
392A ILE* 4.0 31.7 - - + +
447A THR* 3.9 19.7 - - + -
448A VAL* 6.0 2.2 - - + -
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Residues in contact with LYS 367 (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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363A PRO* 3.1 30.4 + - - +
364A ASN* 4.1 18.8 + - - +
366A ALA* 1.4 72.2 - - - +
368A THR* 1.4 57.6 + - - +
370A ASN* 3.3 5.0 + - - +
371A ASN* 2.9 41.4 + - - +
447A THR* 3.9 28.7 - - + +
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Residues in contact with THR 368 (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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328A SER* 4.3 5.2 + - - -
347A TYR* 3.4 34.7 - - + +
350A ALA* 4.1 6.7 - - + -
351A LEU* 3.7 25.4 - - + +
354A TYR* 3.4 21.1 - - - -
364A ASN 2.9 20.4 + - - -
365A VAL 3.8 2.9 - - - -
367A LYS* 1.4 73.6 - - - +
369A LYS* 1.3 57.6 + - - +
371A ASN* 3.2 10.9 + - - +
372A LEU* 2.9 29.3 + - + +
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Residues in contact with LYS 369 (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* 3.8 28.7 - - + -
355A ALA* 6.1 0.9 - - - -
365A VAL* 2.9 40.3 + - + +
366A ALA 3.6 3.6 - - - +
368A THR* 1.3 73.5 - - - +
370A ASN* 1.3 53.2 + - - +
372A LEU* 3.3 5.5 + - - -
373A ALA* 2.8 36.1 + - - +
388A LEU* 3.7 20.4 - - + +
391A GLU* 2.8 43.6 + - - +
392A ILE* 3.7 27.6 - - + +
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Residues in contact with ASN 370 (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 2.7 20.9 + - - +
367A LYS* 3.5 6.5 - - - +
369A LYS* 1.3 72.7 - - - +
371A ASN* 1.3 57.9 + - - +
373A ALA* 3.2 6.0 + - - +
374A SER* 3.0 29.3 + - - -
389A TYR* 3.5 17.2 + - - -
392A ILE* 3.2 11.2 - - - +
447A THR* 3.1 37.8 + - - +
450A THR* 3.8 20.5 - - + +
451A THR* 2.7 20.0 + - - -
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Residues in contact with ASN 371 (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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328A SER* 5.8 2.0 - - - -
332A LEU* 6.3 0.2 - - - -
335A GLN* 4.9 5.6 + - - +
347A TYR* 3.5 46.8 + - + -
367A LYS* 2.9 25.4 + - - +
368A THR* 3.5 9.1 + - - +
370A ASN* 1.3 75.1 - - - +
372A LEU* 1.4 61.6 + - - +
374A SER* 3.5 7.9 + - - -
375A CYS* 3.3 20.3 + - - +
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Residues in contact with LEU 372 (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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344A GLU* 3.9 34.8 - - + +
347A TYR* 3.9 16.7 - - + -
348A ARG* 3.9 16.4 - - + +
351A LEU* 4.7 14.8 - - + -
368A THR* 2.9 19.5 + - + +
369A LYS* 3.8 4.5 - - - +
371A ASN* 1.4 69.2 - - - +
373A ALA* 1.4 65.7 + - - +
375A CYS* 3.1 9.8 + - + +
376A TYR* 3.0 57.8 + - + +
388A LEU* 3.7 18.2 - - + -
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Residues in contact with ALA 373 (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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369A LYS 2.8 19.0 + - - +
370A ASN 3.2 1.8 + - - +
372A LEU* 1.4 76.6 - - - +
374A SER* 1.4 56.7 + - - +
376A TYR* 3.1 9.5 + - - +
377A LEU* 3.0 30.8 + - - +
385A ALA* 3.6 5.3 - - - +
388A LEU* 3.7 21.0 - - + +
389A TYR* 3.3 39.9 - - + -
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Residues in contact with SER 374 (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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335A GLN* 6.1 1.8 - - - -
370A ASN 3.0 16.3 + - - -
371A ASN* 3.6 8.7 - - - -
372A LEU 3.2 0.2 - - - -
373A ALA* 1.4 74.7 - - - +
375A CYS* 1.3 60.9 + - - +
377A LEU* 3.4 15.9 + - - +
378A LYS* 3.2 46.9 + - - +
389A TYR* 3.9 2.8 + - - -
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Residues in contact with CYS 375 (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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335A GLN* 5.5 2.4 - - - +
340A ALA* 3.7 17.7 - - - -
343A VAL* 3.6 32.1 - - + -
344A GLU* 4.1 8.5 - - - -
371A ASN 3.3 11.1 + - - +
372A LEU* 3.1 15.1 + - + +
374A SER* 1.3 76.3 - - - +
376A TYR* 1.3 62.9 + - - +
378A LYS* 3.4 13.4 + - - +
379A GLN* 3.2 46.9 + - - +
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Residues in contact with TYR 376 (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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344A GLU* 3.8 17.7 - - - -
348A ARG* 2.8 44.4 + - - -
372A LEU* 3.0 35.2 + - + +
373A ALA 3.1 6.7 + - - +
375A CYS* 1.3 73.0 - - + +
377A LEU* 1.3 59.9 - - - +
379A GLN* 3.4 3.9 + - - +
380A GLY 3.1 3.3 + - - -
381A LYS* 2.7 67.1 + - + +
384A ASP* 3.6 32.1 - - + -
385A ALA* 3.7 3.8 - - + +
388A LEU* 3.4 27.6 - - + -
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Residues in contact with LEU 377 (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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373A ALA 3.0 14.9 + - - +
374A SER* 3.6 13.7 - - - +
375A CYS 3.3 0.4 - - - -
376A TYR* 1.3 71.9 - - - +
378A LYS* 1.4 59.0 + - + +
379A GLN 3.1 1.6 - - - -
380A GLY* 2.8 23.0 + - - -
382A TYR* 3.5 38.4 + - + -
385A ALA* 3.8 12.1 - - + -
389A TYR* 3.5 27.6 - - + +
454A SER* 5.3 5.6 - - - +
458A LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 378 (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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335A GLN* 5.3 19.6 - - - +
340A ALA* 6.1 2.2 - - + -
374A SER* 3.2 37.8 + - - +
375A CYS* 3.6 14.1 - - - +
377A LEU* 1.4 77.7 - - + +
379A GLN* 1.3 59.7 + - + +
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Residues in contact with GLN 379 (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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340A ALA* 3.9 26.4 + - + +
341A GLU* 5.0 6.6 + - - +
344A GLU* 2.7 30.0 + - - +
375A CYS* 3.2 37.4 + - - +
376A TYR* 3.7 10.1 - - - +
377A LEU 3.1 0.8 - - - -
378A LYS* 1.3 76.4 - - + +
380A GLY* 1.3 60.7 + - - +
381A LYS* 3.7 20.1 + - + +
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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
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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