Contacts of the helix formed by residues 381 - 402 (chain A) in PDB entry 4NZP
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 ASN 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A VAL* 5.7 6.8 - - + +
380A TYR* 1.3 86.8 - - - +
382A GLN* 1.3 67.0 + - - +
383A LYS* 3.4 13.5 + - - +
384A ASP* 3.1 41.7 + - - +
385A ALA* 3.2 17.0 + - - +
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Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASN* 1.3 74.9 - - - +
383A LYS* 1.3 59.8 + - - +
385A ALA* 3.2 9.4 + - - +
386A ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASN* 3.3 11.9 + - - +
382A GLN* 1.3 74.7 - - - +
384A ASP* 1.3 67.4 + - - +
386A ALA* 3.3 20.4 + - - +
387A GLY* 3.4 5.5 + - - -
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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
----------------------------------------------------------
379A VAL 4.7 1.0 - - - +
380A TYR* 3.4 18.7 - - + +
381A ASN* 3.1 42.7 + - - +
382A GLN 3.2 0.2 - - - -
383A LYS* 1.3 79.0 - - - +
385A ALA* 1.3 60.4 + - - +
387A GLY* 3.2 11.1 + - - -
388A PHE* 3.2 13.2 + - - +
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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
----------------------------------------------------------
380A TYR* 4.9 13.4 - - + -
381A ASN 3.2 9.1 + - - +
382A GLN* 3.2 12.6 + - - +
384A ASP* 1.3 78.8 - - - +
386A ALA* 1.3 63.1 + - - +
388A PHE* 3.3 10.3 + - + +
389A ILE* 3.0 33.8 + - + +
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Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN 3.0 12.3 + - - +
383A LYS* 3.4 14.4 - - - +
384A ASP 3.2 0.2 - - - -
385A ALA* 1.3 78.0 - - - +
387A GLY* 1.3 56.6 + - - +
389A ILE* 3.4 8.9 + - - +
390A LYS* 3.0 28.2 + - - +
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Residues in contact with GLY 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS 3.4 6.0 + - - -
384A ASP* 3.2 7.5 + - - -
386A ALA* 1.3 76.9 - - - +
388A PHE* 1.3 64.0 + - - +
390A LYS* 4.3 5.4 - - - -
391A LEU* 3.2 33.7 + - - +
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Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 3.2 12.4 + - - +
385A ALA* 3.3 14.1 + - + +
387A GLY* 1.3 76.1 - - - +
389A ILE* 1.3 66.1 + - + +
391A LEU* 3.6 3.3 + - - +
392A ASN* 2.7 60.5 + - - -
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Residues in contact with ILE 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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385A ALA* 3.0 23.7 + - + +
386A ALA* 3.6 8.1 - - - +
387A GLY 3.2 0.2 - - - -
388A PHE* 1.3 81.1 - - + +
390A LYS* 1.3 66.8 + - - +
392A ASN* 3.3 6.7 + - - +
393A ALA* 3.0 29.4 + - + +
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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
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386A ALA 3.0 17.9 + - - +
387A GLY* 3.8 9.4 - - - +
389A ILE* 1.3 80.1 - - - +
391A LEU* 1.3 65.4 + - + +
393A ALA* 3.5 4.9 + - - +
394A LEU* 3.0 30.1 + - + +
397A ILE* 5.4 2.1 - - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLY* 3.2 21.1 + - - +
388A PHE* 4.3 3.1 - - - +
389A ILE 3.2 0.6 - - - -
390A LYS* 1.3 84.3 - - + +
392A ASN* 1.3 67.6 + - - +
393A ALA 3.2 0.4 + - - -
394A LEU* 3.7 26.5 - - + +
395A ARG 5.0 0.5 + - - -
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Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 2.7 59.3 + - - +
389A ILE* 3.3 6.7 + - - +
391A LEU* 1.3 78.9 - - - +
393A ALA* 1.3 60.3 + - - +
394A LEU 3.3 0.6 + - - -
395A ARG* 4.2 12.0 + - - +
396A PHE* 3.7 18.1 - - - -
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Residues in contact with ALA 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 ILE* 3.0 23.9 + - + +
390A LYS* 3.9 5.8 - - - +
391A LEU 3.2 0.2 - - - -
392A ASN* 1.3 77.7 - - - +
394A LEU* 1.3 64.0 + - - +
395A ARG 3.3 2.5 - - - -
396A PHE* 3.0 24.8 + - + +
397A ILE* 3.1 24.2 + - + +
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Residues in contact with LEU 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* 3.0 30.4 + - + +
391A LEU* 3.7 27.4 - - + +
392A ASN 3.3 0.6 - - - -
393A ALA* 1.3 77.0 - - - +
395A ARG* 1.3 63.5 + - - +
397A ILE* 3.1 11.8 + - + -
398A ILE* 3.0 40.6 + - + +
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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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391A LEU 5.0 0.4 + - - -
392A ASN 4.2 8.7 + - - +
394A LEU* 1.3 78.9 - - - +
396A PHE* 1.3 98.5 + - + +
398A ILE* 3.9 7.5 - - - +
399A ALA* 2.9 30.5 + - - +
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Residues in contact with PHE 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 ASN 3.7 22.4 - - - -
393A ALA* 3.0 14.8 + - + +
395A ARG* 1.3 118.2 - - + +
397A ILE* 1.3 57.7 - - + +
399A ALA* 3.8 5.8 - - + +
400A GLY* 2.9 23.9 + - - -
406A PHE* 5.0 20.6 - + - -
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Residues in contact with ILE 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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390A LYS 5.4 2.5 - - - +
393A ALA* 3.1 25.0 + - + +
394A LEU* 3.1 12.1 + - + +
396A PHE* 1.3 78.3 - - + +
398A ILE* 1.3 69.6 + - + +
400A GLY* 3.4 1.2 + - - -
401A LYS* 3.1 24.2 + - + +
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Residues in contact with ILE 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 LEU* 3.0 38.5 + - + +
395A ARG* 3.9 7.2 - - - +
397A ILE* 1.3 83.7 - - + +
399A ALA* 1.3 64.7 + - - +
401A LYS* 3.3 6.5 + - - +
402A ASN* 3.1 23.0 + - + +
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Residues in contact with ALA 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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395A ARG 2.9 19.3 + - - +
396A PHE* 3.8 7.6 - - + +
398A ILE* 1.3 80.6 - - + +
400A GLY* 1.3 57.2 - - - +
402A ASN* 2.9 22.8 + - - +
403A GLY 3.3 0.3 + - - -
404A ARG* 3.1 43.9 + - + +
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Residues in contact with GLY 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 PHE 2.9 17.5 + - - -
397A ILE* 3.4 2.4 + - - -
398A ILE 3.4 0.2 - - - -
399A ALA* 1.3 74.7 - - - +
401A LYS* 1.3 60.8 + - - +
403A GLY* 3.3 13.2 + - - -
404A ARG 4.2 1.0 + - - -
405A LYS* 4.4 21.9 + - - +
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Residues in contact with LYS 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 ILE* 3.1 18.8 + - + +
398A ILE* 3.7 7.2 - - - +
399A ALA 3.2 0.2 - - - -
400A GLY* 1.3 76.2 - - - +
402A ASN* 1.3 56.8 + - - +
403A GLY 3.3 3.8 + - - -
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Residues in contact with ASN 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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398A ILE* 3.1 14.3 + - + +
399A ALA* 2.9 12.9 + - - +
401A LYS* 1.3 77.5 - - - +
403A GLY* 1.3 56.2 + - - +
404A ARG* 3.3 24.4 + - + +
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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
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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