Contacts of the helix formed by residues 464 - 479 (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 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A GLU* 3.4 24.7 + - + +
419A GLU* 3.3 35.0 - - + +
420A GLU* 5.6 5.6 + - - -
459A TYR* 2.8 26.9 + - + +
462A GLN* 3.6 33.2 + - + +
463A GLY* 1.3 73.8 - - - +
465A LEU* 1.4 57.0 + - - +
466A GLU 3.4 0.2 - - - -
467A ALA* 3.2 8.6 + - + +
468A ALA* 2.9 24.1 + - - +
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Residues in contact with LEU 465 (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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419A GLU* 3.1 2.2 + - - +
460A ARG* 3.3 46.9 - - + +
463A GLY* 3.0 22.4 + - - +
464A LYS* 1.4 71.7 - - - +
466A GLU* 1.3 60.0 + - - +
468A ALA* 3.5 5.2 - - - +
469A HIS* 2.8 53.8 + - + -
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Residues in contact with GLU 466 (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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415A ALA 4.6 0.4 - - - -
418A ARG* 3.3 60.7 + - + +
419A GLU* 2.9 21.5 + - + +
465A LEU* 1.3 76.1 - - - +
467A ALA* 1.4 52.4 + - - +
469A HIS* 3.6 9.9 + - - +
470A THR* 2.6 37.6 + - - -
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA* 3.5 31.6 + - - +
416A GLU* 4.4 2.5 - - + +
419A GLU* 3.4 12.6 - - + +
459A TYR* 3.6 26.5 - - + -
464A LYS* 3.2 13.8 + - + +
466A GLU* 1.4 75.1 - - - +
468A ALA* 1.4 63.2 + - - +
470A THR* 3.2 13.2 + - - -
471A LEU* 3.2 18.5 + - - +
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Residues in contact with ALA 468 (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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456A GLY* 3.3 28.3 - - - +
459A TYR* 3.5 3.7 - - - +
460A ARG* 3.6 31.9 - - - +
464A LYS 2.9 13.9 + - - +
465A LEU* 3.3 10.7 + - - +
467A ALA* 1.4 76.4 - - - +
469A HIS* 1.4 60.5 + - - +
471A LEU* 3.4 3.3 + - - +
472A GLU* 3.0 28.6 + - - +
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Residues in contact with HIS 469 (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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460A ARG* 2.9 31.2 + - - -
465A LEU* 2.8 46.3 + - + +
466A GLU* 4.0 11.5 + - - +
468A ALA* 1.4 69.7 - - - +
470A THR* 1.4 57.0 + - - +
472A GLU* 3.1 8.5 + - + +
473A ASP* 2.8 52.2 + - - +
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Residues in contact with THR 470 (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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411A ILE* 4.3 18.8 - - + +
414A HIS* 5.0 2.0 - - + -
415A ALA* 3.9 24.7 - - + +
418A ARG* 3.3 42.6 + - - +
466A GLU* 2.6 23.5 + - - -
467A ALA* 3.2 9.7 + - - -
469A HIS* 1.4 74.8 - - - +
471A LEU* 1.4 56.8 + - - +
473A ASP* 3.5 5.9 + - - +
474A CYS* 3.1 27.3 + - - +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.6 2.5 - - + -
411A ILE* 3.9 24.9 - - + -
412A TRP* 4.3 11.4 - - - +
415A ALA* 4.5 3.4 - - + -
452A LEU* 3.5 40.5 - - + +
455A LEU* 3.6 17.7 - - + -
456A GLY* 3.5 20.4 - - - +
459A TYR* 3.4 29.2 - - + -
467A ALA 3.2 11.1 + - - +
468A ALA 3.9 5.2 - - - +
470A THR* 1.4 70.8 - - - +
472A GLU* 1.4 59.2 + - - +
474A CYS* 3.4 6.3 + - - +
475A ALA* 3.1 28.1 + - - +
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Residues in contact with GLU 472 (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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453A ARG* 4.8 12.5 - - + +
456A GLY* 3.9 21.0 - - - -
457A ALA* 4.1 3.1 + - - +
460A ARG* 2.7 47.4 + - - -
468A ALA 3.0 20.3 + - - +
469A HIS* 3.1 8.3 + - + +
471A LEU* 1.4 72.5 - - - +
473A ASP* 1.3 57.1 + - - +
475A ALA* 3.5 7.8 + - - +
476A SER* 2.8 35.2 + - - -
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Residues in contact with ASP 473 (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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418A ARG* 5.0 6.2 + - - -
469A HIS* 2.8 40.5 + - - +
470A THR* 3.7 7.3 + - - +
472A GLU* 1.3 70.7 - - - +
474A CYS* 1.3 60.1 + - - +
476A SER* 3.2 9.7 + - - -
477A ARG* 3.0 29.5 + - - +
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Residues in contact with CYS 474 (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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411A ILE* 4.3 9.6 - - + -
441A CYS* 2.0 54.5 - - - -
442A LYS* 4.4 4.0 - - - -
443A VAL* 5.2 4.9 + - - -
449A ASN* 5.3 0.3 + - - -
452A LEU* 4.0 25.4 - - + +
470A THR 3.1 14.5 + - - +
471A LEU* 3.4 13.2 + - - +
473A ASP* 1.3 77.8 - - - +
475A ALA* 1.3 59.3 + - - +
477A ARG* 3.5 15.9 + - - +
478A SER* 3.9 5.2 + - - -
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Residues in contact with ALA 475 (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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449A ASN* 3.0 38.0 - - - +
452A LEU* 4.3 8.5 - - + +
453A ARG* 3.7 36.2 + - + +
471A LEU 3.1 15.6 + - - +
472A GLU 3.6 6.3 - - - +
474A CYS* 1.3 77.6 - - - +
476A SER* 1.3 60.5 + - - +
477A ARG 3.6 0.3 + - - -
478A SER* 3.6 12.1 + - - -
479A ARG* 3.9 2.4 + - - +
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 4.9 5.2 + - - +
472A GLU 2.8 19.5 + - - -
473A ASP* 3.2 12.4 + - - -
475A ALA* 1.3 75.7 - - - +
477A ARG* 1.4 62.8 - - - +
478A SER 3.3 0.2 - - - -
479A ARG* 3.2 23.4 + - - +
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Residues in contact with ARG 477 (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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441A CYS* 5.4 2.9 - - - -
442A LYS* 3.8 46.5 + - + +
473A ASP 3.0 12.4 + - - +
474A CYS* 3.6 14.1 - - - +
475A ALA 3.4 0.8 - - - -
476A SER* 1.4 77.4 - - - +
478A SER* 1.4 61.0 + - - +
479A ARG 3.5 4.0 + - - +
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Residues in contact with SER 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS* 3.9 24.4 + - - +
443A VAL 4.6 6.1 - - - -
444A ASP* 4.5 16.7 + - - +
449A ASN* 3.5 29.3 + - - -
474A CYS 3.9 4.6 + - - -
475A ALA 3.6 5.3 + - - -
476A SER 3.3 0.4 - - - -
477A ARG* 1.4 78.6 - - - +
479A ARG* 1.4 70.3 + - - +
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Residues in contact with ARG 479 (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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444A ASP 5.5 1.4 + - - -
445A SER 5.0 0.4 - - - -
446A PRO* 3.6 35.6 + - - +
449A ASN* 3.7 21.5 + - - +
453A ARG* 3.5 31.9 - - - +
475A ALA 3.9 4.3 - - - +
476A SER* 3.2 19.1 + - - +
477A ARG 4.3 3.6 - - - +
478A SER* 1.4 92.8 + - - +
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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