Contacts of the helix formed by residues 417 - 430 (chain E) in PDB entry 5ZR1
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 417 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C LYS* 3.5 26.3 - - - +
480C PHE* 4.4 7.5 + - - +
481C PRO 3.5 16.8 - - - +
482C SER* 3.8 16.4 - - - +
483C TYR 4.6 2.0 - - - -
414E MET* 4.1 10.9 - - - +
415E LYS 3.2 6.9 + - - +
416E ALA* 1.3 78.0 - - - +
418E ILE* 1.3 64.8 + - - +
419E GLU* 3.2 21.1 + - - +
420E VAL* 3.4 25.7 + - - +
421E PHE* 3.6 14.2 + - - -
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Residues in contact with ILE 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B PRO* 3.6 36.6 - - + +
465B TRP* 5.5 1.3 - - + -
477B PHE* 3.8 35.9 - - + -
479C ILE 3.8 7.6 - - - +
480C PHE* 3.7 33.9 - - + -
481C PRO* 2.9 19.4 + - + +
483C TYR* 4.0 14.8 - - + -
417E ASN* 1.3 77.3 - - - +
419E GLU* 1.3 61.1 + - + +
420E VAL 3.5 0.2 - - - -
421E PHE* 3.9 2.5 + - - +
422E GLN* 3.2 32.8 + - - +
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Residues in contact with GLU 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LYS* 3.3 34.5 + - - +
308C ASN* 2.9 34.2 + - + +
309C ASN* 5.8 2.8 - - + +
480C PHE* 3.2 40.6 - - + -
327E ILE* 4.1 5.5 - - + +
414E MET* 5.7 1.0 - - - +
417E ASN* 3.1 12.6 + - - +
418E ILE* 1.3 78.6 - - + +
420E VAL* 1.3 60.4 + - - +
421E PHE 3.3 0.4 - - - -
422E GLN* 4.1 12.1 - - - +
423E ASN* 2.9 45.9 + - - +
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Residues in contact with VAL 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E ILE* 4.0 12.3 - - + -
331E LEU* 3.8 13.3 - - + +
387E LEU* 3.9 27.6 - - + -
390E PHE* 4.0 22.4 - - + -
414E MET* 3.8 21.8 - - + -
416E ALA* 4.0 14.1 - - + -
417E ASN* 3.4 28.8 + - - +
419E GLU* 1.3 77.0 - - - +
421E PHE* 1.3 56.5 + - + +
423E ASN* 4.8 0.9 - - - -
424E LEU* 3.0 27.9 + - - +
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Residues in contact with PHE 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE 5.0 2.9 - - - -
460B TYR* 3.5 39.5 - + + -
462B PRO* 3.5 37.7 - - + +
463B LEU* 3.8 32.8 - - + -
483C TYR* 5.6 1.1 - - + -
484C LYS* 3.8 17.9 - - + -
383E ILE* 5.1 3.1 - - + -
387E LEU* 3.8 26.7 - - + -
416E ALA* 3.8 24.0 - - + -
417E ASN 3.6 13.8 + - - -
418E ILE 4.3 1.1 - - - +
419E GLU 3.3 0.2 - - - -
420E VAL* 1.3 75.4 - - + +
422E GLN* 1.3 61.1 + - - +
424E LEU* 3.9 7.6 - - + +
425E SER* 3.1 28.1 + - - -
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Residues in contact with GLN 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B PRO 4.1 1.7 + - - +
465B TRP 3.8 11.2 - - - +
466B ASP* 3.9 13.4 - - - +
467B ASN* 2.7 32.6 + - - +
470B ALA* 3.4 27.1 - - + +
309C ASN* 4.0 13.7 + - - +
480C PHE* 5.6 3.1 - - - -
418E ILE* 3.2 27.4 + - - +
419E GLU* 3.8 15.9 - - - +
420E VAL 3.4 0.2 - - - -
421E PHE* 1.3 76.3 - - - +
423E ASN* 1.3 59.9 + - - +
425E SER* 3.6 2.3 + - - -
426E GLU* 3.0 26.3 + - - +
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Residues in contact with ASN 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASN* 4.2 18.5 + - - +
308C ASN 3.1 26.3 + - - +
309C ASN* 4.9 1.6 - - - +
325E SER* 4.4 1.4 - - - -
327E ILE* 3.4 25.7 - - + +
328E SER* 3.2 28.6 + - - +
331E LEU* 4.2 6.9 - - + +
419E GLU* 2.9 27.5 + - - +
420E VAL 4.1 2.5 - - - +
422E GLN* 1.3 75.9 - - - +
424E LEU* 1.3 60.6 + - - +
426E GLU* 3.8 5.5 - - - +
427E LEU* 3.1 28.4 + - - +
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Residues in contact with LEU 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 3.7 21.5 - - + -
331E LEU* 3.8 19.3 - - + +
383E ILE* 3.9 22.4 - - + -
386E LEU* 3.7 28.9 - - + -
387E LEU* 4.2 20.0 - - + -
420E VAL 3.0 16.6 + - - +
421E PHE* 3.9 8.3 - - + +
422E GLN 3.4 0.4 - - - -
423E ASN* 1.3 76.5 - - - +
425E SER* 1.3 61.4 + - - +
427E LEU* 3.5 7.4 + - + +
428E HIS* 3.3 18.4 + - - +
433E ILE* 5.0 7.8 - - + +
450E TRP* 4.6 17.5 - - + -
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Residues in contact with SER 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 3.3 30.5 + - - +
464B LEU 4.4 1.7 + - - -
465B TRP 3.7 13.6 + - - -
466B ASP* 3.4 18.0 + - - +
421E PHE 3.1 15.3 + - - -
422E GLN 3.9 0.9 - - - -
424E LEU* 1.3 75.6 - - - +
426E GLU* 1.3 63.6 + - - +
428E HIS* 3.3 8.2 + - - +
429E THR* 3.2 25.5 + - - +
443E TYR* 4.7 11.7 + - - -
450E TRP* 6.3 0.4 - - - -
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Residues in contact with GLU 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ASP* 3.4 12.1 - - - +
467B ASN* 3.0 49.0 + - - +
468B MET* 4.1 2.3 + - - +
241C ASN* 4.2 1.6 + - - -
311C ASN* 3.6 19.6 + - + +
312C HIS* 5.7 0.2 - - - -
324E LEU* 6.3 1.1 - - + -
328E SER* 6.0 0.2 - - - +
422E GLN 3.0 19.2 + - - +
423E ASN* 4.0 7.9 - - - +
425E SER* 1.3 75.7 - - - +
427E LEU* 1.3 62.5 + - - +
429E THR* 3.0 18.0 + - - -
430E LEU* 3.3 40.5 + - + +
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Residues in contact with LEU 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E LEU* 4.1 14.8 - - + -
328E SER* 4.2 14.4 - - - +
331E LEU* 4.1 24.2 - - + +
332E LEU* 3.7 38.1 - - + +
335E SER* 4.9 0.2 - - - +
423E ASN 3.1 18.3 + - - +
424E LEU* 3.6 8.3 - - + +
425E SER 3.2 0.2 - - - -
426E GLU* 1.3 77.1 - - - +
428E HIS* 1.3 57.9 + - - +
430E LEU* 3.9 4.4 + - + -
431E LYS 3.9 1.0 + - - -
432E LEU* 3.1 46.1 + - + +
433E ILE* 3.2 29.6 + - + -
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Residues in contact with HIS 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E LEU 3.3 12.5 + - - +
425E SER* 3.6 10.8 - - - +
426E GLU 3.2 0.8 - - - -
427E LEU* 1.3 75.6 - - - +
429E THR* 1.3 66.0 + - - +
430E LEU 3.2 1.8 - - - -
431E LYS* 3.3 22.0 + - + +
433E ILE* 3.4 27.8 - - + +
434E ALA* 4.8 1.3 - - - -
435E THR* 3.8 22.8 + - + +
441E ILE* 4.6 10.4 - - + +
443E TYR* 3.3 32.8 + + + -
450E TRP* 3.4 30.0 - + + -
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Residues in contact with THR 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B ASP* 3.4 27.2 + - + +
210C SER* 3.4 22.0 + - - -
425E SER* 3.2 13.2 + - - +
426E GLU* 3.0 21.1 + - - -
428E HIS* 1.3 83.7 - - - +
430E LEU* 1.3 67.7 + - - +
431E LYS* 3.2 15.0 + - - +
443E TYR* 4.7 7.6 - - - +
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Residues in contact with LEU 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ASP* 4.1 18.3 - - + +
241C ASN* 4.0 16.2 - - - +
242C THR* 3.7 30.9 - - + +
246C ASN* 5.1 3.3 + - - -
311C ASN* 6.2 0.2 - - - +
324E LEU* 4.2 22.9 - - + -
426E GLU* 3.3 48.6 + - + +
427E LEU* 4.2 6.7 - - - +
428E HIS 3.2 0.8 - - - -
429E THR* 1.3 84.3 + - - +
431E LYS* 1.3 69.9 + - - +
432E LEU* 3.2 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
------------------------------------------------------------
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