Contacts of the helix formed by residues 444 - 459 (chain E) in PDB entry 3ZXR
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 THR 444 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E SER* 3.9 16.0 + - - -
114E LYS* 4.0 10.3 - - - +
438E THR* 4.7 0.9 - - - -
441E GLY* 3.7 23.6 - - - +
442E VAL 4.2 0.4 + - - -
443E PHE* 1.3 74.5 - - - +
445E ASN* 1.3 66.4 + - - +
446E ASP* 2.5 28.1 + - - +
447E LEU* 3.0 21.4 + - - +
448E ILE* 3.2 15.2 + - - +
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Residues in contact with ASN 445 (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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434E HIS* 3.5 23.8 + - - -
435E GLU* 5.5 0.5 - - - +
438E THR* 3.9 14.0 - - - +
444E THR* 1.3 73.2 - - - +
446E ASP* 1.3 56.3 + - - +
448E ILE* 3.8 5.6 - - - +
449E GLU* 2.8 48.2 + - - +
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Residues in contact with ASP 446 (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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105E SER* 2.6 28.5 + - - -
106E ARG* 2.9 25.9 + - - +
444E THR* 2.5 29.0 + - - -
445E ASN* 1.3 74.7 - - - +
447E LEU* 1.3 63.6 + - - +
449E GLU* 4.1 10.5 + - - +
450E THR* 2.7 33.8 + - - +
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Residues in contact with LEU 447 (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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28E LEU* 3.8 30.5 - - + -
105E SER 3.9 11.2 - - - +
106E ARG* 4.0 13.5 - - + -
111E ILE* 3.4 35.9 - - + -
319E PHE* 4.8 6.1 - - + -
378E LEU* 4.6 10.8 - - + -
443E PHE* 3.7 30.5 - - + -
444E THR* 3.0 18.0 + - - +
446E ASP* 1.3 82.2 - - - +
448E ILE* 1.3 57.0 + - + +
450E THR* 3.3 2.8 + - - -
451E TRP* 2.9 30.8 + - + +
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Residues in contact with ILE 448 (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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319E PHE* 4.6 8.7 - - + -
430E LEU* 4.1 16.3 - - + +
434E HIS* 3.7 44.0 - - + +
437E LEU* 4.3 6.3 - - + -
438E THR* 3.8 18.6 - - + -
443E PHE* 3.9 28.5 - - + -
444E THR 3.2 8.8 + - - +
445E ASN* 3.9 7.4 - - - +
447E LEU* 1.3 78.5 - - - +
449E GLU* 1.3 58.7 + - + +
451E TRP* 3.3 6.6 + - - +
452E ILE* 2.9 47.3 + - + +
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Residues in contact with GLU 449 (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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445E ASN* 2.8 33.6 + - - +
446E ASP* 4.1 7.0 - - - +
448E ILE* 1.3 78.8 - - + +
450E THR* 1.3 56.4 + - - +
452E ILE* 3.4 10.4 + - + +
453E SER* 2.9 31.8 + - - -
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Residues in contact with THR 450 (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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28E LEU* 3.7 20.0 - - + -
60E GLY* 3.8 24.0 - - - +
106E ARG* 3.5 18.2 + - - +
446E ASP 2.7 23.4 + - - -
447E LEU 3.3 3.8 + - - -
449E GLU* 1.3 72.7 - - - +
451E TRP* 1.3 56.6 + - - +
453E SER* 3.7 5.4 - - - -
454E PHE* 2.8 35.5 + - + +
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Residues in contact with TRP 451 (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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28E LEU* 3.4 43.5 - - + +
29E PRO* 4.1 15.7 - - + -
318E ALA 3.0 29.9 + - - -
319E PHE* 3.4 35.6 - + + -
322E PRO* 3.7 12.6 - - + -
375E ASN* 4.7 4.3 - - + -
378E LEU* 3.5 22.7 - - + -
427E ILE* 4.2 8.3 - - + +
430E LEU* 3.9 15.0 - - + -
447E LEU* 2.9 18.9 + - + +
448E ILE* 3.5 5.8 - - - +
450E THR* 1.3 73.2 - - - +
452E ILE* 1.3 65.2 + - - +
454E PHE* 3.2 7.8 + + + +
455E LYS* 3.0 59.4 + - - +
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Residues in contact with ILE 452 (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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427E ILE* 3.7 21.8 - - + +
430E LEU* 3.9 16.2 - - + -
431E GLU* 3.5 39.5 - - + +
434E HIS* 5.7 0.7 - - + -
448E ILE* 2.9 37.7 + - + +
449E GLU* 3.7 10.1 - - + +
451E TRP* 1.3 75.9 - - - +
453E SER* 1.3 65.9 + - - +
455E LYS* 3.4 1.9 + - - +
456E ARG* 3.1 62.4 + - - +
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Residues in contact with SER 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E GLU 2.9 18.9 + - - -
450E THR* 3.7 6.3 - - - -
452E ILE* 1.3 78.4 - - - +
454E PHE* 1.3 62.5 + - - +
456E ARG* 3.4 5.5 + - - +
457E GLU* 3.1 48.1 + - - +
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Residues in contact with PHE 454 (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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28E LEU* 5.8 2.7 - - + -
29E PRO* 3.8 27.8 - - + -
59E ARG* 3.9 42.2 - - + -
60E GLY* 4.9 9.2 - - - -
450E THR* 2.8 26.6 + - + +
451E TRP* 3.2 7.4 + + + +
453E SER* 1.3 72.3 + - - +
455E LYS* 1.3 69.0 + - + +
457E GLU* 5.2 0.7 - - - -
458E ASN* 2.9 73.5 + - + +
459E GLU* 3.4 24.9 - - + -
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Residues in contact with LYS 455 (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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29E PRO* 5.3 7.6 + - - +
322E PRO* 2.9 32.9 + - - +
323E THR* 4.4 5.1 - - - +
373E SER 5.3 1.2 + - - -
374E GLY* 5.8 0.2 - - - -
423E LEU* 4.4 2.9 - - + -
427E ILE* 4.0 30.3 - - + -
451E TRP* 3.0 55.7 + - - +
452E ILE 3.9 3.4 - - - +
454E PHE* 1.3 85.2 - - + +
456E ARG* 1.3 59.5 + - - +
459E GLU* 2.8 42.7 + - - +
460E ILE* 2.9 32.1 + - + +
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Residues in contact with ARG 456 (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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427E ILE* 3.7 9.9 + - + +
428E ASP* 2.9 37.1 + - - +
431E GLU* 2.9 42.6 + - - -
452E ILE* 3.1 34.3 + - - +
453E SER* 3.8 5.4 - - - +
455E LYS* 1.3 77.4 - - - +
457E GLU* 1.3 62.3 + - + +
460E ILE* 3.8 22.3 - - + +
461E GLU* 3.0 34.7 + - - +
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Residues in contact with GLU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453E SER* 3.1 33.7 + - - +
454E PHE* 5.7 0.2 - - - -
456E ARG* 1.3 81.5 - - + +
458E ASN* 1.3 67.7 + - - +
461E GLU* 4.5 14.2 - - - +
462E PRO* 3.4 16.9 - - - +
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Residues in contact with ASN 458 (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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454E PHE* 2.9 65.4 + - + +
457E GLU* 1.3 84.7 + - - +
459E GLU* 1.3 62.6 + - + +
462E PRO* 3.5 16.9 - - - +
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Residues in contact with GLU 459 (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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29E PRO* 5.6 0.9 - - - +
322E PRO 3.4 10.2 - - - +
323E THR* 3.7 17.9 - - - +
324E VAL* 4.2 12.8 + - + -
423E LEU* 3.8 3.4 - - + +
454E PHE* 3.4 16.1 - - + -
455E LYS* 2.8 51.9 + - - +
458E ASN* 1.3 87.6 - - + +
460E ILE* 1.3 70.3 + - - +
461E GLU 3.5 0.9 - - - -
462E PRO* 3.4 3.1 - - - +
463E VAL* 3.2 28.8 + - + +
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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