Contacts of the helix formed by residues 435 - 446 (chain E) in PDB entry 4ZXB
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 CYS 435 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409E ARG 4.9 1.9 + - - -
433E LYS 3.8 2.3 + - - -
434E LEU* 1.3 74.7 - - - +
436E LEU* 1.3 65.4 + - - +
437E SER* 3.3 20.4 - - - +
438E GLU* 3.0 28.9 + - + +
439E ILE* 3.5 6.6 + - - +
463E GLY* 4.2 3.6 - - - -
466E ALA* 4.3 4.7 - - - -
467E SER 3.8 7.6 - - - -
468E CYS* 2.0 55.6 - - + -
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Residues in contact with LEU 436 (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 LEU 3.5 2.0 + - - -
435E CYS* 1.3 70.3 - - - +
437E SER* 1.3 50.7 + - - +
439E ILE* 3.1 10.0 + - + +
440E HIS* 2.7 64.1 + - + -
457E ILE* 3.8 29.2 - - + -
458E ALA 3.8 9.6 - - - +
459E LEU* 3.7 38.6 - - + +
462E ASN* 3.9 22.2 + - + +
463E GLY* 5.0 0.2 - - - -
468E CYS* 5.2 0.6 - - - -
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Residues in contact with SER 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E CYS* 3.3 18.4 - - - +
436E LEU* 1.3 76.9 - - - +
438E GLU* 1.3 59.0 + - - +
440E HIS* 3.3 8.9 + - - +
441E LYS* 2.8 49.9 + - - +
468E CYS* 5.4 2.1 - - - +
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Residues in contact with GLU 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E ARG 4.4 8.3 - - - +
410E GLN* 5.5 4.4 - - - +
411E LEU* 3.9 9.8 + - + +
412E TRP 4.6 4.0 - - - +
414E TRP* 3.4 31.5 + - - +
434E LEU* 3.9 22.9 - - + -
435E CYS* 3.0 23.6 + - + +
437E SER* 1.3 76.8 + - - +
439E ILE* 1.3 61.1 + - - +
441E LYS* 3.2 27.1 + - - +
442E MET* 2.9 25.6 + - - +
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Residues in contact with ILE 439 (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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411E LEU* 4.3 6.1 - - + -
426E LEU* 4.7 0.3 - - - +
428E PHE* 3.6 54.5 - - + -
434E LEU* 3.8 19.5 - - + -
435E CYS 3.5 8.7 + - - +
436E LEU* 3.1 12.7 + - + +
438E GLU* 1.3 76.4 - - - +
440E HIS* 1.3 64.3 + - + +
442E MET* 3.1 6.0 + - - +
443E GLU* 3.0 22.0 + - + +
457E ILE* 3.7 29.6 - - + -
462E ASN* 3.8 31.2 - - + +
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Residues in contact with HIS 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LEU* 2.7 62.1 + - + +
437E SER* 3.8 6.5 + - - +
439E ILE* 1.3 74.8 - - + +
441E LYS* 1.4 60.9 + - - +
443E GLU* 2.9 33.8 + - - +
444E GLU* 3.1 20.6 + - - +
457E ILE* 5.4 4.8 - - - +
459E LEU* 5.4 7.9 - - + +
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Residues in contact with LYS 441 (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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414E TRP* 3.6 24.8 - - + +
437E SER* 2.8 32.1 + - - +
438E GLU* 3.2 36.3 + - - +
439E ILE 3.3 0.2 - - - -
440E HIS* 1.4 69.9 - - - +
442E MET* 1.3 58.9 + - - +
444E GLU* 3.0 10.1 + - - +
445E VAL* 2.8 33.0 + - + +
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Residues in contact with MET 442 (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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400E PHE* 3.6 40.4 - - + -
411E LEU* 3.9 21.3 - - + -
412E TRP* 4.4 2.0 - - + -
414E TRP* 3.5 30.9 - - + +
419E LEU* 4.0 14.1 - - + -
421E ILE* 3.8 21.3 - - + -
426E LEU* 4.3 6.7 - - + -
428E PHE* 4.0 15.3 - - - -
438E GLU 2.9 12.1 + - - +
439E ILE* 3.1 10.1 + - - +
441E LYS* 1.3 76.8 - - - +
443E GLU* 1.3 53.0 + - - +
445E VAL* 3.9 1.1 - - - +
446E SER* 2.7 45.2 + - - +
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Residues in contact with GLU 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E LEU* 3.7 18.1 - - + +
439E ILE 3.0 15.3 + - - +
440E HIS* 2.9 40.1 - - - +
442E MET* 1.3 75.5 - - - +
444E GLU* 1.3 62.0 + - - +
447E GLY* 3.3 3.3 + - - -
448E THR* 3.1 34.2 + - - -
449E LYS* 3.3 35.6 + - + +
452E GLN* 3.0 24.7 - - - +
457E ILE* 3.9 16.2 - - + +
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Residues in contact with GLU 444 (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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440E HIS 3.1 9.2 + - - +
441E LYS* 3.0 12.4 + - - +
443E GLU* 1.3 79.3 - - - +
445E VAL* 1.3 68.4 + - + +
447E GLY* 3.6 7.1 + - - -
449E LYS* 3.0 43.9 + - + +
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Residues in contact with VAL 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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414E TRP* 3.7 47.1 - - + +
417E HIS 4.0 4.7 - - - +
418E ASN* 3.5 25.5 - - - +
419E LEU 3.5 19.5 - - - +
420E THR* 5.0 1.9 + - - -
441E LYS* 2.8 22.2 + - + +
442E MET 3.9 2.5 - - - +
444E GLU* 1.3 75.9 - - + +
446E SER* 1.3 60.7 + - - +
447E GLY 3.5 0.5 + - - -
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Residues in contact with SER 446 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E LEU* 3.0 18.6 - - - -
420E THR* 3.9 7.4 - - - +
421E ILE* 3.2 51.0 + - - +
442E MET* 2.7 29.6 + - - +
445E VAL* 1.3 73.6 - - - +
447E GLY* 1.3 59.8 + - - +
448E THR* 2.7 30.0 + - - +
451E ARG* 4.8 0.2 + - - -
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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