Contacts of the helix formed by residues 473 - 484 (chain E) in PDB entry 5CBZ
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 473 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456E LEU 5.0 0.2 - - - -
457E CYS* 3.8 18.6 - - - -
458E ALA 4.8 1.8 - - - -
463E CYS* 3.8 17.9 - - + -
465E ILE* 3.5 8.4 - - + +
469E ARG 3.8 2.4 + - - -
470E ARG 3.8 5.9 + - - -
471E LYS 3.4 0.8 - - - -
472E ASN* 1.3 83.9 - - + +
474E PRO* 1.3 65.1 - - - +
475E ALA 3.1 3.8 - - - -
476E CYS* 3.1 12.9 + - + -
477E ARG* 2.9 18.7 + - - +
502E ZN 2.3 37.5 - - - -
458F ALA* 5.3 0.4 - - + -
472F ASN* 4.8 4.7 - - - +
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Residues in contact with PRO 474 (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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444E PHE* 3.5 11.0 - - + -
455E TYR* 3.3 47.1 - - + -
456E LEU 5.8 0.4 - - - +
470E ARG 4.1 2.9 - - - +
471E LYS 3.3 17.0 - - - +
472E ASN 3.4 4.9 - - - +
473E CYS* 1.3 87.5 - - - +
475E ALA* 1.3 57.3 + - - +
477E ARG* 3.4 9.6 - - + +
478E LEU* 2.9 27.9 + - - +
472F ASN* 5.1 8.7 - - - +
11H C 5.5 0.2 - - - +
12H T 3.6 15.5 - - - +
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Residues in contact with ALA 475 (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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455E TYR* 3.7 19.1 - - + +
456E LEU* 3.8 9.0 - - - +
457E CYS* 3.5 34.1 - - + +
461E ASN* 5.9 1.3 - - - +
473E CYS* 3.1 2.2 - - - -
474E PRO* 1.3 81.6 - - - +
476E CYS* 1.3 61.6 - - - +
478E LEU* 3.4 6.1 + - - +
479E ARG* 3.1 23.0 + - - +
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Residues in contact with CYS 476 (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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457E CYS* 3.6 4.3 - - - -
461E ASN* 3.5 14.4 - - - -
463E CYS* 3.4 16.4 - - + +
465E ILE* 3.9 16.6 - - + -
473E CYS* 3.1 9.9 + - - +
475E ALA* 1.3 75.7 - - - +
477E ARG* 1.3 65.8 + - - +
479E ARG* 3.4 30.1 + - - +
480E LYS* 2.9 28.1 + - - +
502E ZN 2.2 35.2 - - - -
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Residues in contact with ARG 477 (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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423E VAL* 4.0 10.9 - - + +
440E SER* 3.0 36.4 + - - -
441E CYS* 3.3 25.5 - - - -
444E PHE* 3.4 43.4 - - + -
465E ILE* 3.8 18.3 - - + +
470E ARG* 3.5 37.5 + - - +
471E LYS* 5.4 0.2 - - - +
473E CYS 2.9 13.6 + - - +
474E PRO* 3.4 10.8 - - + +
476E CYS* 1.3 78.8 - - - +
478E LEU* 1.3 56.3 + - - +
480E LYS* 3.3 4.9 + - - +
481E CYS* 3.0 30.6 + - - -
12H T 4.4 7.3 + - - -
13H G 2.7 23.8 + - - -
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Residues in contact with LEU 478 (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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478A LEU* 5.9 4.0 - - + -
482A LEU* 6.0 2.2 - - + -
444E PHE* 3.9 12.3 - - + -
445E PHE* 4.1 25.6 - - + -
448E ALA* 3.9 32.5 - - + +
449E VAL* 5.4 1.1 - - - +
455E TYR* 4.6 12.8 - - + -
474E PRO 2.9 15.7 + - - +
475E ALA* 3.9 5.4 - - - +
477E ARG* 1.3 73.4 - - - +
479E ARG* 1.3 68.7 + - - +
481E CYS* 3.1 4.5 + - - +
482E LEU* 3.0 38.7 + - + +
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Residues in contact with ARG 479 (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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451A GLY 4.1 11.2 - - - +
452A GLN* 4.2 17.7 - - - +
461E ASN* 2.8 34.8 + - - +
462E ASP* 4.1 8.1 + - - +
463E CYS 4.4 1.2 - - - +
475E ALA 3.1 17.1 + - - +
476E CYS* 3.4 32.3 + - - +
478E LEU* 1.3 76.2 - - - +
480E LYS* 1.3 79.9 + - - +
482E LEU* 3.2 8.1 + - - +
483E GLN* 2.8 69.4 + - + +
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Residues in contact with LYS 480 (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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422E LEU 5.8 0.7 - - - +
423E VAL* 3.8 30.5 - - + +
462E ASP* 5.9 1.2 + - - -
463E CYS 4.0 12.9 + - - -
465E ILE* 3.5 36.6 - - + +
476E CYS 2.9 16.7 + - - +
477E ARG 3.6 4.0 - - - +
478E LEU 3.1 0.2 - - - -
479E ARG* 1.3 97.7 - - - +
481E CYS* 1.3 62.9 + - - +
483E GLN* 3.8 7.8 - - - +
484E ALA* 2.9 27.3 + - - +
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Residues in contact with CYS 481 (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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423E VAL* 3.9 19.7 - - - +
441E CYS* 4.7 5.2 - - - -
444E PHE* 4.2 21.1 - - - -
445E PHE* 3.7 20.2 - - + -
477E ARG* 3.0 23.1 + - - -
478E LEU* 3.4 7.4 - - - +
480E LYS* 1.3 75.2 - - - +
482E LEU* 1.3 60.8 + - - +
484E ALA* 3.4 1.7 + - - +
485E GLY 3.3 3.8 + - - -
486E MET* 3.0 56.4 + - - +
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Residues in contact with LEU 482 (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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448A ALA 4.9 2.5 - - - +
449A VAL* 3.2 44.6 - - + +
478A LEU* 4.0 26.9 - - + -
482A LEU* 3.9 28.5 - - + -
445E PHE* 3.9 19.7 - - + -
478E LEU* 3.0 36.3 + - + +
479E ARG* 3.6 9.0 - - - +
481E CYS* 1.3 75.2 - - - +
483E GLN* 1.3 60.5 + - - +
485E GLY* 2.8 19.4 + - - -
486E MET 4.0 8.0 - - - +
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Residues in contact with GLN 483 (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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449A VAL* 3.3 19.7 - - - +
450A GLU* 3.0 25.8 + - - +
451A GLY 3.1 16.8 + - - -
452A GLN* 5.2 0.6 - - - +
479E ARG* 2.8 56.4 + - + +
480E LYS* 4.0 6.1 - - - +
482E LEU* 1.3 72.3 - - - +
484E ALA* 1.3 59.2 + - - +
485E GLY 3.5 0.7 + - - -
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Residues in contact with ALA 484 (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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422E LEU* 4.9 17.8 - - + +
423E VAL* 5.0 3.4 - - + -
435E VAL* 3.2 31.0 - - + +
480E LYS 2.9 18.9 + - - +
481E CYS* 3.7 7.2 - - - +
482E LEU 3.1 0.2 - - - -
483E GLN* 1.3 78.7 - - - +
485E GLY* 1.3 56.4 + - - +
486E MET 3.7 0.7 - - - -
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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