Contacts of the helix formed by residues 498 - 507 (chain E) in PDB entry 4CYM
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 498 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468E HIS* 3.8 2.2 - - - -
489E VAL 4.0 11.0 - - - +
490E ASN* 4.0 17.8 + - - +
491E ALA 3.5 4.2 + - - -
492E THR* 3.9 7.8 - - - +
497E ALA* 1.3 74.9 - - - +
499E PRO* 1.3 80.5 - - + +
500E LEU* 3.4 24.2 - - + +
501E HIS* 2.8 32.1 + - + +
502E LEU* 3.1 11.1 + - - +
520E ALA* 5.3 0.9 - - + -
521E SER 4.8 5.2 - - - +
524E VAL* 3.7 22.6 - - - +
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Residues in contact with PRO 499 (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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467E LEU* 3.9 37.0 - - + +
468E HIS* 3.5 26.6 - - + +
471E ALA* 3.8 15.3 - - + +
488E MET 5.1 1.1 - - - +
489E VAL 3.5 15.7 - - - +
491E ALA* 3.4 16.4 - - + +
498E THR* 1.3 88.4 - - + +
500E LEU* 1.3 56.9 + - - +
502E LEU* 3.0 7.0 + - + +
503E ALA* 2.9 25.5 + - - +
515E LEU* 3.8 12.3 - - + -
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Residues in contact with LEU 500 (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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498E THR* 3.1 15.6 - - + +
499E PRO* 1.3 81.0 - - - +
501E HIS* 1.3 60.0 + - - +
503E ALA* 3.4 0.7 + - - +
504E CYS* 3.0 25.4 + - - +
512E THR* 3.8 44.2 - - + +
515E LEU* 3.6 16.4 - - + +
516E LEU* 4.0 18.4 - - + -
520E ALA* 4.2 9.9 - - + -
521E SER 3.6 23.1 - - - +
522E ALA* 3.9 10.8 - - - -
532E PRO* 3.7 21.5 - - + -
548E LEU* 4.3 3.6 - - + -
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Residues in contact with HIS 501 (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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496E GLY 4.1 6.7 - - - -
497E ALA* 4.0 11.4 - - + -
498E THR* 2.8 36.8 + - - +
500E LEU* 1.3 74.2 - - - +
502E LEU* 1.3 64.2 + - + +
504E CYS* 3.4 1.0 + - - +
505E GLN* 3.1 24.8 + - - +
524E VAL* 3.0 40.4 + - + -
526E ASP* 3.9 11.2 + - + -
530E ASN 2.6 28.6 + - - -
531E THR 3.8 0.2 - - - -
532E PRO* 3.5 29.0 - - + +
535E LEU* 3.6 26.5 - - + +
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Residues in contact with LEU 502 (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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464E HIS* 4.7 11.9 - - + +
468E HIS* 3.5 50.9 - - + +
471E ALA* 4.8 0.9 - - + -
472E VAL* 4.2 26.9 - - + -
493E ASP* 5.2 3.4 - - - +
497E ALA* 4.5 15.5 - - + -
498E THR 3.7 7.9 - - - +
499E PRO* 3.0 7.1 + - + +
501E HIS* 1.3 74.9 - - + +
503E ALA* 1.3 65.9 + - - +
505E GLN* 3.3 19.9 + - - +
506E LYS* 3.1 29.2 + - - +
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Residues in contact with ALA 503 (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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471E ALA* 4.7 7.9 - - + +
499E PRO 2.9 17.9 + - - +
500E LEU 3.8 3.8 - - - +
502E LEU* 1.3 71.7 - - - +
504E CYS* 1.3 58.2 + - - +
506E LYS* 3.2 5.1 + - - -
507E GLY 2.8 25.3 + - - -
508E TYR* 3.2 13.6 + - + +
511E VAL* 3.5 33.7 - - + -
512E THR* 3.6 18.4 - - - +
515E LEU* 4.2 4.0 - - + -
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Residues in contact with CYS 504 (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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500E LEU* 3.0 22.5 + - - +
501E HIS 4.1 2.2 - - - +
502E LEU 3.3 0.2 - - - -
503E ALA* 1.3 71.9 - - - +
505E GLN* 1.3 64.1 + - - +
507E GLY* 3.6 5.3 + - - +
512E THR* 3.7 27.1 - - - -
532E PRO* 3.4 28.9 - - + +
535E LEU* 4.9 0.2 - - + -
536E ALA* 3.6 23.8 - - + +
541E HIS* 3.9 7.6 + - - +
544E CYS* 4.4 9.6 - - - -
548E LEU* 3.6 27.6 - - - -
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Residues in contact with GLN 505 (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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501E HIS 3.1 16.2 + - - +
502E LEU* 3.5 23.0 + - - +
504E CYS* 1.3 77.5 - - - +
506E LYS* 1.3 64.3 + - + +
535E LEU* 4.3 24.5 - - + +
539E TYR* 3.2 44.6 + - + -
541E HIS* 3.0 24.1 + - - -
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Residues in contact with LYS 506 (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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472E VAL* 3.2 46.2 + - + +
502E LEU 3.1 17.7 + - - +
503E ALA* 3.8 1.8 - - - +
505E GLN* 1.3 86.6 - - + +
507E GLY* 1.3 58.9 + - - +
508E TYR* 3.2 45.4 + - + -
541E HIS* 3.4 8.7 + - - -
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Residues in contact with GLY 507 (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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503E ALA 2.8 9.9 + - - -
504E CYS 3.6 1.0 + - - -
505E GLN 3.2 3.8 - - - -
506E LYS* 1.3 77.8 - - - +
508E TYR* 1.3 59.5 + - - -
509E GLN 3.3 6.8 + - - -
541E HIS* 2.8 29.4 - - - -
543E ASP* 3.9 10.7 - - - +
544E CYS* 3.5 11.4 - - - -
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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