Contacts of the helix formed by residues 448 - 459 (chain K) in PDB entry 5ANC
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 ARG 448 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3K LEU* 4.6 18.4 - - - +
47K SER* 5.2 9.3 + - - +
443K GLU* 4.1 15.7 + - - +
444K ARG* 3.3 41.1 + - + +
446K ARG* 3.9 0.9 - - + +
447K GLN* 1.3 92.1 - - + +
449K HIS* 1.3 64.7 + - - +
450K ALA 3.3 1.1 + - - -
451K GLU* 3.9 21.6 + - - +
452K LYS* 3.9 13.5 + - - +
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Residues in contact with HIS 449 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441K ARG* 6.0 5.5 - - + -
444K ARG* 3.0 33.5 + - + +
445K ALA* 4.1 12.5 - - + +
448K ARG* 1.3 71.7 - - - +
450K ALA* 1.3 59.1 + - - +
451K GLU 3.2 2.5 - - - -
452K LYS* 3.2 24.1 + - + +
453K LEU* 2.9 55.0 + - + +
492K PRO 4.9 0.7 - - - +
493K LYS* 4.8 14.3 - - + +
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Residues in contact with ALA 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K ALA* 5.5 0.2 - - - +
446K ARG 5.5 0.4 - - - -
447K GLN* 4.2 16.6 - - - +
448K ARG 3.3 1.0 - - - +
449K HIS* 1.3 78.1 - - - +
451K GLU* 1.3 56.7 + - - +
453K LEU* 3.2 4.3 + - - +
454K ALA* 2.9 28.6 + - - +
485K GLN* 3.6 22.9 - - - +
489K SER* 4.3 2.0 - - - -
490K MET 3.7 6.4 - - - +
491K THR 3.6 13.1 - - - +
492K PRO* 3.7 29.1 + - + +
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Residues in contact with GLU 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447K GLN 3.0 21.9 - - - +
448K ARG* 3.9 13.6 - - - +
449K HIS 3.2 0.2 - - - -
450K ALA* 1.3 78.9 - - - +
452K LYS* 1.3 69.4 + - - +
454K ALA* 3.2 5.0 + - - +
455K ALA* 2.9 29.2 + - - +
477K GLY* 4.1 17.6 - - - +
478K GLU 5.6 0.3 - - - +
481K ARG* 3.5 30.1 - - + +
482K GLY* 4.5 7.4 - - - +
485K GLN* 3.3 26.1 - - + +
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Residues in contact with LYS 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448K ARG 3.9 18.3 + - - +
449K HIS* 3.2 29.7 + - + +
451K GLU* 1.3 92.1 + - - +
453K LEU* 1.3 58.1 + - - +
455K ALA* 3.2 8.8 + - - +
456K ALA* 2.9 28.5 + - - +
476K LYS 3.9 23.3 - - - +
477K GLY* 4.3 8.4 + - - -
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Residues in contact with LEU 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449K HIS* 2.9 41.9 + - + +
450K ALA 3.2 2.2 + - - +
452K LYS* 1.3 78.0 - - - +
454K ALA* 1.3 55.6 - - - +
456K ALA* 3.2 10.6 + - + +
457K GLN* 2.9 30.2 + - - +
491K THR* 3.2 36.1 - - - +
492K PRO 3.8 4.5 - - - -
493K LYS* 3.7 29.2 - - + +
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Residues in contact with ALA 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450K ALA 2.9 13.4 + - - +
451K GLU* 3.3 11.9 - - - +
453K LEU* 1.3 75.5 - - - +
455K ALA* 1.3 62.8 + - - +
457K GLN* 3.2 5.5 + - - +
458K GLY* 3.1 23.2 + - - -
481K ARG* 3.9 24.1 + - - +
490K MET* 4.0 23.3 - - + -
491K THR* 3.8 10.9 + - - +
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Residues in contact with ALA 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451K GLU 2.9 12.9 + - - +
452K LYS* 3.2 11.2 + - - +
454K ALA* 1.3 75.7 - - - +
456K ALA* 1.3 63.7 + - - +
459K GLN* 3.4 29.1 + - - +
475K PRO 3.7 23.0 - - - +
476K LYS* 4.5 2.9 - - - -
477K GLY 4.0 14.4 - - - +
481K ARG* 4.2 14.3 - - + +
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Residues in contact with ALA 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452K LYS 2.9 12.6 + - - +
453K LEU* 3.3 16.2 - - + +
455K ALA* 1.3 78.8 - - - +
457K GLN* 1.3 62.0 + - - +
460K ALA* 3.2 27.9 + - - +
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Residues in contact with GLN 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E THR* 3.2 38.6 + - - +
131E ASN* 5.8 0.4 - - - +
132E ALA 5.2 3.2 - - - +
133E GLY* 4.5 5.9 + - - -
453K LEU 2.9 14.7 + - - +
454K ALA* 3.2 5.8 + - - +
456K ALA* 1.3 81.0 - - - +
458K GLY* 1.3 61.3 - - - +
459K GLN 3.4 0.2 + - - -
460K ALA* 4.1 3.8 + - - +
461K PRO* 4.1 10.2 - - - +
491K THR* 3.5 29.6 + - - +
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Residues in contact with GLY 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ALA 5.6 1.6 - - - -
133E GLY* 4.2 12.8 - - - +
454K ALA 3.1 11.3 + - - -
457K GLN* 1.3 79.9 - - - +
459K GLN* 1.3 76.8 + - - +
460K ALA 3.7 1.0 + - - -
462K LEU 5.5 0.2 + - - -
464K PRO* 3.6 17.7 - - - +
481K ARG* 5.0 4.3 - - - -
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Residues in contact with GLN 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455K ALA* 3.4 15.7 + - - +
456K ALA 4.1 3.1 - - - -
457K GLN 3.3 1.0 - - - -
458K GLY* 1.3 88.5 - - - +
460K ALA* 1.3 58.3 + - - +
462K LEU* 4.6 14.4 - - - +
463K GLU 5.3 0.4 - - - +
464K PRO* 3.4 32.6 - - - +
470K ALA* 4.2 26.3 + - - +
471K ILE* 4.4 5.5 - - - +
474K CYS* 5.5 11.9 - - - +
475K PRO* 4.2 20.6 - - + +
481K ARG* 3.3 30.2 + - - +
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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