Contacts of the helix formed by residues 445 - 454 (chain A) in PDB entry 5ODS
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 LYS 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A LEU* 4.5 7.4 - - + -
443A GLY* 4.2 12.5 + - - -
444A ARG* 1.3 78.6 - - - +
446A GLN* 1.3 67.5 + - - +
447A LEU 3.2 2.9 - - - -
448A LEU* 3.2 30.6 + - + +
449A GLU* 3.9 2.8 + - - +
470A VAL* 3.2 35.7 + - + +
471A ASP* 4.3 23.3 - - + +
474A LEU* 3.9 18.6 - - + +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ARG* 4.8 0.2 - - - +
445A LYS* 1.3 78.6 - - - +
447A LEU* 1.3 56.3 + - - +
449A GLU* 2.9 46.2 + - - +
450A LYS* 3.7 2.9 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A VAL* 4.3 18.6 - - + -
444A ARG* 5.3 8.5 - - + -
445A LYS 3.2 0.8 - - - +
446A GLN* 1.3 77.7 - - - +
448A LEU* 1.3 61.7 + - - +
450A LYS* 3.4 9.7 + - + +
451A TRP* 3.2 63.5 + - + -
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A CYS* 4.1 19.7 - - + -
439A VAL* 4.3 11.7 - - + -
440A LEU* 4.0 18.6 - - + -
444A ARG 4.3 3.4 - - - +
445A LYS* 3.2 35.9 + - + +
446A GLN 3.1 0.2 - - - -
447A LEU* 1.3 79.4 - - - +
449A GLU* 1.3 56.5 + - - +
451A TRP* 3.2 16.1 + - + -
452A LEU* 2.8 53.6 + - + +
457A LEU* 6.1 0.4 - - + -
463A LEU* 5.6 2.0 - - + -
467A VAL* 3.7 28.9 - - + -
474A LEU* 4.0 16.2 - - + -
478A VAL* 5.4 1.8 - - + -
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A LYS 4.7 2.6 - - - +
446A GLN* 2.9 32.0 + - - +
448A LEU* 1.3 78.1 - - - +
450A LYS* 1.3 56.9 + - - +
452A LEU* 4.0 3.3 - - - +
453A LYS* 3.0 32.1 + - - +
474A LEU* 4.5 20.0 - - + +
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Residues in contact with LYS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLN 3.7 2.7 + - - +
447A LEU* 3.4 12.6 + - + +
448A LEU 3.3 0.4 - - - -
449A GLU* 1.3 76.0 - - - +
451A TRP* 1.3 63.2 + - + +
453A LYS* 3.4 3.8 + - - +
454A GLU* 2.9 40.0 + - - +
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Residues in contact with TRP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LEU* 3.7 20.8 - - + +
435A LEU* 4.5 30.7 - - + -
436A CYS* 5.1 5.4 - - - -
439A VAL* 4.3 27.1 - - + -
447A LEU* 3.2 61.2 + - + +
448A LEU* 3.2 19.6 + - + +
450A LYS* 1.3 82.9 - - + +
452A LEU* 1.3 57.2 + - + +
455A ASP 3.0 20.4 + - - -
456A LYS* 3.3 43.4 + - + +
457A LEU* 3.4 21.0 - - + +
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A LEU* 2.8 54.4 + - + +
449A GLU* 4.2 2.7 - - - +
451A TRP* 1.3 71.1 - - + +
453A LYS* 1.3 62.5 + - - +
455A ASP* 2.8 28.8 + - - +
457A LEU* 4.5 23.3 - - + -
459A CYS* 5.9 3.6 - - - -
474A LEU* 4.9 7.0 - - + -
477A SER* 3.9 13.5 - - - +
478A VAL* 3.7 32.3 - - + +
481A ARG* 3.6 38.6 + - - +
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLU 3.0 20.7 + - - +
450A LYS* 3.9 4.3 - - - +
452A LEU* 1.3 76.1 - - - +
454A GLU* 1.3 58.9 + - - +
455A ASP* 3.1 17.2 - - - +
481A ARG* 4.7 7.2 + - - +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A LYS* 2.9 21.9 + - - +
453A LYS* 1.3 74.7 - - - +
455A ASP* 1.3 70.7 + - - +
456A LYS* 3.1 41.9 + - + +
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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