Contacts of the helix formed by residues 458 - 469 (chain B) in PDB entry 5DSG
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 ALA 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457B ASN* 1.3 75.1 + - - +
459B THR* 1.3 61.7 + - - +
460B PHE 3.3 0.7 - - - -
461B LYS* 3.3 11.3 + - + +
462B LYS* 3.1 27.0 + - - +
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Residues in contact with THR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASN* 3.5 25.6 - - - +
62B GLN* 4.2 17.7 + - + +
63B LEU* 3.7 17.9 - - + -
457B ASN* 2.8 12.3 + - - -
458B ALA* 1.3 76.3 - - - +
460B PHE* 1.3 55.4 + - - -
462B LYS* 3.4 6.3 + - + +
463B THR* 2.5 37.4 + - - -
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Residues in contact with PHE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.1 15.5 - - + -
56B SER* 4.2 9.4 - - - -
57B ILE* 3.7 27.8 - - + -
63B LEU* 3.7 24.9 - - + -
68B ASN* 3.7 29.4 - - - -
71B LEU* 4.7 12.1 - - + -
453B TYR* 3.8 32.8 - + + +
454B ALA* 4.8 0.2 - - - -
457B ASN* 3.6 34.5 + - + -
458B ALA 3.3 0.2 - - - -
459B THR* 1.3 78.2 - - - +
461B LYS* 1.3 57.9 - - - +
463B THR* 3.8 4.7 - - - -
464B PHE* 2.9 52.2 + + + -
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Residues in contact with LYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ALA* 4.4 15.4 - - + +
457B ASN 3.9 11.8 + - - +
458B ALA* 3.3 14.4 + - + +
459B THR 3.2 0.4 - - - -
460B PHE* 1.3 76.7 - - - +
462B LYS* 1.3 59.8 + - - +
464B PHE* 3.2 12.8 + - + +
465B ARG* 2.9 61.1 + - - +
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ALA 3.1 15.7 + - - +
459B THR* 3.8 6.3 - - + +
461B LYS* 1.3 76.8 - - - +
463B THR* 1.3 54.7 + - - +
465B ARG* 3.4 10.5 + - - +
466B HIS* 2.3 52.2 + - + -
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER* 3.6 42.2 - - - +
59B VAL* 4.3 9.4 - - + -
60B ASN* 3.3 28.4 + - + -
63B LEU* 3.5 3.4 - - - +
459B THR* 2.5 23.7 + - - +
460B PHE 3.8 3.8 - - - -
462B LYS* 1.3 73.8 - - - +
464B PHE* 1.3 61.7 + - - +
466B HIS* 3.3 5.6 + - - +
467B LEU* 2.9 36.0 + - + +
472B TYR* 4.4 9.4 + - + +
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY* 4.7 1.1 - - - -
52B LEU* 3.3 45.4 - - + +
53B VAL* 3.6 25.8 - - + -
56B SER* 3.1 26.5 - - - -
450B PRO* 4.7 3.1 - - + -
453B TYR* 5.2 0.7 - - + -
454B ALA* 3.6 35.0 - - + -
460B PHE* 2.9 34.2 + + + -
461B LYS* 3.2 10.3 + - + +
463B THR* 1.3 76.3 - - - +
465B ARG* 1.3 58.0 + - - +
467B LEU* 3.1 5.8 + - + +
468B LEU* 2.9 38.5 + - + +
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Residues in contact with ARG 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B LYS* 2.9 53.9 + - - +
462B LYS* 3.7 9.3 - - - +
464B PHE* 1.3 76.4 - - - +
466B HIS* 1.3 67.0 + - + +
467B LEU 3.5 0.2 + - - -
468B LEU* 3.6 8.6 + - - +
469B LEU* 3.5 37.0 + - + +
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Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B LYS* 2.3 46.7 + - + +
463B THR* 3.6 3.4 - - - +
464B PHE 3.2 0.4 - - - -
465B ARG* 1.3 85.1 - - + +
467B LEU* 1.3 59.3 + - - +
469B LEU* 3.8 2.3 + - - -
470B CYS 3.7 1.4 + - - -
471B GLN* 3.0 44.7 + - + +
472B TYR* 3.5 32.1 - + + -
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.0 18.2 - - + +
55B LEU* 3.8 20.4 - - + -
56B SER* 3.4 44.9 - - - +
59B VAL* 4.0 13.0 - - + -
463B THR* 2.9 17.8 + - + +
464B PHE* 3.6 4.5 - - - +
466B HIS* 1.3 74.0 - - - +
468B LEU* 1.3 62.0 + - - +
469B LEU 3.1 6.4 + - - -
470B CYS* 3.2 15.2 + - - +
471B GLN 5.0 0.2 - - - +
472B TYR* 3.6 33.7 - - + -
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 6.1 2.7 - - + -
52B LEU* 4.7 27.4 - - + -
464B PHE* 2.9 22.8 + - + +
465B ARG* 4.0 9.0 - - - +
466B HIS 3.4 0.2 - - - -
467B LEU* 1.3 77.6 - - - +
469B LEU* 1.3 66.5 + - + +
470B CYS* 3.5 4.1 + - - -
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ARG* 3.5 29.7 + - + +
466B HIS* 3.8 3.8 + - - +
467B LEU 3.1 0.8 - - - -
468B LEU* 1.3 85.1 - - + +
470B CYS* 1.3 72.2 + - - +
471B GLN* 3.3 6.3 + - + +
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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