Contacts of the helix formed by residues 450 - 459 (chain J) in PDB entry 5LS6
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 ASN 450 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317J ASN* 4.8 19.8 + - - +
447J TYR* 3.4 36.9 + - + +
448J TYR 3.3 1.0 - - - +
449J ASP* 1.3 74.2 - - - +
451J PHE* 1.3 61.7 + - - +
452J CYS* 3.5 11.8 - - - +
453J ALA* 3.0 20.6 + - - +
454J ILE* 3.0 23.7 + - - +
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Residues in contact with PHE 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325J TYR* 3.9 27.9 - + + -
335J ALA* 3.6 24.5 - - + -
440J PHE* 5.0 0.2 - + - -
444J ILE* 4.9 5.2 - - + -
449J ASP* 3.3 42.7 + - + -
450J ASN* 1.3 69.1 - - - +
452J CYS* 1.3 64.5 - - - +
454J ILE* 3.8 12.5 - - + +
455J ALA* 2.9 28.2 + - - +
463J CYS* 3.7 16.9 - - - +
466J VAL* 3.5 28.0 - - + +
467J TYR* 3.7 15.5 - + + -
470J ARG* 3.6 35.9 - - + -
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Residues in contact with CYS 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317J ASN* 3.9 25.6 - - - +
319J PRO 4.4 10.8 - - - -
320J CYS* 4.4 10.6 - - - +
324J CYS* 4.6 1.3 - - - -
325J TYR* 4.5 12.5 - - - -
450J ASN* 3.1 12.1 - - - +
451J PHE* 1.3 78.0 - - - +
453J ALA* 1.3 58.1 + - - +
455J ALA* 4.0 2.8 - - - +
456J ARG* 3.4 19.0 + - - +
463J CYS* 3.6 10.4 - - - -
802J ZN 3.4 22.9 - - - -
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Residues in contact with ALA 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447J TYR* 3.4 34.8 - - + -
450J ASN* 3.0 14.4 + - - +
452J CYS* 1.3 76.0 - - - +
454J ILE* 1.3 60.3 + - - +
455J ALA 3.4 0.4 - - - -
456J ARG* 3.8 8.5 - - - +
457J LEU* 2.9 34.6 + - + +
675L ASP* 4.3 13.9 - - - +
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Residues in contact with ILE 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440J PHE* 4.1 9.0 - - + -
443J LEU* 3.9 29.2 - - + -
444J ILE* 4.1 18.8 - - + -
447J TYR* 3.6 22.7 - - + -
449J ASP 4.4 0.7 - - - +
450J ASN 3.0 41.1 + - - +
451J PHE* 3.2 8.0 + - + +
453J ALA* 1.3 75.2 - - - +
455J ALA* 1.3 57.6 + - - +
457J LEU* 3.8 0.6 - - - +
458J ILE* 2.8 51.0 + - + +
466J VAL* 3.3 28.0 - - + -
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Residues in contact with ALA 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J CYS* 6.1 0.7 - - - -
451J PHE 2.9 15.2 + - - +
452J CYS 4.0 2.9 - - - +
454J ILE* 1.3 73.5 - - - +
456J ARG* 1.3 57.7 + - - +
458J ILE* 4.1 2.6 - - - +
459J GLY* 2.8 33.8 + - - -
461J LYS 4.1 7.1 - - - +
462J THR* 3.4 13.5 - - - +
463J CYS* 3.3 32.3 - - + +
466J VAL* 3.6 12.3 - - + +
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Residues in contact with ARG 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452J CYS 3.4 14.0 + - - +
453J ALA* 3.6 11.7 - - - +
455J ALA* 1.3 79.5 - - - +
457J LEU* 1.3 52.6 + - + +
459J GLY* 3.7 5.1 + - - -
675L ASP* 3.1 36.4 + - - +
679L THR* 3.7 24.6 + - - +
682L ARG* 2.6 33.2 + - - +
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Residues in contact with LEU 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443J LEU* 3.9 16.8 - - + -
447J TYR* 3.1 40.6 - - + +
453J ALA 2.9 19.0 + - - +
454J ILE 4.1 2.0 - - - +
456J ARG* 1.3 81.0 - - + +
458J ILE* 1.3 64.5 + - - +
459J GLY 3.2 0.4 - - - -
657L MET* 3.4 23.4 - - + +
674L ILE* 3.9 24.2 - - + +
675L ASP* 3.0 37.5 - - - +
678L VAL* 4.8 11.4 - - + -
682L ARG* 3.4 15.1 + - - +
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Residues in contact with ILE 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432J TRP* 4.1 21.3 - - + -
436J GLU* 4.2 17.9 - - + +
439J MET* 4.6 14.4 - - + -
440J PHE* 4.2 13.7 - - + +
443J LEU* 3.6 15.9 - - + -
454J ILE* 2.8 44.5 + - + +
455J ALA* 4.1 3.8 - - - +
457J LEU* 1.3 73.0 - - - +
459J GLY* 1.3 57.5 + - - +
460J THR* 3.1 31.0 + - + +
461J LYS* 4.5 9.0 - - + +
466J VAL* 4.2 7.6 - - + -
657L MET* 5.5 0.2 - - - -
682L ARG* 4.0 3.6 + - - -
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Residues in contact with GLY 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455J ALA 2.8 17.4 + - - -
456J ARG 3.7 6.5 - - - -
457J LEU 3.2 1.0 - - - -
458J ILE* 1.3 74.1 - - - +
460J THR* 1.3 58.5 + - - +
461J LYS 3.5 6.9 + - - +
682L ARG* 3.6 18.8 - - - -
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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