Contacts of the helix formed by residues 450 - 459 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317G ASN* 3.8 25.0 + - - +
447G TYR* 3.6 25.7 + - + +
448G TYR 3.3 2.8 + - - +
449G ASP* 1.3 73.4 - - - +
451G PHE* 1.3 52.7 + - - +
452G CYS* 3.4 13.4 - - - +
453G ALA* 2.7 51.5 + - + +
454G ILE* 2.8 18.4 + - - +
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Residues in contact with PHE 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G TYR* 3.7 32.0 - + - -
335G ALA* 3.9 10.8 - - + -
440G PHE* 5.1 3.4 - + - -
444G ILE* 5.3 2.9 - - + -
449G ASP* 3.0 45.1 + - + -
450G ASN* 1.3 71.6 - - - +
452G CYS* 1.3 57.3 + - - +
454G ILE* 3.9 13.2 - - + +
455G ALA* 2.7 35.7 + - - +
463G CYS* 4.0 20.4 - - - +
466G VAL* 3.6 25.3 - - + +
467G TYR* 3.6 24.9 - + + -
470G ARG* 3.7 38.6 - - + -
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Residues in contact with CYS 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317G ASN* 3.7 29.6 - - - +
319G PRO 4.9 0.2 - - - -
320G CYS* 4.5 16.7 - - - -
324G CYS* 4.3 4.5 - - - -
325G TYR* 4.4 11.0 - - - -
450G ASN* 3.4 11.4 - - - +
451G PHE* 1.3 77.7 - - - +
453G ALA* 1.3 58.4 + - - +
455G ALA* 4.4 1.6 - - - +
456G ARG* 3.7 18.4 + - - +
463G CYS* 3.6 6.1 - - - -
802G ZN 2.7 35.4 - - - -
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Residues in contact with ALA 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G TYR* 3.5 27.4 - - + -
450G ASN* 2.7 37.9 + - - +
452G CYS* 1.3 74.6 - - - +
454G ILE* 1.3 58.5 + - - +
455G ALA 3.4 0.2 - - - -
456G ARG* 3.4 7.7 + - - +
457G LEU* 3.0 33.9 + - + +
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Residues in contact with ILE 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440G PHE* 4.2 8.7 - - + -
443G LEU* 3.8 31.1 - - + +
444G ILE* 4.4 15.7 - - + +
447G TYR* 3.7 22.0 - - + -
449G ASP 4.5 2.5 - - - +
450G ASN 2.8 42.9 + - - +
451G PHE* 3.8 14.6 - - + +
453G ALA* 1.3 69.2 - - - +
455G ALA* 1.3 57.4 + - - +
457G LEU* 3.3 0.4 + - - -
458G ILE* 2.7 59.2 + - + +
466G VAL* 3.4 19.7 - - + -
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Residues in contact with ALA 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320G CYS* 5.8 1.6 - - - -
451G PHE 2.7 19.7 + - - +
452G CYS 4.4 2.0 - - - +
454G ILE* 1.3 68.9 - - - +
456G ARG* 1.3 66.7 + - - +
458G ILE* 4.0 1.3 - - - +
459G GLY* 2.9 22.7 + - - -
461G LYS 3.6 10.3 - - - +
462G THR* 3.5 12.1 - - - -
463G CYS* 3.2 34.1 - - + +
466G VAL* 3.8 10.7 - - + +
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Residues in contact with ARG 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593D HIS* 4.2 27.6 + - - -
452G CYS 3.7 14.3 + - - +
453G ALA* 3.4 11.4 + - - +
455G ALA* 1.3 80.4 - - - +
457G LEU* 1.3 56.0 + - + +
459G GLY* 3.4 4.9 + - - -
675I ASP* 3.0 35.6 + - - +
679I THR* 2.9 36.6 + - - +
682I ARG* 2.7 33.2 + - - +
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Residues in contact with LEU 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443G LEU* 4.0 20.4 - - + -
447G TYR* 3.2 43.3 - - + +
453G ALA* 3.0 21.3 + - + +
456G ARG* 1.3 80.6 - - + +
458G ILE* 1.3 66.9 + - - +
657I MET* 3.3 24.4 - - + +
674I ILE* 3.4 22.2 - - + -
675I ASP* 3.2 37.7 - - + +
678I VAL* 4.6 10.3 - - + +
682I ARG* 3.7 11.0 + - - +
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Residues in contact with ILE 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432G TRP* 4.5 9.4 - - + -
436G GLU* 4.3 18.6 - - + +
439G MET* 5.0 8.7 - - + -
440G PHE* 4.4 22.9 - - + +
443G LEU* 3.7 15.7 - - + -
454G ILE* 2.7 43.7 + - + +
455G ALA* 4.0 2.9 - - - +
457G LEU* 1.3 73.1 - - - +
459G GLY* 1.3 58.0 + - - +
460G THR* 3.4 30.8 + - + +
461G LYS* 4.4 9.2 - - + +
466G VAL* 3.9 15.7 - - + -
657I MET* 5.1 5.7 - - - +
682I ARG* 3.7 6.4 + - - -
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Residues in contact with GLY 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G ALA 2.9 12.7 + - - -
456G ARG 3.6 13.5 - - - -
457G LEU 3.3 0.8 - - - -
458G ILE* 1.3 75.0 - - - +
460G THR* 1.3 56.2 + - - +
461G LYS 3.5 9.2 + - - +
682I ARG* 3.7 14.4 - - - -
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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