Contacts of the helix formed by residues 445 - 458 (chain B) in PDB entry 5Y7G
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 SER 445 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B ARG* 3.1 33.7 + - - +
443B ASP* 2.2 28.0 + - - -
444B GLY* 1.3 70.4 - - - +
446B TYR* 1.3 64.7 + - - +
447B ARG 3.2 2.2 - - - -
448B ASP* 4.2 8.1 - - - +
449B ALA* 3.3 23.6 + - - +
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Residues in contact with TYR 446 (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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397B LEU* 4.2 17.0 - - + -
440B ARG* 2.6 27.6 + - - +
441B LEU* 3.7 27.6 - - + +
443B ASP 4.2 3.1 - - - -
444B GLY 3.0 5.4 + - - -
445B SER* 1.3 74.7 - - - +
447B ARG* 1.3 106.0 + - + +
449B ALA* 3.2 1.9 + - - +
450B ILE* 2.9 46.8 + - + +
479B LEU* 3.4 26.8 + - + -
482B LEU 3.2 22.6 + - - -
484B ALA* 3.9 21.8 + - + -
487B LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLY* 3.5 28.1 + - - +
445B SER 3.2 0.2 - - - -
446B TYR* 1.3 110.9 + - + +
448B ASP* 1.3 63.6 + - - +
451B ARG* 3.1 56.3 + - - +
479B LEU* 3.3 38.9 + - + +
480B ASP* 4.8 8.0 + - - +
484B ALA* 6.0 1.6 - - - +
516B ARG* 5.7 4.9 - - - +
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Residues in contact with ASP 448 (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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444B GLY 4.8 0.6 + - - -
445B SER* 3.9 9.8 + - - +
447B ARG* 1.3 80.0 - - - +
449B ALA* 1.3 58.0 + - - +
451B ARG* 3.3 27.8 + - - +
452B CYS* 2.9 32.5 + - - +
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Residues in contact with ALA 449 (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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396B LEU 5.7 0.2 - - - -
397B LEU* 4.3 15.0 - - + -
440B ARG* 4.7 11.4 - - + -
445B SER 3.3 18.5 + - - +
446B TYR 3.2 5.0 + - - +
448B ASP* 1.3 78.9 - - - +
450B ILE* 1.3 58.3 + - - +
452B CYS* 3.2 7.3 + - - +
453B ARG* 2.9 48.1 + - - +
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Residues in contact with ILE 450 (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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393B LEU* 4.1 21.8 - - + +
396B LEU* 4.2 15.3 - - + +
397B LEU* 3.9 40.6 - - + +
446B TYR* 2.9 38.2 + - + +
447B ARG 3.9 2.7 - - - +
449B ALA* 1.3 73.2 - - - +
451B ARG* 1.3 61.9 + - - +
452B CYS 3.1 0.2 - - - -
453B ARG* 3.9 2.8 - - - +
454B TYR* 2.9 28.6 + - - +
475B LEU* 3.7 28.5 - - + -
479B LEU* 3.9 13.7 - - + -
487B LEU* 5.6 3.6 - - + -
491B PHE* 6.0 0.9 - - + -
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Residues in contact with ARG 451 (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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447B ARG* 3.1 50.2 + - - +
448B ASP* 3.7 22.8 + - - +
450B ILE* 1.3 77.7 - - - +
452B CYS* 1.3 60.3 + - - +
454B TYR* 3.9 5.4 - - - +
455B ARG* 3.3 23.0 + - - +
475B LEU* 4.8 5.8 - - + -
476B GLU* 3.2 39.1 + - - +
479B LEU* 3.7 14.6 - - + +
480B ASP* 5.3 4.9 + - - -
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Residues in contact with CYS 452 (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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448B ASP* 2.9 16.3 + - - +
449B ALA* 3.5 11.0 - - - +
450B ILE 3.1 0.2 - - - -
451B ARG* 1.3 74.5 - - - +
453B ARG* 1.3 72.5 + - - +
454B TYR 3.1 1.2 + - - -
455B ARG* 3.3 6.4 + - - +
456B ASP* 2.9 27.4 + - + +
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Residues in contact with ARG 453 (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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396B LEU* 3.3 32.7 + - + +
397B LEU 3.9 17.6 + - - -
399B TRP* 3.7 28.3 - - + +
400B GLU* 2.4 50.5 + - - +
437B CYS* 4.2 4.9 - - - -
440B ARG* 6.3 0.8 - - - +
449B ALA* 2.9 33.2 + - - +
450B ILE 4.2 1.6 - - - +
452B CYS* 1.3 79.7 - - - +
454B TYR* 1.3 57.8 + - - +
456B ASP* 4.3 5.6 - - - -
457B LYS* 2.9 39.0 + - + +
467B TRP* 4.0 3.1 - - - -
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Residues in contact with TYR 454 (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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396B LEU* 4.0 12.7 - - + +
450B ILE 2.9 19.6 + - - +
451B ARG* 4.0 4.9 - - - +
452B CYS 3.1 0.2 - - - -
453B ARG* 1.3 76.0 - - - +
455B ARG* 1.3 71.5 + - + +
458B PHE* 3.2 46.8 + + - +
467B TRP* 3.6 17.2 - + - -
470B LEU* 2.5 58.3 + - + -
471B GLY* 3.7 11.8 - - - -
472B GLU* 3.9 9.7 + - + -
475B LEU* 3.6 27.4 - - + -
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Residues in contact with ARG 455 (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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451B ARG 3.3 13.8 + - - +
452B CYS* 4.2 6.3 - - - +
454B TYR* 1.3 86.6 - - + +
456B ASP* 1.3 90.0 + - + +
458B PHE* 4.0 10.0 + - - +
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Residues in contact with ASP 456 (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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452B CYS* 2.9 22.2 + - + +
453B ARG* 4.1 4.5 - - - +
455B ARG* 1.3 102.5 + - + +
457B LYS* 1.3 81.0 + - + +
458B PHE 3.4 1.1 + - - +
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Residues in contact with LYS 457 (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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201B GLU* 2.6 32.0 + - - +
399B TRP* 3.4 47.1 - - + +
400B GLU* 6.1 1.1 - - - -
453B ARG* 2.9 28.7 + - - +
456B ASP* 1.3 90.2 + - + +
458B PHE* 1.3 68.3 + - - +
460B LEU* 3.2 32.2 + - + +
467B TRP* 3.3 10.7 - - + -
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Residues in contact with PHE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 3.9 13.4 + - - -
454B TYR* 3.2 45.3 + + - +
455B ARG* 4.1 8.5 - - - +
456B ASP 3.4 3.3 + - - +
457B LYS* 1.3 78.8 - - - +
459B GLY* 1.3 79.9 + - - +
460B LEU* 3.3 5.2 + - - +
467B TRP* 3.3 54.7 - + + -
470B LEU 4.7 0.4 - - - -
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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