Contacts of the helix formed by residues 471 - 482 (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 GLY 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B TYR* 3.7 4.9 - - - -
469B LEU 3.3 7.9 + - - -
470B LEU* 1.3 75.4 - - - +
472B GLU* 1.3 67.7 + - - -
473B GLU* 3.1 4.4 + - - -
474B LEU* 3.2 7.1 + - - +
475B LEU* 3.0 22.2 + - - +
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Residues in contact with GLU 472 (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 TYR* 3.9 13.4 + - + +
471B GLY* 1.3 72.1 - - - -
473B GLU* 1.3 63.4 + - + +
475B LEU* 4.4 9.6 - - + -
476B GLU* 3.0 41.9 + - + +
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Residues in contact with GLU 473 (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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383B HIS* 4.7 9.4 - - + -
471B GLY* 3.1 1.9 - - - -
472B GLU* 1.3 77.7 - - + +
474B LEU* 1.3 58.0 + - - +
476B GLU* 4.7 0.8 - - - +
477B GLN* 2.9 55.6 + - - +
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Residues in contact with LEU 474 (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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383B HIS* 3.3 43.6 - - + +
385B VAL* 4.2 17.3 - - + -
389B LEU* 3.7 27.8 - - + -
469B LEU* 3.5 28.3 - - + +
470B LEU* 4.0 18.4 - - + -
471B GLY* 3.2 12.6 + - - +
473B GLU* 1.3 76.7 - - - +
475B LEU* 1.3 66.9 + - - +
477B GLN* 3.3 2.0 + - - +
478B ALA* 2.9 23.7 + - - +
509B ILE* 5.5 0.4 - - + -
511B PHE* 3.9 9.6 - - + -
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Residues in contact with LEU 475 (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* 4.0 11.7 - - + -
396B LEU* 4.4 0.2 - - + -
450B ILE* 3.7 25.4 - - + -
451B ARG* 4.8 10.3 - - + -
454B TYR* 3.6 38.6 - - + -
470B LEU* 4.0 24.8 - - + +
471B GLY 3.0 16.4 + - - +
472B GLU* 3.8 8.1 - - + +
474B LEU* 1.3 77.4 - - - +
476B GLU* 1.3 79.4 + - + +
478B ALA* 3.2 4.7 + - - +
479B LEU* 3.0 37.1 + - + +
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Residues in contact with GLU 476 (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* 3.2 53.5 + - - +
472B GLU* 3.0 34.0 + - + +
473B GLU* 4.7 0.9 - - - +
475B LEU* 1.3 85.6 - - + +
477B GLN* 1.3 67.6 + - + +
478B ALA 3.4 0.2 + - - -
479B LEU* 4.3 5.4 - - - +
480B ASP* 3.5 28.3 + - - +
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Residues in contact with GLN 477 (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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381B ALA* 3.3 26.1 - - - +
383B HIS* 3.5 8.9 + - - -
473B GLU* 2.9 45.1 + - - +
474B LEU* 3.8 3.1 - - - +
475B LEU 3.3 0.2 - - - -
476B GLU* 1.3 78.7 - - + +
478B ALA* 1.3 61.4 + - - +
480B ASP* 3.7 1.4 + - - +
481B CYS* 3.2 32.1 + - - +
511B PHE* 3.1 36.8 - - + +
513B PRO* 4.3 17.6 - - + +
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Residues in contact with ALA 478 (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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389B LEU* 4.1 10.1 - - + -
393B LEU* 4.1 14.6 - - + -
474B LEU 2.9 17.1 + - - +
475B LEU 3.7 4.0 - - - +
477B GLN* 1.3 74.8 - - - +
479B LEU* 1.3 62.1 + - + +
481B CYS 2.9 1.0 + - - -
482B LEU* 2.8 55.3 + - + +
511B PHE* 3.9 19.0 - - + -
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Residues in contact with LEU 479 (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* 3.9 29.8 - - + -
446B TYR* 3.4 22.9 + - + -
447B ARG* 3.3 67.3 + - - +
450B ILE* 3.9 16.2 - - + -
451B ARG* 3.7 21.5 - - + +
475B LEU* 3.0 25.7 + - + +
476B GLU* 3.5 11.2 + - - +
477B GLN 3.4 0.2 - - - -
478B ALA* 1.3 79.3 - - + +
480B ASP* 1.3 60.8 + - - +
482B LEU* 4.4 2.5 - - - +
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Residues in contact with ASP 480 (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* 4.8 9.3 + - - +
451B ARG* 5.3 4.2 + - - -
476B GLU* 3.5 16.8 + - - +
477B GLN* 4.4 2.5 - - - +
478B ALA 3.1 0.2 - - - -
479B LEU* 1.3 79.9 - - - +
481B CYS* 1.3 65.7 + - - +
482B LEU 3.6 0.8 - - - -
513B PRO* 6.4 1.3 - - + -
516B ARG* 2.9 51.1 + - + +
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Residues in contact with CYS 481 (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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477B GLN* 3.2 18.8 + - - +
478B ALA 2.9 2.0 + - - -
480B ASP* 1.3 85.7 - - - +
482B LEU* 1.3 58.6 + - - +
483B PRO* 3.3 5.5 - - - +
511B PHE* 3.6 29.6 - - + -
513B PRO* 4.1 27.4 - - - -
516B ARG* 4.2 13.5 - - - +
517B ARG* 3.7 23.6 - - - +
518B TYR* 3.2 18.6 - - + -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 5.0 6.5 - - + -
390B ILE* 6.3 1.8 - - + -
393B LEU* 3.7 29.4 - - + -
446B TYR* 3.2 20.1 + - - +
478B ALA* 2.8 32.6 + - + +
479B LEU* 4.4 2.5 - - - +
480B ASP 3.6 1.8 - - - -
481B CYS* 1.3 72.3 - - - +
483B PRO* 1.3 70.7 - - + +
484B ALA 3.4 0.2 + - - -
487B LEU* 3.8 23.6 - - + +
490B TRP* 4.3 14.4 - - + -
509B ILE* 5.8 1.1 - - + -
511B PHE* 4.5 7.4 - - + -
518B TYR* 3.6 40.6 - - + -
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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