Contacts of the helix formed by residues 472 - 485 (chain B) in PDB entry 3E0D
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 GLU 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B GLY 3.6 17.1 - - - +
418B VAL* 3.7 25.6 - - + -
469B SER* 3.0 20.0 + - - +
471B ARG* 1.3 99.2 - - + +
473B ARG* 1.3 66.4 + - - +
474B ASP 3.2 2.9 - - - -
475B ARG* 2.8 57.7 + - - +
476B VAL* 3.5 4.3 + - - +
629B ASP* 5.0 2.5 - - - +
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PHE* 4.2 16.6 - - + -
469B SER 3.0 13.3 + - - +
470B ASP 4.2 7.4 + - - +
471B ARG 3.6 1.2 - - - -
472B GLU* 1.3 76.2 - - - +
474B ASP* 1.3 77.9 + - - +
476B VAL* 3.0 17.8 + - - +
477B ILE* 3.1 32.9 + - + +
491B GLN* 3.6 13.7 - - - +
576B ALA* 3.4 14.3 + - - +
577B ALA* 4.3 2.8 + - - +
579B VAL* 5.1 0.2 - - - +
599B ARG* 3.5 18.4 - - - +
619B PHE* 3.1 43.6 + - + +
620B LEU 3.8 2.5 - - - +
621B GLY* 3.5 20.6 - - - +
10E G 2.6 30.8 + - - -
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Residues in contact with ASP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ASP 5.5 1.8 + - - -
471B ARG 4.9 5.1 + - - +
472B GLU 3.1 1.1 + - - -
473B ARG* 1.3 104.5 + - - +
475B ARG* 1.3 57.6 + - + +
477B ILE* 3.3 10.6 + - - +
478B GLN* 2.9 29.6 + - - +
599B ARG* 2.8 31.7 + - - -
10E G 4.5 1.0 + - - -
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Residues in contact with ARG 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B TRP* 3.7 19.6 - - + -
416B HIS* 2.7 46.1 + - - +
417B GLY* 4.0 2.0 + - - -
418B VAL* 3.9 10.3 - - + +
471B ARG 5.7 0.9 - - - +
472B GLU* 2.8 51.3 + - - +
474B ASP* 1.3 74.1 - - + +
476B VAL* 1.3 57.5 + - - +
478B GLN* 3.4 9.1 + - - +
479B TYR* 2.9 26.9 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR* 4.1 20.6 - - + +
412B TRP* 4.0 10.5 - - + -
413B ALA* 3.9 11.0 - - + -
418B VAL* 3.6 32.1 - - + -
468B PHE* 3.7 24.2 - - + -
472B GLU 3.9 3.1 - - - +
473B ARG* 3.0 12.3 + - - +
475B ARG* 1.3 74.1 - - - +
477B ILE* 1.3 63.8 + - - +
479B TYR* 3.1 5.2 + - - +
480B VAL* 3.1 21.7 + - - +
619B PHE* 3.5 24.9 - - + -
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ARG* 3.1 49.5 + - + +
474B ASP* 3.5 16.6 - - - +
476B VAL* 1.3 74.7 - - - +
478B GLN* 1.3 57.0 + - - +
480B VAL* 3.2 9.0 + - + +
481B ARG* 2.8 48.5 + - + +
489B VAL* 5.0 6.3 - - + -
491B GLN* 3.7 26.9 - - + +
579B VAL* 4.3 17.3 - - + -
599B ARG* 4.7 0.9 - - - +
619B PHE* 4.0 19.1 - - + -
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Residues in contact with GLN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B ASP 2.9 17.7 + - - +
475B ARG* 3.4 10.8 - - - +
477B ILE* 1.3 73.5 - - - +
479B TYR* 1.3 65.3 + - - +
481B ARG* 3.4 34.1 + - - +
482B GLU* 3.0 62.1 + - - +
486B GLU* 5.3 5.1 + - - -
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Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP* 2.9 36.6 + - - -
409B TYR* 3.9 26.9 - - + -
412B TRP* 3.2 60.8 - + + +
475B ARG 2.9 13.7 + - - +
476B VAL 3.1 8.7 + - - +
478B GLN* 1.3 77.1 - - - +
480B VAL* 1.3 59.0 + - + +
482B GLU* 3.3 10.2 + - - +
483B ARG* 2.8 62.3 + - + +
484B TYR* 5.4 1.1 - + - -
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR* 4.1 24.5 - - + -
476B VAL 3.1 14.2 + - - +
477B ILE* 3.4 9.0 - - - +
479B TYR* 1.3 79.9 - - + +
481B ARG* 1.3 56.2 + - - +
483B ARG* 3.0 0.4 + - - -
484B TYR* 2.7 56.6 + - + +
489B VAL* 3.9 13.4 - - + +
579B VAL* 5.2 3.4 - - + -
581B ILE* 3.7 24.9 - - + -
619B PHE* 4.0 23.3 - - + -
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Residues in contact with ARG 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ILE* 2.8 33.6 + - + +
478B GLN* 3.6 31.9 + - - +
480B VAL* 1.3 72.4 - - - +
482B GLU* 1.3 57.3 + - - +
485B GLY* 3.0 34.0 + - - -
486B GLU* 3.1 40.4 + - - +
489B VAL* 3.7 31.9 - - + -
490B ALA* 5.7 0.2 - - - +
594B ARG* 4.6 8.9 - - - +
598B GLY 4.7 6.7 + - - -
599B ARG* 5.5 0.6 - - - +
600B PRO* 3.5 41.3 - - - +
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Residues in contact with GLU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLN* 3.0 44.1 + - - +
479B TYR* 3.7 9.2 - - - +
481B ARG* 1.3 77.5 - - + +
483B ARG* 1.3 63.2 + - - +
484B TYR 3.6 0.2 + - - -
485B GLY* 3.9 5.4 + - - -
486B GLU* 5.7 4.0 - - - +
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Residues in contact with ARG 483 (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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298B PHE* 4.0 16.2 - - - -
299B PRO* 4.5 17.8 + - - +
408B ASP* 3.6 21.0 + - - -
479B TYR* 2.8 53.6 + - + +
480B VAL 3.8 2.5 - - - +
482B GLU* 1.3 78.9 - - - +
484B TYR* 1.3 88.0 + - + +
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Residues in contact with TYR 484 (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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296B PRO* 5.5 3.1 - - + -
297B ARG 4.5 13.2 - - - -
298B PHE* 3.0 35.1 - + - -
299B PRO* 5.0 7.0 - - + -
405B ILE* 3.4 38.4 + - + +
408B ASP* 3.8 10.1 + - - -
409B TYR* 5.3 1.8 - + - -
479B TYR* 5.4 1.3 - + - -
480B VAL* 2.7 45.1 + - + +
483B ARG* 1.3 96.9 - - + +
485B GLY* 1.3 57.6 + - - +
488B LYS* 3.4 26.4 + - + +
489B VAL* 3.9 5.4 - - + -
581B ILE* 3.7 25.8 - - + -
582B ALA 5.7 0.2 - - - +
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Residues in contact with GLY 485 (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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481B ARG 3.0 14.9 + - - +
482B GLU 3.9 4.3 + - - -
483B ARG 3.6 2.2 - - - -
484B TYR* 1.3 80.6 - - - +
486B GLU* 1.3 64.7 + - - -
487B ASP* 3.1 10.5 - - - -
488B LYS* 3.1 13.0 + - - -
489B VAL* 3.3 12.8 + - - +
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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