Contacts of the helix formed by residues 420 - 427 (chain B) in PDB entry 5W5G
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 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ARG* 2.9 18.8 + - - +
419B GLY* 1.3 77.9 - - - +
421B PHE* 1.3 64.6 + - - -
422B ARG* 3.2 4.4 + - - -
423B ASP* 3.2 20.5 + - - +
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Residues in contact with PHE 421 (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 16.5 - - + +
397B PHE* 3.6 62.6 - + + -
398B ASP 4.7 4.9 - - - -
399B ALA 5.7 0.7 - - - -
401B GLY* 3.6 28.7 - - - -
417B ARG* 5.2 0.2 - - - +
420B GLY* 1.3 67.7 - - - -
422B ARG* 1.3 93.6 + - + +
423B ASP 3.1 5.6 - - - -
424B TYR* 3.1 37.9 + - + +
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Residues in contact with ARG 422 (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* 4.3 9.4 - - + +
419B GLY 5.9 1.3 - - - +
420B GLY 3.2 1.8 - - - -
421B PHE* 1.3 107.2 - - + +
423B ASP* 1.3 59.0 + - - +
424B TYR 3.2 0.9 - - - -
425B GLU* 3.2 36.3 + - - +
426B LYS* 5.8 0.2 - - - +
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Residues in contact with ASP 423 (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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417B ARG* 3.2 29.7 + - - +
418B SER 4.3 2.8 - - - +
419B GLY* 3.3 27.6 + - - -
420B GLY 3.2 13.9 + - - +
421B PHE 3.1 0.6 - - - -
422B ARG* 1.3 78.1 - - - +
424B TYR* 1.3 60.6 + - - +
425B GLU 3.2 1.4 + - - -
426B LYS* 3.5 12.7 + - - +
427B ASP* 3.7 15.2 + - - +
502B ALA* 4.0 24.1 + - + +
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Residues in contact with TYR 424 (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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392B TRP* 3.6 23.9 + + + -
393B LEU* 4.0 3.1 - - + -
397B PHE* 4.3 21.5 - + - -
414B LEU* 3.5 9.7 - - + +
415B PRO* 2.4 50.6 + - + +
417B ARG* 3.6 31.3 - - + +
421B PHE* 3.1 31.4 + - + +
423B ASP* 1.3 74.7 - - - +
425B GLU* 1.3 65.6 + - - +
426B LYS 3.1 1.1 - - - -
427B ASP 3.1 19.6 + - - -
428B ALA* 3.4 13.7 + - - +
429B PRO* 4.2 15.9 - - + -
461B LEU* 3.5 24.5 - - + -
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Residues in contact with GLU 425 (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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385B ASP* 5.4 4.2 - - - +
390B LYS 4.1 15.1 - - - +
392B TRP* 5.1 7.5 + - - +
393B LEU* 3.8 25.9 - - + +
422B ARG* 3.2 30.9 + - - +
424B TYR* 1.3 78.3 - - - +
426B LYS* 1.3 59.5 + - + +
427B ASP 3.8 0.2 + - - -
428B ALA* 5.3 1.4 + - - +
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Residues in contact with LYS 426 (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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422B ARG 5.8 0.4 - - - +
423B ASP* 3.5 7.3 + - - +
424B TYR 3.1 0.2 - - - -
425B GLU* 1.3 78.5 - - + +
427B ASP* 1.3 60.2 + - - +
428B ALA 4.1 0.2 - - - -
462B ARG* 5.2 3.7 + - - -
495B VAL* 6.6 0.2 - - + -
496B ALA 5.8 4.7 - - - +
501B PRO* 3.2 42.2 - - + +
502B ALA 5.1 1.6 - - - +
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Residues in contact with ASP 427 (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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417B ARG* 2.8 45.5 + - - +
423B ASP 3.7 12.3 - - - +
424B TYR* 3.1 11.7 + - - -
425B GLU 3.5 0.6 + - - -
426B LYS* 1.3 81.3 - - - +
428B ALA* 1.3 65.1 + - - +
459B PRO 5.0 0.3 - - - +
460B SER* 3.6 12.1 + - - -
461B LEU* 3.1 33.8 + - - +
462B ARG* 4.7 6.9 + - - +
501B PRO* 4.4 3.4 - - + -
502B ALA 3.8 5.0 - - - +
503B TRP* 3.7 17.4 + - - -
504B ILE* 4.5 1.9 + - - +
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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