Contacts of the helix formed by residues 417 - 428 (chain B) in PDB entry 4IYM
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 ASP 417 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A TRP* 4.2 1.6 - - - -
255B MSE 6.4 0.2 - - + -
257B ASP* 3.2 15.1 + - - +
415B THR* 3.2 15.4 + - - +
416B ARG* 1.3 75.5 - - - +
418B GLY* 1.3 68.2 + - - +
419B ASP* 3.4 15.1 + - - +
420B ALA* 2.9 29.3 + - + +
421B ALA* 3.1 18.9 + - - +
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Residues in contact with GLY 418 (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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480A TRP* 3.9 16.4 - - - -
416B ARG 3.6 5.7 + - - -
417B ASP* 1.3 71.9 + - - +
419B ASP* 1.3 56.0 + - - +
421B ALA* 3.4 0.5 + - - +
422B ARG* 3.0 33.3 + - - +
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Residues in contact with ASP 419 (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 ASP* 3.3 14.0 + - - +
418B GLY* 1.3 74.9 - - - +
420B ALA* 1.3 59.2 + - - +
422B ARG* 4.0 3.5 - - - +
423B ASP* 2.9 41.3 + - - +
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Residues in contact with ALA 420 (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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255B MSE 4.5 13.9 - - + -
395B TYR* 3.7 21.3 + - + -
413B ILE* 4.3 6.7 - - + -
415B THR* 4.0 17.3 - - + +
417B ASP* 2.9 22.5 + - + +
418B GLY 3.4 0.2 - - - -
419B ASP* 1.3 75.8 + - - +
421B ALA* 1.3 62.9 + - - +
423B ASP* 4.7 1.6 - - - -
424B PHE* 2.9 27.9 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A TRP* 3.5 33.4 - - + -
413B ILE* 4.4 9.5 - - - +
415B THR* 4.0 9.3 - - + +
417B ASP 3.1 10.0 + - - +
418B GLY 3.8 1.1 - - - +
419B ASP 3.3 0.2 - - - -
420B ALA* 1.3 77.6 - - - +
422B ARG* 1.3 57.2 + - - +
424B PHE* 3.6 1.4 - - - +
425B ALA* 2.9 32.7 + - - +
435B VAL* 3.7 21.8 - - + +
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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
----------------------------------------------------------
418B GLY 3.0 18.2 + - - +
419B ASP* 4.0 4.5 - - - +
421B ALA* 1.3 75.4 - - - +
423B ASP* 1.3 74.0 + - - +
425B ALA* 3.5 4.4 + - - +
426B SER* 3.0 51.9 + - - -
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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
----------------------------------------------------------
395B TYR* 2.7 25.8 + - + +
419B ASP* 2.9 27.9 + - - +
420B ALA* 3.9 1.1 - - - +
422B ARG* 1.3 89.3 + - - +
424B PHE* 1.3 58.3 + - - +
426B SER* 3.4 2.7 + - - -
427B ARG* 3.1 64.2 + - - +
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Residues in contact with PHE 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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253B ILE* 3.9 29.8 - - + -
395B TYR* 3.0 20.6 + + - +
399B LEU* 3.5 41.0 - - + +
402B PRO* 4.3 4.3 - - + -
411B VAL* 3.8 38.8 - - + -
412B ALA 4.4 2.0 - - - -
413B ILE* 3.7 37.0 - - + -
420B ALA 2.9 19.0 + - - +
421B ALA 3.6 3.1 - - - +
423B ASP* 1.3 74.1 - - - +
425B ALA* 1.3 68.0 + - - +
427B ARG* 3.4 0.6 + - - +
428B ILE* 3.0 35.8 + - + +
433B VAL* 4.8 3.4 - - + -
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Residues in contact with ALA 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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132A TYR* 5.6 0.9 - - - +
474A LYS* 2.7 41.0 + - - +
476A ILE* 3.7 26.5 - - + -
413B ILE* 6.0 0.2 - - + -
421B ALA 2.9 17.3 + - - +
422B ARG* 4.0 4.7 - - - +
424B PHE* 1.3 78.1 - - - +
426B SER* 1.3 51.9 + - - +
428B ILE* 3.9 1.7 - - - +
433B VAL* 3.9 24.9 - - + -
435B VAL* 4.7 8.5 - - + -
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Residues in contact with SER 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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134A ILE* 5.5 7.4 - - - +
136A GLN* 3.0 33.5 + - - +
474A LYS* 3.1 7.2 + - - -
422B ARG* 3.0 46.1 + - - -
423B ASP 3.7 4.0 - - - -
425B ALA* 1.3 77.9 - - - +
427B ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 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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474A LYS* 4.3 0.2 - - - -
395B TYR* 3.8 1.0 - - - -
396B GLU* 2.8 41.6 + - - -
399B LEU* 3.4 23.4 - - + +
403B MSE 3.4 23.4 - - + +
423B ASP* 3.1 48.4 + - - +
424B PHE 4.3 0.9 - - - +
426B SER* 1.3 81.0 - - - +
428B ILE* 1.3 65.8 + - - +
429B ASN* 3.4 3.1 + - - +
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Residues in contact with ILE 428 (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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474A LYS* 2.7 28.4 + - - -
399B LEU* 3.8 17.9 - - + +
402B PRO* 3.8 18.4 - - + -
403B MSE 3.5 40.2 - - + +
411B VAL* 4.0 12.8 - - + -
424B PHE* 3.0 27.5 + - + +
425B ALA* 3.9 3.8 - - - +
426B SER 3.6 0.2 - - - -
427B ARG* 1.3 77.4 - - - +
429B ASN* 1.3 61.0 + - - +
430B ILE* 3.0 26.4 + - + +
433B VAL* 3.8 28.5 - - + -
451B TRP* 4.1 1.0 - - - -
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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