Contacts of the helix formed by residues 446 - 456 (chain A) in PDB entry 1ISR
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 446 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 5.6 1.0 - - - +
427A MET* 3.5 7.3 - - + +
431A LEU* 6.1 0.7 - - + -
441A ALA 5.5 1.0 + - - -
444A PRO* 3.5 5.1 + - - +
445A ILE* 1.3 73.5 - - - +
447A GLY* 1.3 61.6 + - - +
448A ARG* 3.0 50.5 + - - +
449A LYS* 3.8 28.5 - - + -
450A LEU* 3.0 27.2 + - - +
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA 5.5 1.1 - - - -
179A ASP* 3.4 26.2 + - - +
181A PRO* 4.1 9.5 - - - +
200A TYR* 4.0 6.0 - - - -
445A ILE 3.4 5.0 + - - -
446A ASP* 1.3 71.9 + - - +
448A ARG* 1.3 64.8 + - - +
450A LEU* 3.2 9.7 + - - +
451A LEU* 3.0 23.0 + - - +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 4.2 9.9 - - + +
199A LYS* 6.3 0.4 - - - +
200A TYR* 3.4 28.6 + - - +
446A ASP* 3.0 35.6 + - - +
447A GLY* 1.3 76.3 - - - +
449A LYS* 1.3 82.3 + - + +
451A LEU* 3.5 13.0 - - - +
452A ASP* 3.2 15.3 - - - +
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Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A MET* 3.5 15.3 - - + -
431A LEU* 4.5 22.9 - - + -
446A ASP* 3.5 29.9 + - + +
447A GLY 3.2 0.2 - - - -
448A ARG* 1.3 94.7 - - + +
450A LEU* 1.3 67.0 + - - +
451A LEU 3.1 2.0 - - - -
452A ASP* 3.1 20.9 + - - +
453A PHE* 3.2 22.2 + - + -
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA* 3.6 26.7 - - + +
181A PRO* 3.6 15.7 - - + -
420A MET* 4.7 8.5 - - - +
423A GLY* 3.9 23.1 - - - +
424A LEU* 3.6 33.7 - - + -
427A MET* 3.2 16.7 - - + +
445A ILE* 4.6 8.1 - - + -
446A ASP 3.0 19.0 + - - +
447A GLY* 3.2 7.2 + - - +
449A LYS* 1.3 75.1 - - - +
451A LEU* 1.3 62.6 + - - +
453A PHE* 3.4 2.7 + - - -
454A LEU* 3.0 36.6 + - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 4.2 16.1 - - + +
199A LYS* 3.2 47.6 - - + +
200A TYR* 3.8 36.6 - - + -
201A PHE 4.7 0.4 - - - +
202A LEU* 4.2 12.8 - - + -
447A GLY 3.0 11.7 + - - +
448A ARG* 3.5 11.2 - - - +
449A LYS 3.1 0.2 - - - -
450A LEU* 1.3 78.3 - - - +
452A ASP* 1.3 65.1 + - - +
454A LEU* 3.4 7.9 + - + +
455A ILE* 3.1 37.8 + - + +
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ARG 3.2 17.6 - - - +
449A LYS* 3.1 13.0 + - - +
451A LEU* 1.3 79.6 - - - +
453A PHE* 1.3 66.4 + - + +
455A ILE* 3.4 6.0 + - - +
456A LYS* 3.1 50.4 + - + +
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Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A GLY* 3.8 17.9 - - - +
426A ASN* 3.8 29.8 + - + +
427A MET* 3.5 43.5 - - + -
430A ALA* 3.8 24.7 - - + -
431A LEU* 4.5 11.2 - - + -
449A LYS* 3.2 25.8 + - + -
450A LEU* 3.8 4.9 - - - +
451A LEU 3.3 0.2 - - - -
452A ASP* 1.3 76.6 - - + +
454A LEU* 1.3 59.8 + - - +
456A LYS* 3.2 17.9 + - + +
457A SER* 2.7 26.1 + - - -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 3.5 35.9 - - + -
183A ILE* 4.2 13.7 - - + -
202A LEU* 3.8 26.0 - - + -
419A ALA 3.2 28.9 - - - +
420A MET* 4.3 11.0 - - - -
423A GLY* 3.7 15.7 - - - -
450A LEU* 3.0 29.6 + - + +
451A LEU* 3.6 6.3 - - - +
452A ASP 3.3 0.2 - - - -
453A PHE* 1.3 76.5 - - - +
455A ILE* 1.3 64.1 + - - +
457A SER* 3.0 22.4 + - - -
469A PHE* 3.6 14.2 - - + -
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Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 6.4 0.7 - - + -
201A PHE 5.2 1.8 - - - +
202A LEU* 4.1 32.3 - - + -
451A LEU* 3.1 25.9 + - + +
452A ASP* 3.8 8.3 - - - +
454A LEU* 1.3 76.0 - - - +
456A LYS* 1.3 62.3 + - + +
457A SER 3.2 5.8 + - - +
469A PHE* 3.8 23.8 - - + +
470A ASP 3.4 24.0 - - - +
471A GLU* 4.7 6.5 - - - +
473A GLY* 4.2 14.8 - - - +
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ASN* 4.8 4.7 + - - -
452A ASP* 3.1 43.0 + - + +
453A PHE* 3.4 13.2 - - + +
454A LEU 3.1 0.6 - - - -
455A ILE* 1.3 82.0 - - + +
457A SER* 1.3 58.6 + - - +
458A SER* 4.3 0.7 + - - -
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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