Contacts of the helix formed by residues 449 - 460 (chain A) in PDB entry 3S3J
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 SER 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A TYR* 3.5 0.7 - - - +
446A PRO* 2.6 46.5 + - - +
447A GLU 3.2 3.0 + - - -
448A GLY* 1.3 82.0 - - - +
450A SER* 1.3 63.3 + - - +
451A GLU* 3.4 14.3 + - - -
452A GLU* 3.0 26.0 + - - +
453A ARG* 3.4 12.8 + - - +
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Residues in contact with SER 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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448A GLY 3.6 0.8 + - - -
449A SER* 1.3 71.3 - - - +
451A GLU* 1.3 79.3 + - - +
453A ARG* 3.3 20.5 + - - +
454A GLU* 3.1 35.1 + - - +
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Residues in contact with GLU 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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381A GLU* 5.4 0.5 - - - +
445A TYR* 3.5 43.8 - - + +
446A PRO* 5.1 0.9 - - - +
449A SER* 3.4 17.7 - - - -
450A SER* 1.3 85.7 + - - +
452A GLU* 1.3 65.8 + - - +
453A ARG 3.3 0.2 + - - -
454A GLU* 3.3 17.4 + - - +
455A ALA* 3.2 21.1 + - - +
458A ARG* 5.9 0.2 + - - -
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Residues in contact with GLU 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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444A LYS* 6.0 2.3 - - - -
445A TYR* 3.6 19.8 - - + +
446A PRO 3.3 5.1 - - - +
447A GLU* 3.2 26.2 + - - +
448A GLY* 2.9 26.2 + - - -
449A SER* 3.0 24.1 + - - +
450A SER 3.3 0.2 - - - -
451A GLU* 1.3 76.8 - - - +
453A ARG* 1.3 67.6 + - - +
455A ALA* 3.2 6.6 + - - +
456A PHE* 3.2 22.6 + - + +
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Residues in contact with ARG 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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448A GLY* 3.2 29.9 + - - -
449A SER 3.4 6.6 + - - +
450A SER* 3.3 25.0 + - - +
451A GLU 3.2 0.8 - - - -
452A GLU* 1.3 82.8 - - + +
454A GLU* 1.3 67.2 + - + +
456A PHE* 3.5 6.7 + - - +
457A THR* 3.1 26.5 + - - -
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Residues in contact with GLU 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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450A SER* 3.1 24.6 + - - +
451A GLU* 3.3 16.2 + - - +
453A ARG* 1.3 76.7 - - - +
455A ALA* 1.3 57.5 + - - +
457A THR* 3.4 8.8 - - - +
458A ARG* 3.0 46.0 + - - +
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Residues in contact with ALA 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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379A ILE 5.6 0.2 - - - +
380A LYS 3.5 20.4 - - - +
381A GLU* 3.3 24.2 - - - +
382A GLY* 3.7 6.5 - - - +
394A PHE* 5.8 3.8 - - + -
445A TYR* 4.9 1.8 - - + -
451A GLU 3.2 12.3 + - - +
452A GLU* 3.5 11.4 - - - +
453A ARG 3.2 0.2 - - - -
454A GLU* 1.3 73.8 - - - +
456A PHE* 1.3 60.7 + - - +
457A THR 3.0 1.8 - - - -
458A ARG* 3.3 1.4 + - - +
459A ALA* 2.8 31.5 + - - +
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Residues in contact with PHE 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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394A PHE* 5.5 4.5 - - - -
452A GLU* 3.2 13.2 + - + +
453A ARG* 3.5 9.6 + - - +
455A ALA* 1.3 78.0 - - - +
457A THR* 1.3 56.7 + - - +
459A ALA* 4.2 5.6 - - - -
460A ASN* 3.0 46.5 + - - +
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Residues in contact with THR 457 (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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453A ARG 3.1 14.4 + - - -
454A GLU* 3.4 13.0 - - - +
455A ALA 3.0 0.2 - - - -
456A PHE* 1.3 75.2 - - - +
458A ARG* 1.3 69.3 + - - +
459A ALA 3.1 1.1 - - - -
460A ASN* 3.5 17.9 - - - +
461A HIS* 4.0 6.6 - - - -
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Residues in contact with ARG 458 (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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381A GLU* 3.1 49.2 + - - +
382A GLY 3.4 14.1 - - - +
383A ASP* 4.2 21.0 - - - +
384A LEU 5.5 0.9 + - - -
454A GLU* 3.0 36.4 + - - +
455A ALA* 3.3 0.8 + - - +
457A THR* 1.3 78.2 - - - +
459A ALA* 1.3 64.6 + - - +
461A HIS* 3.9 10.7 + - - -
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Residues in contact with ALA 459 (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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382A GLY* 3.2 16.0 + - - +
384A LEU* 3.6 32.1 - - + +
394A PHE* 4.1 16.2 - - + -
455A ALA 2.8 17.9 + - - +
456A PHE* 3.6 5.8 - - - +
458A ARG* 1.3 80.6 - - - +
460A ASN* 1.3 63.2 + - - +
461A HIS* 3.2 17.8 + - - -
572A ILE* 5.2 2.9 - - + -
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Residues in contact with ASN 460 (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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394A PHE* 5.8 1.2 - - - -
400A ASP* 5.5 3.5 - - - +
456A PHE* 3.0 25.8 + - - +
457A THR* 3.5 11.2 - - - +
459A ALA* 1.3 78.5 - - - +
461A HIS* 1.3 68.4 + - - +
572A ILE* 4.1 28.7 - - + +
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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