Contacts of the helix formed by residues 447 - 454 (chain A) in PDB entry 1S11
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 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A VAL* 3.4 29.3 - - + +
418A ILE 3.8 9.0 + - - +
419A VAL* 3.4 14.4 - - - +
444A ASN* 2.6 34.0 + - - +
446A THR* 1.4 80.7 - - - +
448A GLU* 1.3 54.1 + - - +
450A PRO* 3.2 6.0 - - - +
451A GLY* 2.6 34.0 + - - -
462A ILE* 4.3 9.3 - - + +
478A LEU* 3.5 24.8 - - + +
480A LEU* 4.9 3.3 - - - +
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Residues in contact with GLU 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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444A ASN* 5.5 1.2 - - - +
445A LYS* 5.4 6.9 - - - -
446A THR 4.9 0.4 - - - +
447A ASP* 1.3 77.2 - - - +
449A GLU* 1.3 65.7 + - + +
451A GLY 4.0 0.7 - - - +
452A TYR* 2.6 47.2 + - + -
462A ILE* 3.8 25.3 - - + +
466A LYS* 2.4 43.8 + - - -
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Residues in contact with GLU 449 (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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422A VAL* 4.4 20.1 - - + +
425A LEU* 5.3 7.2 - - - +
445A LYS 4.7 14.8 + - - +
446A THR 4.6 1.4 + - - +
448A GLU* 1.3 79.9 - - + +
450A PRO* 1.4 59.4 - - + +
452A TYR* 3.6 3.6 - - - +
453A ILE* 2.6 55.5 + - + +
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Residues in contact with PRO 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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418A ILE 3.6 13.5 - - - +
420A GLU* 3.3 42.4 - - + +
422A VAL* 5.6 2.5 - - + -
446A THR 3.0 29.8 - - - +
447A ASP 3.2 9.9 - - - +
449A GLU* 1.4 90.3 - - + +
451A GLY* 1.3 61.3 + - - +
453A ILE* 2.7 6.2 + - + +
454A LYS* 2.6 45.8 + - + +
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Residues in contact with GLY 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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418A ILE* 4.3 4.7 + - - -
447A ASP 2.6 24.1 + - - -
448A GLU 3.0 1.5 + - - -
450A PRO* 1.3 71.2 - - - +
452A TYR* 1.4 58.8 + - - +
454A LYS* 4.7 3.1 - - - -
457A CYS* 3.4 15.9 - - - +
458A LYS 3.4 10.4 + - - -
459A GLY* 3.5 26.7 + - - -
462A ILE* 4.2 10.8 - - - -
796B TRP* 3.6 2.8 - - - -
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Residues in contact with TYR 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 GLU* 2.6 53.4 + - + +
449A GLU* 3.8 3.8 - - - +
450A PRO 3.2 0.7 - - - -
451A GLY* 1.4 71.1 - - - +
453A ILE* 1.3 59.6 + - + +
457A CYS* 2.6 36.5 - - + -
462A ILE* 3.7 7.2 - - + -
463A ASP* 2.4 29.1 + - - -
466A LYS* 2.8 18.1 + - - +
796B TRP* 3.7 18.2 - + - -
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Residues in contact with ILE 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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449A GLU* 2.6 44.2 + - + +
450A PRO* 2.7 4.4 + - + -
452A TYR* 1.3 75.8 - - + +
454A LYS* 1.4 49.1 + - - +
455A LYS* 2.4 24.0 + - - +
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Residues in contact with LYS 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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418A ILE* 3.6 32.5 - - + +
419A VAL 3.8 7.1 + - - -
420A GLU* 2.3 50.2 + - - +
450A PRO* 2.6 35.2 + - + +
451A GLY* 4.3 2.9 - - - +
452A TYR 3.5 2.0 + - - -
453A ILE* 1.4 64.6 - - - +
455A LYS* 1.4 63.2 + - + +
456A CYS 3.1 0.5 + - - -
457A CYS* 2.6 29.9 + - - +
458A LYS* 4.5 9.6 + - + +
459A GLY 6.1 0.2 - - - +
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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