Contacts of the strand formed by residues 449 - 454 (chain A) in PDB entry 3HO5
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 THR 449 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ALA 3.7 0.7 - - - +
437A VAL* 3.4 2.6 - - - -
438A ASP* 2.7 50.0 + - - +
440A HIS* 3.1 18.8 + - - -
448A LEU* 1.3 76.3 + - - +
450A ILE* 1.3 65.6 + - - +
451A LEU 4.2 0.4 - - - +
465A ILE* 3.8 21.5 - - + -
466A LEU 3.3 4.3 - - - +
467A GLN* 3.5 36.0 + - + +
509A TYR* 3.7 19.2 - - + +
530A TRP* 6.0 0.2 - - + -
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Residues in contact with ILE 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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358A LEU* 5.2 4.0 - - + -
366A TYR* 5.5 4.7 - - + -
368A ILE* 4.2 16.6 - - + -
392A VAL* 4.6 13.7 - - + -
435A CYS* 3.9 19.1 - - + -
436A ALA 3.3 5.6 - - - +
437A VAL* 4.4 10.1 - - + -
448A LEU* 3.7 24.0 - - + -
449A THR* 1.3 74.3 - - - +
451A LEU* 1.3 60.2 + - - +
452A CYS* 3.6 18.6 - - - -
464A ARG 5.5 0.4 - - - +
465A ILE* 3.6 1.4 - - - +
466A LEU* 2.7 75.3 + - + +
480A LEU* 5.3 4.0 - - + -
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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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435A CYS* 3.4 0.5 - - - -
436A ALA* 2.8 40.0 + - + +
449A THR* 4.2 0.6 - - + -
450A ILE* 1.3 74.0 - - - +
452A CYS* 1.3 64.8 + - - +
463A ALA* 4.1 24.5 - - + -
464A ARG 3.5 7.2 - - - +
465A ILE* 4.1 20.6 - - + +
483A PHE* 4.3 8.3 - - + -
509A TYR* 3.7 37.2 - - + -
511A PHE* 3.8 25.0 - - + -
521A LEU* 4.9 7.4 - - + -
530A TRP* 4.0 25.1 - - + -
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Residues in contact with CYS 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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368A ILE* 4.7 5.2 - - - -
429A LEU* 5.0 10.8 - - + -
432A PRO* 4.4 7.0 - - + -
435A CYS* 2.0 50.0 - - - +
450A ILE* 3.6 21.1 - - - -
451A LEU* 1.3 78.6 - - - +
453A SER* 1.3 68.6 + - - +
454A ASP* 5.7 0.2 - - + -
463A ALA* 3.2 5.9 - - - +
464A ARG* 2.7 50.1 + - + +
480A LEU* 6.2 0.9 - - - -
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Residues in contact with SER 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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431A ASP 5.3 0.2 + - - -
432A PRO* 3.3 18.4 - - - +
433A GLY* 3.5 20.9 + - - +
434A ARG 5.2 1.8 + - - -
435A CYS* 5.2 0.4 - - - -
452A CYS* 1.3 79.4 - - - +
454A ASP* 1.3 64.4 + - - +
461A SER* 5.8 1.6 - - - -
462A SER 3.6 5.6 - - - -
486A PHE* 4.4 8.7 - - - -
491A LEU* 4.0 34.7 + - - -
493A GLY* 4.2 4.5 - - - -
511A PHE* 4.0 20.6 - - - -
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.1 2.9 - - + +
430A HIS* 3.0 19.2 + - - +
431A ASP 2.6 34.9 + - - -
432A PRO* 4.3 1.6 - - + -
452A CYS* 5.7 0.4 - - + -
453A SER* 1.3 79.3 + - - +
455A SER* 1.3 69.2 + - - +
456A ASN* 3.0 22.8 + - - +
461A SER* 3.6 5.9 + - - -
462A SER* 2.9 34.2 + - - +
464A ARG* 2.7 34.9 + - + +
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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