Contacts of the strand formed by residues 444 - 450 (chain A) in PDB entry 3R2W
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 LEU 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A ARG* 3.1 22.3 + - - -
417A PRO* 3.4 30.2 - - + +
418A LEU 4.8 2.9 - - - +
419A VAL* 4.9 5.2 - - + -
441A MET* 2.6 38.0 + - + +
443A GLU* 1.3 71.1 - - - +
445A ASP* 1.3 67.1 + - - +
446A HIS* 4.1 16.8 - - - +
447A LEU* 4.1 14.8 - - + +
461A LEU* 3.3 51.4 - - + +
463A GLY 3.4 10.1 - - - +
465A VAL* 5.8 1.1 - - + -
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Residues in contact with ASP 445 (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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411A ARG* 4.3 12.8 + - - +
413A PHE* 5.8 0.5 - - - -
415A THR* 4.7 6.2 + - - -
417A PRO* 3.4 11.2 - - - +
418A LEU* 3.2 19.2 + - - +
443A GLU 3.5 12.5 - - - +
444A LEU* 1.3 79.1 - - - +
446A HIS* 1.3 62.4 + - + +
463A GLY* 2.7 21.8 + - - +
464A THR* 5.0 3.8 - - + -
276C ARG* 3.6 26.3 - - - +
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Residues in contact with HIS 446 (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 LEU* 3.5 38.7 - - + +
420A LYS* 5.6 10.3 - - + -
444A LEU* 4.1 4.9 - - - +
445A ASP* 1.3 82.4 - - - +
447A LEU* 1.3 71.1 + - - +
448A THR* 3.4 29.9 - - + +
463A GLY 3.0 5.8 + - - +
464A THR* 3.2 26.3 - - + -
465A VAL* 2.8 25.1 + - - +
466A ILE* 4.7 5.8 - - + -
446C HIS* 4.1 31.2 + + + -
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Residues in contact with LEU 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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391A LEU* 4.1 18.6 - - + -
418A LEU 3.0 14.1 + - - +
419A VAL* 3.5 22.6 - - + -
420A LYS* 3.1 23.3 + - - +
421A LEU* 4.8 6.5 - - + -
435A PHE* 5.8 0.7 - - + -
444A LEU* 4.1 13.9 - - + -
446A HIS* 1.3 79.0 + - - +
448A THR* 1.3 64.7 + - - +
449A VAL* 3.8 25.4 - - + -
455A PHE* 4.8 4.3 - - + -
461A LEU* 3.7 25.1 - - + -
465A VAL* 3.2 35.7 - - + +
467A ILE* 4.7 3.1 - - + -
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Residues in contact with THR 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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420A LYS* 3.3 36.5 + - - +
446A HIS* 3.4 23.3 - - - +
447A LEU* 1.3 75.5 - - - +
449A VAL* 1.3 67.1 + - - +
450A SER* 5.5 2.1 - - - -
465A VAL 3.0 4.3 + - - +
466A ILE* 3.4 32.1 - - + +
467A ILE 3.1 20.8 + - - +
468A ILE* 5.8 2.3 - - - +
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Residues in contact with VAL 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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420A LYS* 3.0 10.4 + - - +
421A LEU* 4.1 8.7 - - + -
422A GLY* 2.9 26.9 + - - +
425A PHE* 3.5 39.0 - - + -
447A LEU* 3.8 31.9 - - + -
448A THR* 1.3 81.2 + - - +
450A SER* 1.3 63.7 + - - +
453A VAL* 4.2 11.2 - - + -
455A PHE* 4.3 15.3 - - + -
467A ILE* 3.1 17.9 - - + +
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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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422A GLY* 4.1 12.3 - - - -
423A SER 5.6 0.7 - - - -
448A THR* 5.5 2.5 - - - -
449A VAL* 1.3 76.3 - - - +
451A GLY* 1.3 58.5 + - - +
453A VAL* 4.4 2.3 - - - +
467A ILE 3.0 7.8 + - - +
468A ILE* 3.3 25.5 - - - +
469A ALA* 2.7 32.4 + - - +
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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