Contacts of the strand formed by residues 445 - 450 (chain B) in PDB entry 3N2Z
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 445 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ILE* 3.0 35.4 - - + +
417B SER* 3.9 10.8 - - - +
419B HIS* 3.3 30.7 - - + +
420B THR* 3.9 4.3 - - - +
422B ILE* 3.5 42.8 - - + -
424B PHE* 4.7 5.8 - - + -
440B ASP* 3.7 0.2 - - - -
441B ILE* 2.9 54.7 + - + -
442B THR* 2.8 20.0 + - - +
444B THR* 1.4 71.7 - - - +
446B VAL* 1.3 58.0 - - - +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ILE 3.1 9.6 + - - +
423B VAL* 3.4 24.1 - - + -
424B PHE* 2.7 36.8 + - - -
437B VAL* 5.0 0.4 - - - -
440B ASP* 3.6 17.3 - - - +
442B THR 3.6 9.4 - - - +
443B ASP* 3.4 27.1 - - - +
444B THR 4.1 2.9 - - - +
445B LEU* 1.3 79.0 - - - +
447B ALA* 1.3 55.9 + - - +
448B VAL* 4.8 4.9 - - + -
480B HIS* 3.8 29.6 - - + +
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B PHE* 3.3 6.5 - - - -
437B VAL* 3.8 13.5 - - + +
438B THR* 3.4 36.3 - - - +
439B LYS* 3.5 16.8 - - - +
440B ASP* 2.9 15.5 + - - +
446B VAL* 1.3 71.0 - - - +
448B VAL* 1.3 69.2 + - - +
449B THR 4.3 0.4 - - - -
476B LEU* 5.5 0.5 - - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B VAL* 3.6 24.0 - - + -
424B PHE 2.9 11.9 + - - +
425B SER* 3.3 8.7 - - - -
426B ASN* 2.9 27.1 + - - +
437B VAL 5.2 0.2 + - - -
446B VAL* 4.8 4.7 - - + -
447B ALA* 1.3 80.1 - - - +
449B THR* 1.3 62.7 + - - +
450B ILE* 3.8 2.5 - - + +
473B ALA* 3.4 37.7 - - + +
476B LEU* 3.7 29.4 - - + -
477B GLU* 4.4 8.3 - - + +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASN* 3.3 12.1 - - + +
427B GLY 5.6 1.1 - - - +
428B GLU* 4.6 21.5 + - + -
438B THR* 4.1 40.5 + - + +
447B ALA 4.3 0.6 - - - -
448B VAL* 1.3 76.9 - - - +
450B ILE* 1.3 61.6 + - - +
451B SER 3.9 2.5 + - - -
469B SER* 4.7 6.4 - - - +
473B ALA* 5.1 0.5 - - - +
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B SER* 4.1 12.8 - - - -
426B ASN 3.0 29.6 + - - +
427B GLY* 4.3 4.3 - - - +
428B GLU* 3.1 16.2 + - - +
448B VAL 3.8 11.4 - - - +
449B THR* 1.3 72.7 - - - +
451B SER* 1.3 65.3 + - - +
452B GLU 4.8 0.2 - - - -
453B GLY* 2.8 34.9 + - - +
457B LEU* 4.6 7.0 - - + +
458B ASP* 4.3 18.2 - - + +
467B PRO* 5.5 0.2 - - + -
469B SER* 4.1 4.5 - - - +
470B VAL* 3.9 32.3 - - + +
473B ALA* 3.8 23.6 - - + -
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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