Contacts of the strand formed by residues 420 - 426 (chain B) in PDB entry 6HYI
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 PRO 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B ILE* 3.7 17.7 - - + -
413B GLY 3.3 9.2 - - - +
414B ARG* 3.9 16.1 - - - +
415B ASP* 4.7 1.9 - - - +
418B GLY 4.3 3.1 - - - +
419B GLU* 1.3 102.1 - - + +
421B THR* 1.3 59.6 + - - +
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Residues in contact with THR 421 (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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412B ILE* 3.4 5.9 - - - +
413B GLY* 2.8 50.3 + - - -
414B ARG 3.8 2.7 - - - +
415B ASP* 3.7 28.9 - - + +
419B GLU 4.1 2.0 - - - -
420B PRO* 1.3 75.1 - - - +
422B LYS* 1.3 67.2 + - - +
423B VAL* 3.4 6.9 + - + -
485B TYR* 4.7 4.7 - - + -
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Residues in contact with LYS 422 (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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410B GLU* 3.8 27.2 + - + +
411B VAL 3.7 9.4 - - - +
412B ILE* 4.5 5.8 - - + +
421B THR* 1.3 78.8 + - - +
423B VAL* 1.3 63.0 + - - +
424B CYS* 4.2 9.2 - - - +
425B GLU* 2.8 43.9 + - - -
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 2.8 21.6 + - + +
413B GLY* 3.6 24.5 - - - +
421B THR* 3.8 5.8 - - + +
422B LYS* 1.3 76.6 - - - +
424B CYS* 1.3 64.3 + - - +
482B LYS* 3.9 6.7 - - - +
485B TYR* 3.7 37.5 - - + -
602B NOS 3.7 35.9 - - + +
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Residues in contact with CYS 424 (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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410B GLU* 3.6 4.3 - - - +
411B VAL* 2.9 30.9 + - - +
422B LYS* 3.9 7.7 - - - +
423B VAL* 1.3 83.8 - - + +
425B GLU* 1.3 66.3 - - - +
426B PHE* 3.7 18.2 - - - -
482B LYS* 3.7 29.8 - - + -
602B NOS 3.5 32.3 - - - -
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Residues in contact with GLU 425 (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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408B THR* 3.6 22.5 - - + +
409B VAL 3.2 13.7 - - - +
410B GLU* 4.4 3.4 - - - +
411B VAL 4.8 0.2 - - - +
422B LYS* 2.8 37.1 + - - -
424B CYS* 1.3 75.4 - - - +
426B PHE* 1.3 61.6 + - - +
450B THR* 4.9 8.1 + - - +
482B LYS* 2.8 32.6 + - - -
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Residues in contact with PHE 426 (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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404B ILE* 3.9 5.6 - - + +
408B THR* 3.4 4.0 - - - +
409B VAL* 2.9 41.0 + - + +
411B VAL* 3.7 18.8 - - + -
424B CYS* 3.7 7.0 - - - -
425B GLU* 1.3 78.2 - - - +
427B THR* 1.3 66.1 + - - +
430B ASP* 3.5 34.1 - - + +
431B HIS 4.5 4.3 - - - -
432B ILE* 3.5 24.7 - - + -
482B LYS* 3.6 23.3 - - + +
483B TYR* 3.3 29.4 - + - -
602B NOS 3.5 30.3 - + - -
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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