Contacts of the strand formed by residues 462 - 468 (chain B) in PDB entry 5DX1
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 LYS 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B SER* 5.1 5.5 - - - -
426B LEU* 3.6 6.5 - - - +
453B VAL* 3.8 24.0 - - + +
454B ALA 3.3 11.7 - - - +
455B GLN* 4.3 17.7 - - + +
460B GLY 3.4 8.5 + - - +
461B SER* 1.3 75.7 - - - +
463B SER* 1.3 68.8 + - - +
464B SER* 4.4 10.2 + - - +
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 3.5 8.1 - - - +
424B SER* 2.9 35.0 + - - -
426B LEU* 3.7 18.6 - - - +
453B VAL* 3.5 2.6 - - - +
454B ALA* 2.8 34.4 + - - +
462B LYS* 1.3 77.6 - - - +
464B SER* 1.3 61.7 + - - +
465B ASN* 3.1 22.0 + - - -
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Residues in contact with SER 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLN* 5.6 2.3 - - - +
424B SER 5.8 0.3 + - - -
452B ILE 3.5 4.5 - - - -
453B VAL* 4.3 18.5 - - - +
462B LYS* 4.4 10.9 + - - +
463B SER* 1.3 73.2 + - - +
465B ASN* 1.3 72.5 + - - +
466B LEU* 6.5 0.2 - - - -
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Residues in contact with ASN 465 (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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335B PHE 6.1 0.4 - - - +
421B LEU 3.6 9.5 - - - +
422B PHE* 3.0 34.4 - - + -
423B GLN* 2.9 32.1 + - - +
424B SER 4.7 0.2 + - - -
450B ILE 3.8 0.5 - - - +
451B SER* 3.5 4.3 + - - -
452B ILE* 2.8 45.9 + - + +
453B VAL* 5.3 0.2 - - - +
463B SER* 3.1 13.5 + - - -
464B SER* 1.3 85.4 - - - +
466B LEU* 1.3 66.5 + - - +
467B LEU* 4.3 11.3 - - + +
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Residues in contact with LEU 466 (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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335B PHE 4.4 1.4 - - - +
336B ARG* 3.4 41.9 - - + +
450B ILE 3.3 4.0 - - - +
451B SER* 3.8 24.9 - - - +
464B SER* 6.5 0.2 - - - -
465B ASN* 1.3 79.8 - - - +
467B LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 467 (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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335B PHE 3.5 21.3 - - - +
336B ARG* 3.5 10.8 + - - +
337B GLN 4.1 2.2 - - - +
338B PRO* 4.0 24.5 - - + -
420B CYS* 3.8 43.1 - - + -
421B LEU 4.4 4.9 - - - +
449B ASP* 3.6 6.2 - - - +
450B ILE* 2.8 50.2 + - + +
452B ILE* 4.2 13.9 - - + -
465B ASN* 4.3 12.1 - - + +
466B LEU* 1.3 88.2 - - - +
468B ASP* 1.3 60.5 - - - +
469B LEU 3.8 0.9 - - - -
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Residues in contact with ASP 468 (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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151A GLN* 5.4 1.4 + - - -
155A TYR* 4.5 5.9 + - - -
336B ARG* 3.0 35.3 + - + +
338B PRO* 3.3 14.2 - - - +
443B ASN* 4.7 0.9 + - - -
445B ARG* 3.1 36.5 + - - -
448B TYR 4.3 4.7 - - - +
449B ASP* 5.0 2.3 - - - +
467B LEU* 1.3 71.6 - - - +
469B LEU* 1.3 65.3 + - - +
470B LYS* 3.6 6.6 + - - +
471B ASN* 3.1 36.6 + - + +
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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