Contacts of the strand formed by residues 459 - 470 (chain E) in PDB entry 2UX0
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 ILE 459 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411E ASN* 3.7 45.6 + - + +
452E LEU* 6.0 4.5 - - + -
455E ASN* 4.1 11.0 - - - +
457E LYS* 3.3 12.7 + - + +
458E PRO* 1.3 84.2 - - - +
460E HIS* 1.3 60.2 + - - +
461E THR* 4.1 2.7 + - - +
484E THR* 4.2 17.9 - - + -
485E GLN 3.2 12.8 - - - +
486E TYR* 4.3 10.8 - - + -
446F PHE* 4.0 2.7 - - - -
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Residues in contact with HIS 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E ILE* 1.3 72.3 + - - +
461E THR* 1.3 72.0 + - - +
462E THR* 4.0 9.5 + - - -
483E LEU 3.7 0.9 - - - +
484E THR* 3.5 2.3 - - - -
485E GLN* 2.8 60.8 + - - +
442F ASP* 2.6 50.0 + - - -
443F PHE* 5.2 0.2 - - - -
446F PHE* 3.8 19.2 - - + -
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Residues in contact with THR 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407E ILE* 4.1 13.6 - - + +
411E ASN* 3.3 28.8 + - - +
459E ILE* 4.1 2.1 + - - +
460E HIS* 1.3 87.8 + - - +
462E THR* 1.3 68.7 + - - +
463E ILE* 4.5 9.0 - - + -
482E ARG* 3.6 33.3 - - + -
483E LEU 3.4 4.0 - - - -
484E THR* 4.0 12.5 + - - +
442F ASP* 5.2 0.2 - - - +
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Residues in contact with THR 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460E HIS* 4.0 14.6 - - - -
461E THR* 1.3 76.3 + - - +
463E ILE* 1.3 67.1 + - - +
464E LEU* 3.9 27.5 + - + +
481E ILE 3.5 1.0 - - - +
482E ARG* 3.4 5.7 - - - -
483E LEU* 2.7 51.7 + - + +
485E GLN* 4.5 1.7 + - - -
438F VAL* 5.5 4.0 - - + -
442F ASP* 4.1 8.7 + - - +
443F PHE* 4.5 13.3 - - + +
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Residues in contact with ILE 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E ILE* 6.2 2.7 - - + -
403E THR* 5.0 5.2 - - + -
404E GLU* 4.1 28.5 - - + +
407E ILE* 3.5 32.1 - - + -
461E THR* 4.3 8.7 - - + -
462E THR* 1.3 81.2 - - - +
464E LEU* 1.3 64.2 + - - +
465E ASN 4.1 0.5 + - - -
466E PRO* 4.2 22.3 - - + +
478E ILE* 6.1 1.6 - - + -
480E TYR* 3.9 34.5 - - + -
481E ILE 3.4 2.9 - - - +
482E ARG* 5.1 0.7 - - + -
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Residues in contact with LEU 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E THR* 4.0 20.0 - - + +
463E ILE* 1.3 75.7 - - - +
465E ASN* 1.3 86.0 + - + +
466E PRO 3.3 2.3 - - - -
480E TYR* 4.1 0.9 - - - -
481E ILE* 2.8 45.0 + - + +
483E LEU* 4.1 20.6 - - + -
436F ASN* 3.6 37.9 - - + +
437F LEU 3.9 18.4 - - - +
438F VAL* 4.5 7.2 - - + -
439F GLU* 5.7 2.2 - - + +
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Residues in contact with ASN 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464E LEU* 1.3 90.4 - - - +
466E PRO* 1.3 76.6 - - - +
467E HIS* 3.6 3.5 + - - +
479E ALA 4.0 3.8 - - - +
480E TYR* 4.6 1.4 - - - -
481E ILE* 5.5 9.7 - - + +
437F LEU 5.6 2.0 + - - -
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Residues in contact with PRO 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E ILE* 4.5 23.3 - - + -
463E ILE* 4.2 17.5 - - + +
464E LEU* 3.3 4.4 - - - -
465E ASN* 1.3 94.0 - - - +
467E HIS* 1.3 61.7 + - - +
468E VAL* 5.5 0.4 - - - -
478E ILE* 4.3 15.3 - - + -
479E ALA 3.4 7.9 - - - +
480E TYR* 4.0 16.6 - - + -
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Residues in contact with HIS 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E LYS* 4.7 8.4 + - - -
465E ASN 4.6 3.4 - - - +
466E PRO* 1.3 76.7 - - - +
468E VAL* 1.3 74.7 + - - +
469E HIS* 3.7 38.5 + + - -
477E CYS 3.8 1.0 - - - +
478E ILE* 3.4 3.1 - - - +
479E ALA* 2.8 40.9 + - + +
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Residues in contact with VAL 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E LYS* 2.8 73.0 + - + +
399E ILE* 3.9 26.5 - - + -
400E ILE* 4.2 9.2 - - + -
466E PRO 5.5 0.2 - - - -
467E HIS* 1.3 82.1 + - - +
469E HIS* 1.3 70.8 + - - +
470E VAL* 4.4 2.9 - - + -
476E ALA* 4.7 0.2 - - + -
477E CYS 3.3 7.6 - - - +
478E ILE* 3.6 33.7 - - + -
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Residues in contact with HIS 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E HIS* 3.7 33.7 + + - -
468E VAL* 1.3 72.3 - - - +
470E VAL* 1.3 62.6 + - - +
471E ILE* 3.6 12.8 + - + +
476E ALA* 3.3 4.9 - - - +
477E CYS* 2.8 53.9 + - + +
479E ALA* 6.0 4.5 - - + -
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Residues in contact with VAL 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E LEU* 3.8 29.0 - - + +
395E ARG* 4.0 38.8 - - + +
396E LYS* 4.1 18.8 - - + +
399E ILE* 5.5 0.7 - - + -
468E VAL* 3.9 8.1 + - + -
469E HIS* 1.3 72.8 - - - +
471E ILE* 1.3 59.8 + - - +
472E GLY* 3.7 23.2 + - - +
475E ALA 4.1 4.0 - - - +
476E ALA* 4.6 5.6 - - + +
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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