Contacts of the strand formed by residues 454 - 465 (chain E) in PDB entry 5IXM
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 454 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431E ARG* 3.7 19.3 - - + +
432E TYR* 3.1 14.4 - - - -
433E ALA* 2.9 46.8 + - + +
438E ILE* 4.4 8.5 - - + -
452E GLN* 5.3 0.4 - - - +
453E GLY* 1.3 81.8 - - - +
455E SER* 1.3 63.4 + - - +
456E GLN* 4.2 13.5 - - + +
478E ASP* 5.6 1.8 - - - -
480E LYS* 5.8 0.2 - - - -
68F SER* 4.3 15.5 - - - +
69F ILE 3.3 26.5 - - - +
70F PHE* 4.0 15.0 - - + -
76F ALA* 4.0 16.6 - - + -
77F GLU* 4.6 3.1 - - - +
107F PHE* 4.7 3.1 - - + -
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Residues in contact with SER 455 (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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430E TYR* 2.8 27.3 + - - -
431E ARG 3.3 5.6 - - - -
432E TYR* 4.4 2.0 - - - -
453E GLY 4.3 0.4 - - - -
454E ILE* 1.3 76.4 - - - +
456E GLN* 1.3 59.4 + - - +
478E ASP* 3.3 10.8 + - - +
479E THR* 2.9 47.6 + - - +
480E LYS* 3.6 26.1 + - - +
602G C8E 3.6 6.2 - - - -
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Residues in contact with GLN 456 (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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429E ASN* 4.0 4.9 + - - +
430E TYR* 3.2 6.6 - - - -
431E ARG* 2.9 44.1 + - + +
454E ILE* 4.2 10.7 - - + +
455E SER* 1.3 73.2 - - - +
457E VAL* 1.3 69.9 + - - +
476E TYR* 3.3 29.9 - - + -
477E TYR 3.3 15.5 - - - +
478E ASP* 5.2 2.7 - - + -
485E ALA* 5.0 3.9 - - + +
550E LEU* 3.9 10.0 - - - +
67F VAL 2.9 25.6 + - - -
68F SER* 3.4 21.4 - - - -
69F ILE* 3.6 12.6 + - - +
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Residues in contact with VAL 457 (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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429E ASN 3.6 8.3 - - - +
430E TYR* 3.7 19.3 - - + -
456E GLN* 1.3 75.3 - - - +
458E GLY* 1.3 66.1 + - - +
459E THR* 5.5 4.9 - - + -
475E TYR 3.6 1.2 - - - +
476E TYR* 3.3 3.3 - - - +
477E TYR* 2.8 40.1 + - + +
479E THR* 3.5 24.7 - - + -
215G LEU* 5.9 0.4 - - + -
219G TRP* 5.9 3.8 - - + -
222G ILE* 6.0 6.3 - - + -
602G C8E 3.7 33.9 - - - +
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Residues in contact with GLY 458 (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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428E LEU* 3.4 1.0 - - - +
429E ASN* 2.9 53.7 + - - +
457E VAL* 1.3 78.0 - - - +
459E THR* 1.3 69.3 + - - +
475E TYR 3.2 7.2 - - - -
476E TYR* 3.6 11.2 - - - -
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Residues in contact with THR 459 (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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426E ILE* 6.5 0.4 - - - -
427E GLN 3.2 4.5 - - - -
428E LEU* 4.0 26.5 - - + -
457E VAL* 5.5 5.8 - - + -
458E GLY* 1.3 79.2 - - - +
460E THR* 1.3 67.7 + - - +
473E GLY 5.2 0.2 - - - -
474E ALA* 3.2 1.4 - - - -
475E TYR* 2.9 52.8 + - - +
476E TYR* 4.5 1.6 - - - -
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Residues in contact with THR 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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425E MET* 3.3 14.9 - - + +
426E ILE* 3.5 2.4 - - - +
427E GLN* 2.9 42.3 + - - -
429E ASN* 5.3 0.3 + - - -
459E THR* 1.3 79.4 + - - +
461E ALA* 1.3 67.2 + - - +
473E GLY 3.2 13.9 - - - +
474E ALA* 4.2 6.9 - - + +
476E TYR* 3.4 23.2 + - - -
545E LEU* 3.7 21.5 - - + -
552E TYR* 4.4 19.8 - - + +
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Residues in contact with ALA 461 (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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425E MET* 3.2 14.8 - - - +
426E ILE* 4.6 12.1 - - + -
460E THR* 1.3 78.3 - - - +
462E SER* 1.3 63.7 + - - +
463E TRP* 5.4 4.0 - - + +
471E ILE 4.5 0.7 - - - -
472E VAL* 3.2 6.0 - - - +
473E GLY* 2.9 36.2 + - - +
545E LEU* 3.9 4.5 - - - +
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Residues in contact with SER 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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423E ASP* 2.8 23.7 + - - +
424E ARG* 3.2 0.9 - - - -
425E MET* 2.9 40.8 + - - -
461E ALA* 1.3 75.3 - - - +
463E TRP* 1.3 60.8 + - - +
470E ALA* 5.9 2.1 - - - +
471E ILE 3.4 6.0 + - - -
472E VAL* 3.6 10.7 - - - +
541E THR* 3.1 30.3 + - - +
545E LEU* 4.2 9.0 - - - -
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Residues in contact with TRP 463 (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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418E TYR* 3.7 25.8 - + - -
423E ASP 4.2 1.3 - - - -
424E ARG* 3.3 34.5 - - + +
425E MET 3.7 14.4 - - - -
426E ILE* 3.5 38.1 - - + -
461E ALA* 5.7 4.0 - - + -
462E SER* 1.3 87.4 + - - +
464E PRO* 1.3 84.9 - - + +
465E ILE* 5.8 1.3 - - + -
470E ALA* 4.5 2.7 - - - -
471E ILE* 2.9 46.2 + - + +
360G PHE* 5.5 7.6 - + - -
603G C8E 4.3 13.2 - - - -
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Residues in contact with PRO 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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423E ASP* 3.5 26.4 - - + +
424E ARG* 3.5 41.6 + - + +
463E TRP* 1.3 104.8 - - + +
465E ILE* 1.3 63.2 + - - +
466E ALA 5.0 3.1 - - - +
469E TRP 3.4 12.3 - - - +
470E ALA* 4.1 4.7 - - + -
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Residues in contact with ILE 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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463E TRP* 4.2 2.2 - - + +
464E PRO* 1.3 78.1 - - - +
466E ALA* 1.3 79.9 + - + +
467E ASP 4.4 0.2 - - - -
469E TRP* 2.9 42.3 + - + +
470E ALA 5.2 0.4 - - - -
471E ILE* 3.7 38.6 - - + +
491E LEU* 5.8 2.9 - - + -
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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