Contacts of the strand formed by residues 483 - 493 (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 GLN 483 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477E TYR* 3.7 8.0 - - - -
478E ASP* 2.9 31.7 + - + +
481E ALA* 3.9 25.3 - - + +
482E LYS* 1.3 80.4 - - - +
484E PRO* 1.3 73.8 - - + +
485E ALA 3.4 0.2 + - - -
508E ILE* 3.4 16.7 - - + +
511E TRP* 5.8 0.2 - - - -
517E THR* 5.1 4.3 + - - -
518E SER* 3.3 28.6 + - - -
520E TYR* 3.2 21.7 + - - +
71F ARG* 4.8 7.9 - - - +
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Residues in contact with PRO 484 (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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475E TYR* 6.3 0.2 - - + -
476E TYR 3.7 8.3 - - - +
477E TYR* 3.4 34.8 - - + +
483E GLN* 1.3 87.3 - - + +
485E ALA* 1.3 60.0 + - - +
486E SER* 4.6 9.0 - - - +
487E GLN* 5.2 11.9 - - + +
506E ARG* 4.7 12.6 - - - +
508E ILE* 3.7 1.9 - - - +
520E TYR* 2.4 42.9 + - + +
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Residues in contact with ALA 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456E GLN* 5.0 6.3 - - + +
476E TYR* 2.9 20.1 + - + +
477E TYR 5.1 0.4 - - - -
478E ASP* 4.7 13.0 - - + +
483E GLN 3.4 2.4 + - - +
484E PRO* 1.3 73.5 - - - +
486E SER* 1.3 63.9 + - - +
507E LYS* 3.6 0.8 - - - -
508E ILE* 2.9 41.8 + - + +
520E TYR* 5.0 0.9 - - - -
549E ILE* 4.1 3.6 - - - +
550E LEU* 5.2 0.9 - - + -
69F ILE* 3.9 26.0 - - + -
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Residues in contact with SER 486 (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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474E ALA 4.4 1.1 - - - -
475E TYR* 3.8 1.4 - - - -
476E TYR* 2.9 34.5 + - - +
477E TYR* 5.6 0.2 - - - -
484E PRO* 3.5 3.7 - - - +
485E ALA* 1.3 83.0 - - - +
487E GLN* 1.3 68.5 + - - +
488E LEU* 5.7 1.0 - - - +
505E GLU* 5.8 1.7 - - - +
506E ARG 3.4 9.4 + - - -
507E LYS* 4.5 4.1 - - - +
548E GLY* 5.3 2.9 - - - -
549E ILE* 3.8 31.1 + - - +
550E LEU* 4.2 18.9 + - - +
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Residues in contact with GLN 487 (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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474E ALA 3.3 6.1 - - - -
475E TYR* 3.3 43.9 + - + -
477E TYR* 5.7 0.8 + - - -
484E PRO* 5.2 12.6 - - + +
486E SER* 1.3 80.4 + - - +
488E LEU* 1.3 66.7 + - - +
489E VAL* 4.1 11.5 - - + +
504E TYR* 4.6 16.6 - - + -
505E GLU* 3.3 7.0 - - - +
506E ARG* 2.9 53.1 + - + +
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Residues in contact with LEU 488 (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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472E VAL* 4.4 14.6 - - + -
473E GLY* 3.3 7.1 - - - -
474E ALA* 2.9 55.5 + - + +
475E TYR* 4.9 0.7 - - - -
486E SER* 5.7 0.9 - - - +
487E GLN* 1.3 80.1 - - - +
489E VAL* 1.3 68.9 + - - +
504E TYR 3.4 9.6 - - - +
505E GLU* 4.0 18.2 - - + +
544E MET* 3.5 28.7 - - + +
545E LEU* 4.9 7.6 - - + +
547E SER* 3.3 26.0 - - - +
548E GLY* 4.3 12.3 - - - +
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Residues in contact with VAL 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E ILE* 5.1 11.2 - - + -
472E VAL 3.7 6.3 - - - +
473E GLY* 5.7 0.9 - - - -
475E TYR* 3.7 24.7 - - + +
487E GLN* 4.1 15.3 - - + +
488E LEU* 1.3 83.4 - - - +
490E GLY* 1.3 64.4 + - - +
491E LEU* 6.0 2.7 - - + -
503E GLY* 3.5 1.2 - - - -
504E TYR* 2.8 47.4 + - + +
544E MET* 5.0 0.2 - - - +
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Residues in contact with GLY 490 (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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471E ILE* 3.4 9.6 - - - +
472E VAL* 2.9 45.1 + - - +
489E VAL* 1.3 78.9 - - - +
491E LEU* 1.3 62.3 + - - -
502E LEU 3.4 10.3 - - - -
544E MET* 3.8 11.7 - - - -
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Residues in contact with LEU 491 (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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465E ILE* 5.8 2.7 - - + -
469E TRP* 5.0 21.8 - - + -
470E ALA 3.6 4.9 - - - +
471E ILE* 3.7 29.4 - - + -
489E VAL* 6.0 3.4 - - + -
490E GLY* 1.3 82.0 - - - +
492E GLN* 1.3 61.6 + - - +
500E VAL* 5.9 0.2 - - - +
502E LEU* 2.9 53.5 + - + +
544E MET* 3.8 5.2 - - - +
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Residues in contact with GLN 492 (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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468E ARG 4.5 0.2 - - - +
469E TRP* 3.8 7.3 - - - -
470E ALA* 2.9 45.3 + - + +
491E LEU* 1.3 76.0 - - - +
493E TYR* 1.3 70.8 + - - +
494E ASN* 4.3 11.6 - - + +
499E ALA 4.9 2.8 + - - +
500E VAL 4.0 6.3 - - - +
501E ASN* 3.0 26.5 + - - +
541E THR* 3.4 35.9 + - - +
543E GLN* 5.1 8.0 + - - +
544E MET* 4.8 10.8 - - + +
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Residues in contact with TYR 493 (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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468E ARG* 3.4 22.6 - - + +
469E TRP* 3.4 49.4 - + + -
492E GLN* 1.3 81.4 + - - +
494E ASN* 1.3 71.2 + - - +
495E THR* 4.0 20.7 - - - -
499E ALA* 3.2 41.2 + - + +
500E VAL* 3.4 15.8 + - + +
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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