Contacts of the strand formed by residues 483 - 494 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A TYR* 3.5 7.7 - - - -
478A ASP* 2.9 32.5 + - + +
481A ALA* 4.0 25.4 - - + +
482A LYS* 1.3 79.9 - - - +
484A PRO* 1.3 75.2 - - + +
485A ALA 3.5 0.2 + - - -
508A ILE* 3.3 17.1 - - + +
517A THR* 5.8 0.7 - - - -
518A SER* 2.9 30.2 + - - -
520A TYR* 3.3 20.6 + - - +
71B ARG* 4.6 8.7 - - - +
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Residues in contact with PRO 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A TYR* 3.3 34.3 - - + +
476A TYR 3.6 10.3 - - - +
477A TYR* 4.0 8.3 - - + -
483A GLN* 1.3 88.3 - - + +
485A ALA* 1.3 59.3 + - - +
486A SER* 4.6 6.5 - - - +
487A GLN* 5.1 6.5 - - + +
506A ARG* 4.5 14.1 - - - +
508A ILE* 3.5 4.1 - - - +
520A TYR* 2.4 43.7 + - + +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A GLN* 4.8 8.1 - - + +
476A TYR* 2.9 20.1 + - + +
477A TYR 5.2 0.2 - - - -
478A ASP* 4.8 12.8 - - + +
483A GLN 3.5 2.6 + - - +
484A PRO* 1.3 73.9 - - - +
486A SER* 1.3 64.5 + - - +
506A ARG 4.9 0.4 - - - -
507A LYS* 3.6 0.6 - - - -
508A ILE* 2.9 39.7 + - + +
549A ILE* 3.8 5.0 - - - +
550A LEU* 5.1 1.1 - - + -
69B ILE* 3.7 26.0 - - + -
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ALA 4.3 1.3 + - - -
475A TYR* 3.6 2.1 - - - -
476A TYR* 2.8 38.8 + - - +
484A PRO* 3.6 2.8 - - - +
485A ALA* 1.3 83.6 - - - +
487A GLN* 1.3 67.9 + - - +
488A LEU* 5.6 1.2 - - - +
505A GLU* 5.6 2.4 + - - +
506A ARG 3.6 8.7 + - - -
507A LYS* 4.3 4.5 - - - +
548A GLY* 5.2 3.3 - - - -
549A ILE* 3.9 30.1 + - - +
550A LEU* 4.3 18.4 + - - +
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ALA 3.2 6.3 - - - +
475A TYR* 3.8 32.0 - - + +
484A PRO* 5.1 8.6 - - + +
486A SER* 1.3 80.1 + - - +
488A LEU* 1.3 67.5 + - - +
489A VAL* 4.3 19.2 - - + +
504A TYR* 4.7 15.5 - - + -
505A GLU* 3.3 6.4 - - - +
506A ARG* 2.9 53.5 + - + +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A VAL* 4.4 22.4 - - + -
473A GLY* 3.2 6.3 - - - -
474A ALA* 2.8 55.5 + - + +
486A SER* 5.6 2.2 - - - +
487A GLN* 1.3 78.8 - - - +
489A VAL* 1.3 69.3 + - - +
504A TYR* 3.4 10.5 - - - +
505A GLU* 4.2 18.2 - - + +
544A MET* 3.6 35.0 - - + +
545A LEU* 5.0 8.3 - - + +
547A SER* 3.6 11.4 - - - +
548A GLY* 4.4 11.2 - - - +
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ILE* 5.1 11.4 - - + -
472A VAL 3.7 6.3 - - - +
473A GLY* 5.6 1.8 - - - -
487A GLN* 4.3 22.7 - - + +
488A LEU* 1.3 84.4 - - - +
490A GLY* 1.3 64.8 + - - +
491A LEU* 6.2 1.6 - - + -
503A GLY* 3.5 1.4 - - - -
504A TYR* 2.9 47.0 + - + +
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Residues in contact with GLY 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ILE* 3.2 11.0 - - - +
472A VAL* 2.8 53.6 + - - +
489A VAL* 1.3 78.6 - - - +
491A LEU* 1.3 65.0 + - - -
502A LEU 3.4 9.4 - - - -
503A GLY* 4.3 0.7 - - - -
544A MET* 4.1 6.1 - - - -
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A ILE* 5.0 9.4 - - + -
469A TRP* 5.8 9.6 - - + -
470A ALA 3.4 5.4 - - - +
471A ILE* 3.7 28.9 - - + -
489A VAL* 6.2 2.0 - - + -
490A GLY* 1.3 80.9 - - - +
492A GLN* 1.3 63.1 + - - +
501A ASN* 3.6 2.6 - - - -
502A LEU* 2.9 53.8 + - + +
544A MET* 3.9 4.6 - - - +
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Residues in contact with GLN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ARG 3.8 0.6 - - - +
469A TRP* 3.5 8.1 - - - +
470A ALA* 2.7 45.1 + - + +
472A VAL* 6.6 0.2 - - + -
491A LEU* 1.3 75.7 - - - +
493A TYR* 1.3 63.0 + - - +
494A ASN* 3.3 21.4 + - - +
499A ALA* 3.1 24.6 - - + +
500A VAL 3.2 7.2 - - - +
501A ASN* 3.2 19.8 + - - +
540A GLY* 4.4 4.4 - - - -
541A THR* 2.7 42.4 + - - -
544A MET* 5.1 2.0 - - + +
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ARG* 2.8 40.2 + - - -
469A TRP* 3.8 24.7 - + + -
492A GLN* 1.3 75.1 - - - +
494A ASN* 1.3 70.2 + - - +
495A THR* 3.4 30.4 - - + +
498A TRP 4.0 0.2 - - - +
499A ALA* 3.2 4.7 - - - -
500A VAL* 2.9 52.7 + - + +
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Residues in contact with ASN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ARG* 2.8 56.3 + - + +
469A TRP 5.0 0.6 + - - -
470A ALA* 4.5 8.3 - - - +
492A GLN* 3.3 27.3 + - - +
493A TYR* 1.3 77.8 - - - +
495A THR* 1.3 65.7 + - - +
498A TRP 3.3 8.2 - - - +
499A ALA* 3.2 21.3 - - - +
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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