Contacts of the strand formed by residues 485 - 493 (chain A) in PDB entry 2IBI
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 CYS 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A LEU* 3.7 17.7 - - + -
424A THR 3.1 7.9 - - - +
425A CYS* 3.7 22.7 - - - -
426A THR* 4.3 0.9 - - - +
468A LEU* 2.8 34.4 + - + +
474A PRO* 3.4 37.7 - - + -
475A THR 5.6 0.2 - - - -
476A CYS* 5.1 5.6 - - - -
483A LYS* 3.7 9.9 - - - -
484A ARG* 1.3 78.4 - - - +
486A ILE* 1.3 67.6 + - - +
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Residues in contact with ILE 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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422A SER 3.4 2.1 - - - +
423A LEU* 3.3 3.8 - - - -
424A THR* 2.8 48.6 + - - +
426A THR* 3.9 22.7 - - + -
465A GLU* 3.4 38.6 - - + -
466A ASP 3.5 3.1 - - - +
467A VAL* 3.7 31.6 - - + -
484A ARG* 4.8 5.8 - - - +
485A CYS* 1.3 82.6 - - - +
487A LYS* 1.3 62.1 + - - +
488A LYS* 5.5 1.3 - - + +
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Residues in contact with LYS 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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421A SER* 2.9 27.0 + - - +
422A SER 3.3 4.3 - - - +
423A LEU* 3.8 10.5 - - + -
464A LYS 3.4 2.4 - - - +
465A GLU* 3.3 4.1 - - - -
466A ASP* 2.8 44.0 + - + +
468A LEU* 3.7 19.1 - - + -
485A CYS 4.2 0.2 - - - -
486A ILE* 1.3 73.4 - - - +
488A LYS* 1.3 65.1 + - - +
489A PHE* 3.4 24.7 - - - -
4B PHE* 3.3 30.7 - - + -
6B LYS* 6.1 0.2 - - - +
12B THR* 4.1 25.3 + - + +
66B THR* 2.8 29.8 + - - +
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Residues in contact with LYS 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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420A LYS 3.5 1.7 - - - +
421A SER* 3.5 4.3 - - - -
422A SER* 2.9 44.6 + - - +
463A THR* 3.3 21.8 + - - +
464A LYS 4.2 3.6 - - - +
465A GLU* 3.3 37.5 - - + +
486A ILE* 5.5 1.6 - - + -
487A LYS* 1.3 80.0 - - - +
489A PHE* 1.3 78.8 + - - +
490A SER* 4.0 9.0 + - - -
530A GLU 5.6 4.2 + - - -
531A PHE* 6.1 1.8 - - - +
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Residues in contact with PHE 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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419A LEU* 3.9 26.2 - - + -
420A LYS 3.2 11.7 - - - -
421A SER* 3.9 13.5 - - - -
436A ASP* 4.9 4.5 - - + -
462A PHE* 3.6 52.5 - + + +
463A THR* 3.5 19.3 + - + +
464A LYS 4.8 0.6 + - - -
466A ASP* 5.9 0.4 - - - -
487A LYS* 3.4 26.7 - - - -
488A LYS* 1.3 94.5 + - - +
490A SER* 1.3 61.5 + - - +
6B LYS* 4.1 17.7 - - + -
66B THR* 3.7 21.8 - - + -
68B HIS* 3.9 15.3 - + - -
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Residues in contact with SER 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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419A LEU* 3.7 7.4 - - - +
420A LYS* 2.9 42.0 + - - +
422A SER* 5.0 2.4 + - - -
463A THR* 4.8 2.7 - - - -
488A LYS* 4.7 9.2 - - - -
489A PHE* 1.3 75.8 - - - +
491A ILE* 1.3 62.2 + - - +
531A PHE 3.4 13.5 - - - -
532A ALA 4.2 1.8 - - - -
533A SER* 3.1 30.5 - - - -
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Residues in contact with ILE 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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418A GLN 3.8 4.9 - - - +
419A LEU* 4.2 16.6 - - + -
438A PHE* 4.5 7.9 - - + -
441A LEU* 4.3 21.5 - - + -
459A MET* 5.5 4.3 - - + -
462A PHE* 5.9 0.9 - - + -
463A THR* 5.3 7.2 - - + -
490A SER* 1.3 72.7 - - - +
492A GLN* 1.3 60.5 + - - +
493A ARG 3.4 30.1 - - - +
494A PHE* 3.8 41.6 - - + -
498A LEU* 6.3 0.9 - - + -
528A LEU* 5.3 6.1 - - + -
531A PHE* 2.8 34.1 + - + +
532A ALA* 3.5 4.9 - - - +
533A SER* 3.0 19.2 + - - -
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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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393A ASP* 4.1 30.7 + - - +
396A GLY* 4.9 2.6 - - - -
418A GLN* 2.7 39.3 + - - +
420A LYS* 3.2 31.0 + - + +
435A PHE* 3.7 17.4 - - + -
490A SER 3.6 1.6 + - - -
491A ILE* 1.3 76.0 - - - +
493A ARG* 1.3 64.8 + - + +
494A PHE* 5.4 1.9 - - - -
533A SER* 2.4 28.2 + - - -
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Residues in contact with ARG 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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396A GLY 6.1 0.4 - - - -
397A ARG* 4.4 20.0 - - - +
400A TRP* 3.1 63.1 - - + +
416A VAL 5.8 0.2 - - - +
417A GLY* 3.2 8.8 - - - -
418A GLN* 2.8 51.2 + - + +
438A PHE* 3.9 0.3 - - - -
491A ILE* 3.4 10.8 - - - +
492A GLN* 1.3 84.5 - - + +
494A PHE* 1.3 61.4 - - - +
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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