Contacts of the strand formed by residues 468 - 475 (chain A) in PDB entry 2IO1
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A PRO* 3.9 22.4 - - + +
434A ALA 3.1 4.7 + - - +
435A LEU* 3.4 26.4 - - + +
436A HIS* 3.1 24.1 + - - +
466A GLN* 4.6 0.2 - - - +
467A GLU* 1.3 82.4 + - - +
469A ILE* 1.3 65.7 + - - +
470A LEU* 3.8 17.7 - - + -
483A VAL* 4.4 9.4 - - + -
484A ILE 3.6 5.6 - - - +
485A ASP* 4.5 7.0 - - - +
487A ARG* 3.8 27.4 - - - +
559A ILE* 3.5 27.1 - - + +
560A SER* 3.9 10.1 - - - +
562A ASP* 4.4 1.3 - - - +
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Residues in contact with ILE 469 (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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436A HIS* 3.4 13.2 - - + +
438A PHE* 3.7 28.9 - - + -
463A LEU* 3.6 35.4 - - + +
466A GLN* 4.7 2.7 - - + -
468A ILE* 1.3 77.4 - - - +
470A LEU* 1.3 71.2 + - - +
471A VAL* 4.3 0.7 - - + -
482A VAL 3.9 0.3 - - - +
483A VAL* 3.8 0.5 - - - -
484A ILE* 2.8 59.0 + - + +
486A LEU* 4.1 33.9 - - + -
512A LEU* 4.5 10.3 - - + -
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Residues in contact with LEU 470 (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 MET* 4.9 3.4 - - + -
423A LEU* 4.6 3.8 - - + -
435A LEU* 3.7 26.2 - - + -
436A HIS 2.9 7.3 + - - +
437A VAL* 3.6 21.8 - - + -
438A PHE* 3.1 28.1 + - - +
468A ILE* 3.8 15.0 - - + -
469A ILE* 1.3 80.6 - - - +
471A VAL* 1.3 64.5 + - - +
472A PRO* 3.8 2.2 - - + +
481A LEU* 4.3 9.9 - - + -
482A VAL 3.8 1.6 - - - +
483A VAL* 4.1 23.3 - - + -
556A ALA* 3.5 38.4 - - + +
559A ILE* 4.4 5.6 - - + -
560A SER* 4.9 1.1 - - - -
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Residues in contact with VAL 471 (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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438A PHE* 4.1 16.2 - - + -
439A SER 5.6 0.4 - - - +
442A PHE* 4.2 22.0 - - + -
443A TYR* 4.5 5.8 - - + -
469A ILE* 4.3 9.0 - - + -
470A LEU* 1.3 78.5 - - - +
472A PRO* 1.3 73.9 - - + +
473A ILE* 3.5 9.9 + - + +
481A LEU* 3.2 2.9 - - - +
482A VAL* 3.0 36.4 + - + +
484A ILE* 4.3 9.2 - - + -
508A LEU* 3.9 36.3 - - + -
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Residues in contact with PRO 472 (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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416A ILE* 4.6 2.5 - - + -
417A ASN* 5.1 1.3 - - - +
420A MET* 3.6 31.2 - - + -
437A VAL* 4.4 4.9 - - + -
438A PHE 3.2 31.0 - - - +
439A SER 4.0 5.1 - - - +
440A THR* 4.1 33.8 - - + +
443A TYR* 4.3 6.9 - - - +
470A LEU 3.8 3.8 - - - +
471A VAL* 1.3 88.4 - - + +
473A ILE* 1.3 63.2 + - - +
474A HIS 4.1 1.0 + - - -
479A TRP* 5.0 3.6 - - + -
480A SER 3.8 5.6 - - - +
481A LEU* 4.2 4.7 - - + -
552A THR* 5.1 2.5 - - + -
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Residues in contact with ILE 473 (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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443A TYR* 4.0 29.6 - - + -
471A VAL* 3.7 14.8 - - + +
472A PRO* 1.3 81.0 - - - +
474A HIS* 1.3 63.0 + - - +
475A ARG* 3.7 17.3 + - + -
479A TRP* 3.6 6.0 - - - -
480A SER* 2.6 52.3 + - - +
482A VAL* 3.3 24.9 - - + +
493A TYR* 4.3 2.9 - - + -
504A ILE* 3.3 43.1 - - + -
508A LEU* 4.8 0.2 - - + -
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Residues in contact with HIS 474 (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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440A THR 4.6 5.1 + - - +
443A TYR* 5.3 3.0 - - - -
444A PRO* 4.6 16.3 - - + +
472A PRO 4.1 1.4 + - - -
473A ILE* 1.3 74.6 - - - +
475A ARG* 1.3 80.6 + - - +
476A LYS* 3.4 14.6 + - - -
478A HIS 3.8 4.5 - - - -
479A TRP* 3.7 27.8 - + + -
88B GLN 5.2 0.7 - - - -
89B GLN* 3.5 51.6 + - + +
90B THR 2.9 30.2 + - - -
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Residues in contact with ARG 475 (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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473A ILE* 4.2 17.7 - - + +
474A HIS* 1.3 87.9 + - - +
476A LYS* 1.3 73.5 + - + +
477A VAL 2.5 5.0 + - - -
478A HIS* 2.8 49.4 + - + +
480A SER* 4.2 3.1 - - - -
493A TYR* 2.5 37.5 + - - -
499A GLN* 3.3 39.2 + - - +
500A LYS 3.5 15.5 + - - +
504A ILE* 4.7 9.7 - - + +
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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