Contacts of the strand formed by residues 561 - 573 (chain F) in PDB entry 4OMD
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 GLY 561 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460F ASP* 3.3 13.2 + - - +
461F ILE* 3.0 26.8 + - - +
462F GLY 4.7 1.4 - - - +
494F SER* 3.0 18.2 - - - -
495F TYR* 3.6 8.1 - - - -
560F TYR* 1.3 79.4 - - - +
562F THR* 1.3 63.5 + - - -
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Residues in contact with THR 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458F PRO* 3.9 20.6 - - + -
459F LYS 3.2 16.4 - - - +
460F ASP* 4.0 7.8 + - - -
461F ILE* 4.0 6.0 - - - +
493F LEU* 3.2 3.6 - - - -
494F SER* 2.9 40.3 + - - -
561F GLY* 1.3 77.6 + - - -
563F LEU* 1.3 69.3 + - - +
564F THR* 3.7 14.1 + - + +
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Residues in contact with LEU 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455F LEU* 3.6 22.4 - - + +
458F PRO* 3.5 2.3 - - - +
459F LYS* 2.8 37.3 + - + +
461F ILE* 4.0 7.2 - - + +
465F LEU* 3.9 27.6 - - + -
467F VAL* 4.4 8.1 - - + -
491F LEU* 4.4 9.9 - - + -
492F THR 3.7 9.6 - - - +
493F LEU* 3.9 15.0 - - + -
549F LEU* 4.0 15.5 - - + -
551F ILE* 4.0 18.4 - - + -
562F THR* 1.3 69.9 - - - +
564F THR* 1.3 58.7 + - - +
565F LYS 3.5 21.3 - - - +
566F PHE* 4.3 4.9 - - + -
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Residues in contact with THR 564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455F LEU* 3.8 10.9 - - - +
457F GLU 5.7 0.3 - - - -
458F PRO* 4.5 14.1 - - + +
492F THR* 2.8 32.6 + - - +
493F LEU* 4.8 1.2 - - - -
494F SER* 5.5 1.8 - - - +
562F THR* 3.7 24.2 + - + +
563F LEU* 1.3 75.6 - - - +
565F LYS* 1.3 62.7 + - - +
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Residues in contact with LYS 565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E THR* 6.3 3.4 - - - -
233E ASP* 5.8 9.9 - - + -
269E LEU* 6.4 0.9 - - - -
453F ASP* 4.2 9.9 - - - +
455F LEU* 3.8 6.5 - - - +
490F ARG* 3.4 18.4 + - - +
491F LEU* 3.3 5.0 - - - -
492F THR* 2.9 58.5 + - + +
530F ASP* 3.0 33.0 + - - +
563F LEU* 3.5 8.3 - - - +
564F THR* 1.3 82.5 - - - +
566F PHE* 1.3 63.9 + - - +
567F THR* 3.5 22.0 - - - +
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Residues in contact with PHE 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453F ASP* 3.8 2.0 + - - +
454F ILE* 3.0 62.9 + - + +
455F LEU* 3.9 18.4 + - + +
467F VAL* 4.1 15.9 - - + -
469F LYS* 5.7 2.5 - - + -
489F ALA* 4.0 23.8 - - + -
490F ARG 3.4 2.2 - - - -
491F LEU* 3.4 21.8 - - + -
505F LEU* 4.2 12.3 - - + -
547F TRP* 5.6 6.5 - - + -
548F VAL 5.7 0.2 - - - -
549F LEU* 3.7 33.9 - - + -
563F LEU* 4.3 7.4 - - + -
565F LYS* 1.3 77.8 - - - +
567F THR* 1.3 67.2 + - - +
568F LEU* 4.6 11.7 - - + -
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Residues in contact with THR 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ALA* 4.3 4.4 - - + +
269E LEU* 4.1 12.7 - - + +
451F ILE* 3.7 30.7 - - + -
452F ILE 3.6 9.0 - - - +
453F ASP* 2.8 21.3 + - - +
488F GLN 3.6 0.5 - - - +
489F ALA* 3.6 1.7 - - - -
490F ARG* 2.8 50.8 + - - +
565F LYS* 3.5 21.1 - - - +
566F PHE* 1.3 74.2 - - - +
568F LEU* 1.3 65.0 + - - +
569F VAL* 4.4 2.9 - - + -
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Residues in contact with LEU 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F CYS 3.6 2.3 - - - +
451F ILE* 3.7 0.9 - - - -
452F ILE* 2.8 61.2 + - + +
454F ILE* 4.4 11.9 - - + +
471F VAL* 4.5 5.8 - - + -
487F ALA* 5.3 1.1 - - + -
488F GLN 3.5 15.0 - - - +
505F LEU* 4.3 22.9 - - + -
547F TRP* 3.7 47.3 - - + +
566F PHE* 4.0 13.7 + - + -
567F THR* 1.3 73.7 - - - +
569F VAL* 1.3 61.0 + - - +
570F LEU* 3.8 20.9 - - + -
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Residues in contact with VAL 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E LEU* 4.3 10.8 - - + -
449F LYS* 3.8 29.2 - - + -
450F CYS 3.6 4.3 - - - +
451F ILE* 4.5 6.1 - - + -
487F ALA* 3.4 5.5 - - - -
488F GLN* 2.9 50.8 + - + +
490F ARG* 4.0 32.3 - - + -
567F THR* 4.3 8.1 - - + +
568F LEU* 1.3 78.1 - - - +
570F LEU* 1.3 64.3 + - - +
571F TYR* 3.6 24.2 + - + -
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Residues in contact with LEU 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F LYS* 3.3 4.0 - - - +
450F CYS* 2.7 47.4 + - + +
452F ILE* 3.7 26.7 - - + -
471F VAL* 4.9 0.9 - - + -
473F ALA* 4.0 16.8 - - + -
481F ILE* 3.2 12.1 - - + +
484F LEU* 3.9 19.3 - - + -
487F ALA* 4.5 4.5 - - + -
543F PRO* 3.8 24.0 - - + +
547F TRP* 4.1 17.9 - - + -
568F LEU* 3.8 28.0 - - + -
569F VAL* 1.3 77.2 - - - +
571F TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E GLU* 4.1 3.6 + - - -
276E ARG* 4.3 1.3 - - - -
312F ILE* 3.8 23.0 - - + +
447F GLN* 3.4 29.6 - - - +
448F ARG 3.3 6.7 - - - +
449F LYS* 3.4 37.2 + - + -
481F ILE* 3.5 3.5 - - - +
484F LEU* 3.1 9.0 - - - +
485F GLU* 2.8 26.5 + - + +
486F HIS* 3.1 38.8 + - + +
487F ALA 4.7 0.4 - - - -
488F GLN* 3.3 37.9 + - + -
569F VAL* 3.6 16.8 - - + -
570F LEU* 1.3 76.4 - - - +
572F GLY* 1.3 58.9 + - - +
602F FMT 3.6 18.1 + - - -
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Residues in contact with GLY 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447F GLN* 3.8 1.4 - - - +
448F ARG* 2.8 41.0 + - - +
481F ILE* 3.4 8.4 - - - +
483F ARG 3.3 10.5 - - - -
485F GLU* 3.9 19.0 + - - -
571F TYR* 1.3 76.2 - - - +
573F THR* 1.3 67.8 + - - +
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Residues in contact with THR 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F ARG* 3.3 29.4 - - - +
444F VAL* 5.1 2.2 - - + -
445F ALA* 3.6 28.5 - - + +
446F PRO 3.7 6.7 - - - +
448F ARG* 4.5 6.3 - - - +
480F HIS 4.4 3.6 - - - -
481F ILE* 3.6 1.9 - - - -
482F THR 2.9 22.9 + - - -
483F ARG* 2.9 35.3 + - - +
485F GLU* 4.1 4.9 + - - +
572F GLY* 1.3 76.1 - - - +
574F ALA* 1.3 69.3 + - - +
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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