Contacts of the strand formed by residues 483 - 495 (chain F) in PDB entry 4RYD
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 ARG 483 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395F HIS* 4.0 19.5 + - - -
399F GLN* 4.6 9.9 - - - +
441F TRP* 5.7 2.6 - - - -
444F VAL* 5.8 2.4 - - - +
481F ILE* 3.7 2.5 - - - -
482F THR* 1.3 84.4 - - - +
484F LEU* 1.3 65.0 + - - +
485F GLU* 4.4 1.9 - - - +
540F ASP* 2.6 45.5 + - - +
541F GLU 3.7 2.2 - - - -
572F GLY* 3.4 1.6 - - - -
573F THR* 3.0 47.5 + - - +
574F ALA 5.3 5.6 - - - +
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Residues in contact with LEU 484 (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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481F ILE* 4.0 4.3 - - + +
483F ARG* 1.3 73.7 - - - +
485F GLU* 1.3 69.3 + - - +
486F HIS 3.6 11.2 - - - +
487F ALA* 4.0 15.5 - - + -
538F SER* 3.7 35.4 - - - +
539F TRP* 4.1 1.2 - - - -
540F ASP* 2.6 31.0 + - - +
541F GLU* 2.9 21.9 + - + +
543F PRO* 4.2 13.0 - - + -
547F TRP* 4.1 15.0 - - + -
570F LEU* 3.8 28.7 - - + -
571F TYR 3.3 18.4 - - - +
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Residues in contact with GLU 485 (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* 2.9 48.1 + - - +
395F HIS* 2.8 37.8 + - + +
447F GLN* 4.5 4.2 + - - +
483F ARG 4.4 2.7 - - - +
484F LEU* 1.3 86.7 - - - +
486F HIS* 1.3 72.0 + - - +
487F ALA 4.0 0.2 + - - -
535F THR 4.5 3.5 - - - +
536F THR* 4.9 0.3 - - - -
539F TRP* 3.4 42.4 + - + -
571F TYR* 2.8 14.5 + - - +
572F GLY* 3.7 16.6 + - - -
573F THR* 4.1 6.8 + - - +
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Residues in contact with HIS 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F ILE* 3.4 58.3 + - + +
390F TRP* 4.5 11.0 - + - -
391F ARG* 5.3 2.2 - - + -
394F GLN* 2.7 30.9 + - - -
447F GLN* 5.4 0.8 + - - -
484F LEU* 3.6 3.2 - - - +
485F GLU* 1.3 91.7 + - + +
487F ALA* 1.3 59.6 + - - +
534F MET* 4.2 19.3 - - + -
535F THR 3.9 5.4 - - - -
536F THR* 4.7 5.4 - - + +
539F TRP* 3.5 23.3 - + - -
571F TYR* 3.1 37.8 + - + +
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Residues in contact with ALA 487 (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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484F LEU* 4.0 22.0 - - + -
486F HIS* 1.3 76.0 - - - +
488F GLN* 1.3 62.0 - - - +
505F LEU* 5.4 1.1 - - + -
533F PHE 4.0 0.2 - - - +
534F MET* 3.4 3.6 - - - +
535F THR* 3.0 49.5 + - + +
547F TRP* 4.5 9.6 - - + -
568F LEU* 5.0 3.8 - - + -
569F VAL 3.3 8.5 - - - +
570F LEU* 4.2 11.2 - - + -
571F TYR* 5.0 0.2 - - - -
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Residues in contact with GLN 488 (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* 5.4 0.3 - - - +
272E GLU* 5.1 3.8 + - - +
310F ASN 5.4 2.4 + - - -
311F SER* 6.0 1.2 - - - +
312F ILE* 4.3 14.4 - - + +
487F ALA* 1.3 77.5 - - - +
489F ALA* 1.3 60.3 + - - +
490F ARG* 3.8 18.1 + - + +
505F LEU* 5.5 1.3 - - - -
532F ALA* 3.7 28.9 + - + +
533F PHE 3.2 9.0 - - - +
534F MET* 4.2 14.6 - - + +
567F THR 3.6 0.3 - - - +
568F LEU* 3.5 9.6 - - - +
569F VAL* 2.8 47.0 + - + +
571F TYR* 3.3 35.2 + - + -
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Residues in contact with ALA 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488F GLN* 1.3 72.3 - - - +
490F ARG* 1.3 61.7 + - - +
491F LEU* 3.4 8.2 + - + +
505F LEU* 4.3 11.6 - - + +
515F LEU* 3.6 30.3 - - + -
531F TRP 3.3 2.3 - - - +
533F PHE* 2.8 32.3 + - - +
549F LEU* 4.9 0.9 - - + -
566F PHE* 3.9 21.3 - - + -
567F THR 3.6 5.4 - - - -
568F LEU* 4.7 0.2 - - - +
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Residues in contact with ARG 490 (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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268E ARG* 3.3 26.3 - - - +
269E LEU* 3.9 36.9 - - - +
272E GLU* 4.5 11.3 + - - -
488F GLN* 3.8 16.4 + - + +
489F ALA* 1.3 69.7 - - - +
491F LEU* 1.3 60.8 + - - +
530F ASP* 2.9 53.1 + - - +
531F TRP 3.3 7.2 - - - +
532F ALA* 3.4 29.8 - - + +
565F LYS* 3.1 11.4 + - - +
566F PHE* 3.5 2.8 - - - -
567F THR* 2.8 43.3 + - - +
569F VAL* 3.9 14.8 - - + -
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Residues in contact with LEU 491 (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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489F ALA* 3.7 10.8 - - + +
490F ARG* 1.3 75.7 - - - +
492F THR* 1.3 62.8 + - - +
493F LEU* 4.2 11.2 - - + -
503F ILE* 3.9 31.9 - - + -
515F LEU* 5.0 1.8 - - + -
528F PHE* 3.8 8.3 - - + +
530F ASP 3.1 2.9 + - - -
531F TRP 2.9 29.3 + - - +
533F PHE* 3.8 28.3 - - + -
549F LEU* 4.0 16.4 - - + -
551F ILE* 4.9 2.2 - - + -
563F LEU* 4.4 6.5 - - + -
565F LYS 3.4 2.9 - - - +
566F PHE* 3.5 42.2 - - + -
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Residues in contact with THR 492 (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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491F LEU* 1.3 71.3 - - - +
493F LEU* 1.3 64.9 + - - +
528F PHE 3.2 9.4 - - - +
529F ASN* 4.2 10.7 + - - +
530F ASP* 2.9 20.5 + - - +
563F LEU* 3.7 1.0 - - - +
564F THR* 2.9 38.1 + - - +
565F LYS* 3.0 44.9 + - + +
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Residues in contact with LEU 493 (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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461F ILE* 4.3 7.4 - - + -
491F LEU* 4.6 8.3 - - + -
492F THR* 1.3 77.0 - - - +
494F SER* 1.3 73.5 + - - +
495F TYR* 4.2 3.1 - - + -
501F LEU* 4.0 23.3 - - + -
503F ILE* 4.4 12.8 - - + -
526F ASP 4.4 1.4 - - - +
527F GLY* 3.4 3.7 - - - -
528F PHE* 2.9 61.2 + - + +
551F ILE* 4.2 15.5 - - + -
562F THR 3.1 14.8 - - - +
563F LEU* 3.8 22.9 - - + -
564F THR* 4.4 2.2 - - - +
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Residues in contact with SER 494 (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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461F ILE* 3.8 3.6 - - - +
493F LEU* 1.3 75.7 - - - +
495F TYR* 1.3 66.2 + - - +
525F ALA 5.7 1.6 - - - -
526F ASP 5.4 1.6 - - - -
527F GLY* 4.5 3.4 - - - +
561F GLY* 3.0 5.5 - - - -
562F THR* 2.9 47.4 + - - +
564F THR* 5.8 1.3 - - - +
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Residues in contact with TYR 495 (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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461F ILE* 3.8 24.2 - - + +
462F GLY 3.4 8.1 + - - -
493F LEU* 4.2 5.1 + - + +
494F SER* 1.3 81.7 - - - +
496F ASN* 1.3 63.3 + - - +
497F ARG 3.4 33.9 - - - +
498F ARG* 4.7 5.4 - - - +
500F ASP* 4.6 3.4 - - + -
501F LEU* 3.6 40.8 - - + +
524F SER 4.3 1.0 - - - +
525F ALA* 3.3 24.4 + - - +
527F GLY* 4.4 7.2 + - - +
553F ASN* 3.3 22.9 - - - +
559F ASN* 3.1 37.3 - - + +
560F TYR* 3.4 25.8 - - - -
561F GLY* 3.8 2.7 - - - -
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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