Contacts of the strand formed by residues 483 - 495 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.9 30.7 - - - +
395C HIS* 5.0 11.6 - - - -
399C GLN* 6.0 1.8 - - - +
481C ILE* 3.6 2.4 - - - -
482C THR* 1.3 82.3 + - - +
484C LEU* 1.3 64.5 + - - +
485C GLU* 4.6 2.2 - - - +
540C ASP* 3.1 37.7 + - - +
541C GLU 3.8 2.0 - - - -
572C GLY* 3.4 1.9 - - - -
573C THR* 2.9 48.7 + - - +
574C ALA* 5.3 1.5 - - - -
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C ILE* 4.0 4.2 - - + +
483C ARG* 1.3 75.2 - - - +
485C GLU* 1.3 69.1 + - - +
486C HIS 3.5 11.7 - - - +
487C ALA* 4.0 15.0 - - + -
538C SER* 3.5 36.8 - - - +
539C TRP* 3.6 1.0 - - - -
540C ASP* 2.6 29.9 + - - +
541C GLU* 2.9 22.6 + - + +
543C PRO* 4.4 11.9 - - + -
547C TRP* 4.2 13.2 - - + -
570C LEU* 3.8 29.6 - - + -
571C TYR 3.3 17.7 - - - +
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Residues in contact with GLU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ARG* 2.8 49.2 + - - +
395C HIS* 2.8 33.9 + - + +
444C VAL* 4.6 0.2 - - - +
447C GLN* 4.3 4.3 + - - +
483C ARG* 4.6 2.0 - - - +
484C LEU* 1.3 87.7 - - - +
486C HIS* 1.3 75.3 + - - +
487C ALA 4.0 0.5 + - - -
535C THR 4.5 3.6 - - - +
536C THR* 4.9 0.2 - - - -
538C SER 4.5 0.3 + - - -
539C TRP* 3.5 41.3 + - + -
571C TYR* 2.8 15.6 + - - +
572C GLY* 4.0 15.2 + - - -
573C THR* 4.0 6.6 + - - +
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Residues in contact with HIS 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ILE* 3.4 56.6 + - + +
390C TRP* 4.5 11.2 - + - -
391C ARG* 5.3 2.7 - - + -
394C GLN* 2.8 31.0 + - - -
447C GLN* 5.3 0.8 + - - -
484C LEU* 3.5 3.6 - - - +
485C GLU* 1.3 94.5 + - + +
487C ALA* 1.3 60.0 + - - +
534C MET* 4.1 19.3 - - + -
535C THR 3.9 5.8 - - - -
536C THR* 4.7 4.0 - - + +
539C TRP* 3.6 22.1 - + - -
571C TYR* 3.1 38.5 + - + +
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Residues in contact with ALA 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C LEU* 4.0 20.6 - - + -
486C HIS* 1.3 77.3 - - - +
488C GLN* 1.3 64.2 + - - +
505C LEU* 5.3 1.3 - - + -
533C PHE 3.9 0.2 - - - +
534C MET* 3.4 4.4 - - - +
535C THR* 3.0 48.6 + - + +
547C TRP* 4.4 10.1 - - + -
568C LEU* 5.2 2.7 - - + -
569C VAL 3.3 9.4 - - - +
570C LEU* 4.2 11.9 - - + -
571C TYR* 5.1 0.2 - - - -
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Residues in contact with GLN 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ASN 5.4 2.4 + - - -
311C SER* 6.0 1.0 - - - +
312C ILE* 4.3 14.0 - - + +
487C ALA* 1.3 78.3 - - - +
489C ALA* 1.3 60.6 + - - +
490C ARG* 3.8 16.0 + - + +
505C LEU* 5.5 1.3 - - - -
532C ALA* 3.8 29.0 + - + +
533C PHE 3.1 10.3 - - - +
534C MET* 4.2 14.2 - - + +
567C THR 3.6 0.2 - - - +
568C LEU* 3.5 9.2 - - - +
569C VAL* 2.8 46.5 + - + +
571C TYR* 3.4 34.6 + - + -
269D LEU* 5.6 0.5 - - - +
272D GLU* 5.3 4.0 + - - +
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Residues in contact with ALA 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C GLN* 1.3 73.6 - - - +
490C ARG* 1.3 62.7 + - - +
491C LEU* 3.4 7.6 + - + +
505C LEU* 4.3 11.8 - - + +
515C LEU* 3.5 30.7 - - + -
531C TRP 3.3 2.6 - - - +
533C PHE* 2.8 32.0 + - - -
549C LEU* 5.0 0.4 - - + -
566C PHE* 3.8 22.2 - - + -
567C THR 3.6 4.5 - - - -
568C LEU* 4.7 0.2 - - - +
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Residues in contact with ARG 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C GLN* 4.0 16.2 + - + +
489C ALA* 1.3 69.7 - - - +
491C LEU* 1.3 61.1 + - - +
530C ASP* 2.9 51.9 + - - +
531C TRP 3.4 7.2 - - - +
532C ALA* 3.5 30.1 - - + +
565C LYS* 3.6 11.2 + - - +
566C PHE* 3.4 4.2 - - - -
567C THR* 2.8 43.5 + - - +
569C VAL* 3.9 22.7 - - + -
268D ARG* 3.3 26.5 - - - +
269D LEU* 4.0 28.0 - - - +
272D GLU* 4.5 11.3 + - - -
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ALA* 3.7 11.7 - - + +
490C ARG* 1.3 74.8 - - - +
492C THR* 1.3 62.6 + - - +
493C LEU* 4.2 11.0 - - + -
503C ILE* 3.9 33.2 - - + -
515C LEU* 4.9 2.0 - - + -
528C PHE* 3.8 9.1 - - + +
530C ASP 3.1 2.2 + - - -
531C TRP 3.0 30.0 + - - +
533C PHE* 3.8 28.3 - - + -
549C LEU* 4.0 15.9 - - + -
551C ILE* 5.0 2.5 - - + -
563C LEU* 4.5 6.7 - - + -
565C LYS 3.4 3.1 - - - +
566C PHE* 3.4 42.0 - - + -
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C LEU* 1.3 70.2 - - - +
493C LEU* 1.3 63.7 + - - +
528C PHE 3.2 10.5 - - - +
529C ASN* 4.3 10.6 + - + +
530C ASP* 2.8 27.4 + - - +
563C LEU* 3.5 2.5 - - - +
564C THR* 2.9 38.3 + - - +
565C LYS* 3.1 37.1 + - + -
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Residues in contact with LEU 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ILE* 4.4 5.8 - - + -
491C LEU* 4.7 9.0 - - + -
492C THR* 1.3 77.3 - - - +
494C SER* 1.3 73.6 + - - +
495C TYR* 4.1 3.4 - - + -
501C LEU* 4.0 22.9 - - + -
503C ILE* 4.4 13.0 - - + -
526C ASP 4.4 1.6 - - - +
527C GLY* 3.4 5.7 - - - -
528C PHE* 2.9 58.3 + - + +
551C ILE* 4.3 22.7 - - + -
562C THR 3.1 15.0 - - - +
563C LEU* 3.8 13.9 - - + -
564C THR* 4.4 1.8 - - - +
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Residues in contact with SER 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ILE* 3.9 0.9 - - - +
493C LEU* 1.3 78.2 - - - +
495C TYR* 1.3 65.1 + - - +
525C ALA 5.7 1.6 - - - -
526C ASP 5.4 1.3 - - - -
527C GLY* 4.5 4.0 - - - +
561C GLY* 3.0 5.5 - - - -
562C THR* 2.9 47.5 + - - +
564C THR* 5.9 1.4 - - - +
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Residues in contact with TYR 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ILE* 3.8 28.9 - - + +
462C GLY 3.3 8.7 + - - -
493C LEU* 4.1 12.7 - - + +
494C SER* 1.3 75.7 - - - +
496C ASN* 1.3 63.0 + - - +
497C ARG 3.4 32.1 - - - +
498C ARG* 4.7 4.6 + - - +
500C ASP* 4.6 3.4 - - + -
501C LEU* 3.4 31.4 - - + -
524C SER 4.3 1.0 - - - +
525C ALA* 3.4 24.5 + - - +
527C GLY* 4.5 7.0 + - - -
553C ASN* 3.3 22.7 - - - +
559C ASN* 3.0 36.3 - - + +
560C TYR* 3.3 28.9 - - - -
561C GLY* 3.7 5.8 - - - -
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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