Contacts of the strand formed by residues 563 - 569 (chain C) in PDB entry 4BUR
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 563 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C VAL 3.2 13.7 - - - -
508C PHE* 3.8 11.2 - - - -
562C LYS* 1.3 75.7 - - - +
564C VAL* 1.3 58.4 + - - +
565C ILE* 4.8 0.4 - - - -
579C TRP* 2.7 47.6 + - - +
581C ILE* 3.8 6.8 - - - +
610C ILE* 4.1 9.6 - - - -
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Residues in contact with VAL 564 (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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505C VAL 4.0 0.9 - - - +
506C GLY* 3.4 1.6 - - - -
507C VAL* 2.9 29.5 + - + +
508C PHE* 5.0 0.4 - - - -
563C GLY* 1.3 75.4 - - - +
565C ILE* 1.3 65.9 + - - +
566C PHE* 4.1 29.4 + - + -
576C ILE* 3.6 20.6 - - + -
577C VAL 3.5 12.3 - - - +
578C LEU* 3.9 13.9 - - + -
581C ILE* 5.4 2.0 - - + -
605C ALA* 4.1 6.5 - - + -
608C PHE* 4.3 15.7 - - + -
610C ILE* 3.4 27.4 - - + -
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Residues in contact with ILE 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PRO* 4.4 11.2 - - + -
347C TYR* 4.4 2.7 - - - +
348C LEU* 3.6 27.4 - - + -
504C THR* 3.8 19.3 - - + -
505C VAL 3.4 11.0 - - - +
506C GLY* 4.2 2.9 - - - -
508C PHE* 4.0 19.5 - - + -
564C VAL* 1.3 79.8 - - - +
566C PHE* 1.3 65.0 + - - +
567C TYR* 3.6 24.3 - - + +
576C ILE* 3.4 5.0 - - - -
577C VAL* 3.0 52.0 + - + +
579C TRP* 4.1 14.4 - - + -
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Residues in contact with PHE 566 (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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504C THR* 3.1 7.4 - - - -
505C VAL* 2.7 46.6 + - + +
507C VAL* 4.3 6.5 - - + -
564C VAL* 4.1 19.1 - - + -
565C ILE* 1.3 75.5 - - - +
567C TYR* 1.3 61.0 + - - +
568C LEU* 4.1 5.3 + - + +
573C VAL* 3.9 27.6 - - + -
575C GLY 3.6 2.7 - - - -
576C ILE* 4.2 10.5 - - + -
591C ILE* 5.0 0.4 - - + -
601C LEU* 3.7 44.4 - - + -
604C VAL* 3.9 23.6 - - + -
605C ALA* 4.0 19.3 - - + -
608C PHE* 3.9 27.4 - + - -
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Residues in contact with TYR 567 (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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343C ILE 2.7 26.8 + - - -
344C LEU* 4.1 8.7 - - - +
345C PRO* 4.1 5.4 - - + +
497C LEU 3.6 17.7 - - - +
498C VAL* 4.0 4.4 - - + +
499C ASP 3.4 41.3 - - - -
500C SER* 4.1 1.6 - - - -
502C LEU* 4.4 7.6 - - + -
503C PRO 3.6 4.9 - - - +
504C THR* 3.4 22.4 - - + -
565C ILE* 3.6 22.6 - - + +
566C PHE* 1.3 75.3 - - - +
568C LEU* 1.3 60.8 + - - +
573C VAL* 3.6 3.8 - - - -
574C VAL* 3.0 28.6 + - - +
575C GLY* 2.9 16.9 + - - +
577C VAL* 3.5 33.9 - - + +
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Residues in contact with LEU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C LEU* 3.7 8.9 - - - +
503C PRO* 2.8 50.0 + - + +
504C THR 4.9 0.4 - - - -
505C VAL* 3.7 22.0 - - + +
566C PHE 4.6 4.3 - - - +
567C TYR* 1.3 76.9 - - - +
569C ARG* 1.3 61.1 + - - +
570C ASP 4.1 7.9 - - - +
571C LYS* 3.9 17.7 - - - +
572C VAL 3.5 20.9 - - - +
573C VAL* 4.0 12.6 - - + +
574C VAL* 4.6 2.0 - - - -
598C HIS 5.5 0.2 - - - +
601C LEU* 3.5 35.2 - - + -
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Residues in contact with ARG 569 (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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446C LYS 5.2 0.6 + - - -
447C LEU* 2.8 32.7 + - - +
448C GLY* 5.1 0.4 - - - -
497C LEU* 3.4 26.9 - - - +
502C LEU* 4.7 14.6 - - + +
503C PRO* 5.5 1.1 - - - -
568C LEU* 1.3 76.3 - - - +
570C ASP* 1.3 74.9 + - - +
572C VAL* 2.9 28.6 + - - +
574C VAL* 4.0 23.0 - - + +
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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
------------------------------------------------------------
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