Contacts of the strand formed by residues 491 - 496 (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 491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484C SER 3.4 2.2 - - - -
485C ASP* 3.4 18.2 - - - -
490C VAL* 1.3 75.5 - - - +
492C TYR* 1.3 61.1 + - - +
579C TRP* 5.3 0.8 - - - -
580C ASN* 2.8 42.3 + - - -
581C ILE 4.5 0.5 + - - -
582C PHE* 5.5 8.3 - - - -
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Residues in contact with TYR 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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310C PHE* 3.8 4.2 - - - -
340C MET* 3.4 32.1 - - + +
343C ILE* 4.9 8.5 - - + -
344C LEU* 5.0 4.7 - - + -
482C PHE* 4.3 19.3 - + - -
483C TRP* 3.2 6.2 - - - +
484C SER* 3.0 64.9 + - - +
485C ASP* 4.5 0.4 + - - -
486C LEU* 5.0 6.5 - - + -
490C VAL* 4.3 11.9 - - + -
491C GLY* 1.3 76.3 - - - +
493C GLU* 1.3 69.7 + - - +
494C ALA* 4.9 1.8 - - + -
577C VAL* 3.9 17.9 - - + -
578C LEU 3.0 18.4 - - - +
579C TRP* 3.6 35.7 - + + -
581C ILE 5.9 0.2 - - - +
701C NAD 5.2 0.2 - - - +
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Residues in contact with GLU 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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481C MET* 4.3 4.0 - - + -
482C PHE 3.1 8.7 - - - +
483C TRP* 4.1 7.2 - - + +
492C TYR* 1.3 80.4 - - - +
494C ALA* 1.3 61.5 + - - +
577C VAL* 3.5 1.4 - - - +
578C LEU* 2.7 49.0 + - + +
581C ILE 4.8 8.3 - - - +
582C PHE* 4.8 4.1 - - - -
583C ASN 5.2 0.5 + - - -
585C MET* 3.7 34.1 + - + +
701C NAD 3.0 64.7 + - - +
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Residues in contact with ALA 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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481C MET* 3.1 8.2 - - - +
482C PHE* 2.8 68.2 + - + -
492C TYR* 4.9 2.5 - - + -
493C GLU* 1.3 75.0 - - - +
495C ILE* 1.3 64.2 + - - +
498C VAL* 3.9 7.6 - - + -
576C ILE 3.2 14.1 - - - +
577C VAL* 4.0 10.8 - - + -
578C LEU* 5.8 0.2 - - - -
585C MET* 4.3 2.5 - - - -
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Residues in contact with ILE 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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479C GLN* 3.8 27.8 - - + -
480C SER 3.6 18.8 - - - +
481C MET* 4.2 1.6 - - + +
482C PHE* 5.2 2.2 - - - -
494C ALA* 1.3 78.0 - - - +
496C GLY* 1.3 69.5 + - - +
498C VAL* 3.5 2.5 - - - +
575C GLY* 3.4 1.0 - - - -
576C ILE* 3.0 39.7 + - + +
578C LEU* 6.0 0.4 - - + -
585C MET* 4.0 14.4 - - + -
588C ALA* 3.8 24.7 - - + -
589C ARG* 4.0 36.6 - - + +
592C ILE* 4.5 12.3 - - + -
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Residues in contact with GLY 496 (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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447C LEU* 4.1 12.1 - - - -
450C ARG* 3.4 26.4 + - - +
479C GLN* 4.7 2.8 - - - +
480C SER 4.5 2.4 + - - -
482C PHE* 5.0 5.9 - - - -
495C ILE* 1.3 83.7 - - - +
497C LEU* 1.3 60.0 + - - -
498C VAL* 3.1 9.2 + - - +
574C VAL 3.5 9.2 - - - -
575C GLY* 4.2 0.7 - - - -
592C ILE* 4.9 4.0 - - - -
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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
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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