Contacts of the helix formed by residues 521 - 525 (chain C) in PDB entry 2BT4
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 TYR 521 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B THR* 5.4 2.8 - - + +
316B PHE* 3.9 30.2 - + + +
484C SER 2.8 11.9 + - - +
485C HIS 3.4 28.5 - - - -
486C THR* 4.0 10.1 - - - -
487C SER 3.9 24.2 - - - +
488C VAL* 3.6 28.5 - - + +
491C LEU* 3.4 23.9 - - + +
519C HIS 6.2 0.2 - - - -
520C SER* 1.3 71.9 - - - +
522C VAL* 1.3 63.5 + - + +
524C GLN* 3.1 36.5 + - - +
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Residues in contact with VAL 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ILE* 4.2 6.3 - - + -
480C PRO* 3.9 22.4 - - + -
483C TYR 4.9 2.5 - - - +
484C SER* 4.5 7.6 - - - +
487C SER 4.9 2.2 - - - +
490C ILE* 3.8 28.9 - - + -
491C LEU* 4.6 9.0 - - - +
494C LEU* 3.7 20.0 - - + -
504C GLU* 3.7 27.8 - - + +
520C SER* 3.1 8.4 + - - +
521C TYR* 1.3 77.1 - - - +
523C SER* 1.3 58.4 + - - +
524C GLN 3.1 0.2 - - - -
525C ARG* 3.0 6.4 + - - +
526C ALA* 2.9 26.7 + - + -
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Residues in contact with SER 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C GLU* 2.4 28.2 + - - -
506C HIS* 5.3 0.2 + - - -
520C SER* 3.2 20.9 + - - -
521C TYR 3.1 1.4 - - - -
522C VAL* 1.3 75.1 - - - +
524C GLN* 1.3 61.0 + - - +
525C ARG 3.2 0.9 + - - -
526C ALA* 3.9 1.9 - - - +
529C VAL* 3.6 18.8 - - - +
2415C GOL 4.4 1.8 + - - -
1909J ASN* 3.1 23.9 + - - +
1911J HIS* 3.9 26.3 + - - +
1912J GLN* 3.8 4.0 - - - +
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Residues in contact with GLN 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 5.5 2.8 - - - +
316B PHE* 3.5 28.0 - - - -
491C LEU* 3.9 12.0 - - + +
495C ASN* 5.2 0.9 - - - +
520C SER 4.0 11.0 + - - +
521C TYR* 3.3 32.6 - - - +
522C VAL 3.1 0.8 + - - -
523C SER* 1.3 78.5 - - - +
525C ARG* 1.3 56.8 + - - +
2415C GOL 4.8 11.2 - - - -
1911J HIS 4.6 13.2 + - - +
1912J GLN* 3.1 23.3 + - - +
1918J HIS* 6.0 3.4 - - - -
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Residues in contact with ARG 525 (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* 3.5 14.3 - - + +
494C LEU* 3.4 37.5 + - + -
495C ASN* 3.2 31.9 + - - +
497C CYS* 2.9 23.4 + - - +
498C ASP* 5.0 0.6 - - - +
499C GLY 4.5 3.2 - - - +
500C LEU 2.9 24.4 + - - +
502C VAL* 3.7 14.7 - - + +
522C VAL 3.0 3.7 + - - +
524C GLN* 1.3 79.4 - - - +
526C ALA* 1.3 68.7 + - - +
527C ASP* 3.1 26.3 + - - +
1912J GLN* 3.6 7.8 + - - +
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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