Contacts of the helix formed by residues 526 - 530 (chain C) in PDB entry 5U03
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 HIS 526 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371C GLY* 5.8 2.0 - - - -
398C VAL* 3.6 22.4 - - + +
399C CYS* 4.0 13.2 - - + -
476C GLU* 4.3 0.9 - - - -
477C ARG* 2.7 29.7 + - - +
478C HIS 4.0 2.7 - - - -
479C ARG* 3.1 54.5 + - + +
524C GLN 3.4 17.0 + - - -
525C TYR* 1.4 70.6 - - - +
527C PRO* 1.3 68.1 - - - +
528C GLU* 3.2 22.7 + - - +
529C PHE* 3.5 27.7 + + + +
530C LEU* 4.6 0.9 + - - +
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Residues in contact with PRO 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C VAL* 5.3 1.8 - - + -
476C GLU* 3.3 22.9 - - - +
523C VAL* 4.5 6.5 - - + -
525C TYR* 3.3 27.3 - - + +
526C HIS* 1.3 85.0 - - - +
528C GLU* 1.3 66.4 + - - +
529C PHE 2.9 6.1 - - - -
530C LEU* 2.9 20.0 + - - +
531C SER* 3.0 13.3 + - - -
537C SER* 3.8 19.2 - - - +
539C PRO* 3.6 25.1 - - + -
540C TYR* 3.9 9.2 - - + +
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Residues in contact with GLU 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 6.1 0.4 - - + -
76C ARG* 5.3 4.0 + - - -
316C SER* 4.0 33.7 - - - +
317C VAL* 4.0 16.1 - - + +
320C ALA* 4.0 15.8 - - + +
323C HIS* 5.8 0.7 - - - -
398C VAL* 5.1 3.4 - - - +
526C HIS* 3.4 29.5 + - - +
527C PRO* 1.3 88.6 - - - +
529C PHE* 1.3 74.1 + - + +
530C LEU 3.2 0.6 + - - -
531C SER* 3.9 12.2 + - - +
532C ARG* 5.0 0.2 + - - -
540C TYR* 2.7 37.4 + - + +
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Residues in contact with PHE 529 (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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57C GLU* 4.3 21.3 - - + -
58C VAL 3.5 25.4 - - - -
59C PHE* 3.4 48.9 - + + -
60C VAL* 4.3 13.7 - - + -
69C LEU* 4.7 1.8 - - + -
316C SER* 4.5 10.5 - - - -
477C ARG* 3.6 27.6 - - + -
479C ARG* 5.6 4.3 - - - -
526C HIS* 3.5 45.8 - + + +
527C PRO 2.9 0.6 - - - -
528C GLU* 1.3 90.5 - - + +
530C LEU* 1.3 57.7 + - - +
532C ARG* 2.9 18.1 + - - -
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Residues in contact with LEU 530 (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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59C PHE* 5.9 0.2 - - + -
81C ARG* 4.8 8.5 - - - +
452C LYS* 5.2 7.9 - - - +
475C GLU 3.7 19.5 - - - +
476C GLU* 3.5 33.2 - - - +
477C ARG* 3.6 43.3 - - - +
526C HIS 4.9 0.9 - - - +
527C PRO 2.9 6.3 + - - +
529C PHE* 1.3 79.1 - - + +
531C SER* 1.3 68.1 + - - +
532C ARG* 3.3 20.4 + - - +
535C LYS* 4.4 2.8 - - - +
537C SER* 5.3 1.3 - - - -
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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