Contacts of the helix formed by residues 526 - 530 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 6.2 0.2 - - + -
371A GLY* 5.8 2.2 - - - -
398A VAL* 3.6 22.0 - - + +
399A CYS* 4.0 13.2 - - + -
476A GLU* 4.3 0.4 - - - -
477A ARG* 2.7 30.4 + - - +
478A HIS 4.0 2.9 - - - -
479A ARG* 3.1 53.3 + - + +
524A GLN 3.4 17.0 + - - -
525A TYR* 1.4 71.1 - - - +
527A PRO* 1.3 68.7 - - - +
528A GLU* 3.2 22.5 + - - +
529A PHE* 3.5 27.6 + + + +
530A LEU* 4.7 0.7 + - - +
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Residues in contact with PRO 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 6.4 0.2 - - + -
398A VAL* 5.3 2.5 - - + -
476A GLU* 3.3 23.1 - - - +
523A VAL* 4.5 7.9 - - + -
525A TYR* 3.3 24.7 - - + +
526A HIS* 1.3 83.9 - - - +
528A GLU* 1.3 66.2 + - - +
529A PHE 2.9 6.1 - - - -
530A LEU* 2.9 20.5 + - + +
531A SER* 3.0 13.0 + - - -
537A SER* 3.8 20.1 - - - +
539A PRO* 3.6 25.1 - - + -
540A TYR* 3.9 9.0 - - + +
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Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 6.1 0.4 - - + -
76A ARG* 5.3 3.8 + - - -
316A SER* 4.0 34.1 - - - +
317A VAL* 4.0 16.9 - - + +
320A ALA* 4.0 15.4 - - + +
323A HIS* 5.8 0.5 - - - -
398A VAL* 5.1 3.3 - - - +
526A HIS* 3.4 29.5 + - - +
527A PRO* 1.3 88.2 - - - +
529A PHE* 1.3 72.5 + - + +
530A LEU 3.2 0.4 + - - -
531A SER* 3.9 12.7 + - - +
532A ARG* 5.0 0.2 + - - -
540A TYR* 2.7 39.0 + - + +
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Residues in contact with PHE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 4.3 22.2 - - + -
58A VAL 3.5 25.1 - - - -
59A PHE* 3.4 48.1 - + + -
60A VAL* 4.3 13.0 - - + -
69A LEU* 4.7 1.6 - - + -
316A SER* 4.5 10.3 - - - -
477A ARG* 3.6 26.9 - - + -
479A ARG* 5.6 4.7 - - - -
526A HIS* 3.5 46.2 - + + +
527A PRO 2.9 0.8 - - - -
528A GLU* 1.3 91.8 - - + +
530A LEU* 1.3 58.2 + - - +
532A ARG* 2.9 18.5 + - - -
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 5.9 0.4 - - + -
81A ARG* 4.8 8.3 - - - +
452A LYS* 5.2 7.4 - - - +
475A GLU 3.7 19.1 - - - +
476A GLU* 3.5 33.4 - - - +
477A ARG* 3.6 42.6 - - - +
526A HIS 4.9 0.7 - - - +
527A PRO 2.9 6.5 + - - +
529A PHE* 1.3 79.5 - - + +
531A SER* 1.3 68.1 + - - +
532A ARG* 3.3 21.3 + - - +
535A LYS* 4.4 2.6 - - - +
537A SER* 5.3 1.8 - - - -
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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