Contacts of the helix formed by residues 526 - 532 (chain A) in PDB entry 4Z4Q
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 MET 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A MET 5.6 1.6 - - - +
480A ILE* 5.8 5.8 - - - -
483A ILE* 3.6 26.5 - - + -
486A GLY 4.8 3.1 - - - +
487A VAL* 5.4 1.8 - - + -
488A GLY 5.5 0.4 - - - -
491A PHE* 3.3 38.1 - - + -
521A PHE* 4.0 17.0 + - + +
522A PHE* 3.2 42.2 + - + +
525A TYR* 1.3 89.5 - - + +
527A ARG* 1.3 64.6 + - - +
528A PRO* 3.0 9.2 - - - -
529A LEU* 2.9 47.3 + - + +
530A VAL 3.7 0.3 + - - -
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Residues in contact with ARG 527 (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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522A PHE 3.5 9.4 + - - -
523A TYR* 3.7 25.2 + - + +
524A ARG 4.9 1.5 - - - -
525A TYR 3.9 1.2 - - - +
526A MET* 1.3 75.5 - - - +
528A PRO* 1.3 70.1 - - + +
530A VAL* 3.1 5.8 + - - +
531A GLU* 3.0 22.6 + - - +
611A LEU* 6.4 1.1 - - + -
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Residues in contact with PRO 528 (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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488A GLY 5.7 2.0 - - - +
491A PHE* 3.7 33.2 - - + +
493A ILE* 4.7 12.1 - - + +
526A MET* 3.0 9.4 - - - -
527A ARG* 1.3 95.0 - - + +
529A LEU* 1.3 60.0 + - - +
531A GLU* 3.2 6.9 + - + +
532A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 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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483A ILE* 4.6 2.7 - - + -
491A PHE* 4.0 12.2 - - + -
493A ILE* 5.5 7.6 - - + -
496A ALA* 5.8 5.8 - - + -
498A TYR 5.5 3.1 - - - +
501A ILE* 3.6 32.5 - - + -
522A PHE* 5.1 4.5 - - + -
526A MET* 2.9 45.3 + - + +
528A PRO* 1.3 81.2 - - - +
530A VAL* 1.3 57.9 + - - +
532A ALA* 3.6 2.2 + - + -
533A GLY 3.6 2.4 + - - -
534A HIS* 3.2 67.6 + - + +
535A VAL* 4.2 13.2 + - + -
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Residues in contact with VAL 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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519A LEU* 6.2 1.1 - - + -
522A PHE* 4.1 18.8 - - + +
523A TYR* 5.3 5.8 - - + -
526A MET 3.7 1.4 + - - -
527A ARG* 3.1 9.7 + - - +
529A LEU* 1.3 77.2 - - - +
531A GLU* 1.3 63.0 + - - +
533A GLY 3.2 9.1 + - - +
535A VAL* 4.3 16.1 - - + +
606A VAL* 3.4 32.5 - - + +
607A THR* 4.3 7.6 - - - -
608A ILE* 4.5 5.5 + - + +
1009A LEU* 6.0 4.3 - - + -
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Residues in contact with GLU 531 (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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527A ARG 3.0 16.1 + - - +
528A PRO* 3.2 8.0 + - + +
530A VAL* 1.3 77.8 - - - +
532A ALA* 1.3 57.2 + - - +
533A GLY 3.2 2.6 + - - -
607A THR* 6.0 0.3 - - - -
608A ILE* 5.2 15.4 + - + +
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Residues in contact with ALA 532 (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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528A PRO 3.0 16.2 + - - +
529A LEU* 3.6 3.8 + - + +
530A VAL 3.3 0.2 - - - -
531A GLU* 1.3 75.5 - - - +
533A GLY* 1.3 63.4 + - - +
534A HIS* 3.0 30.2 + - + +
605A ARG* 4.7 4.2 + - - -
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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