Contacts of the helix formed by residues 532 - 538 (chain A) in PDB entry 5SY1
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 ASN 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A LEU* 1.3 81.0 - - - +
533A ARG* 1.3 84.6 + - - +
534A ASN* 3.3 32.1 - - - +
535A VAL* 3.3 23.9 + - + +
536A GLU* 3.3 15.3 + - - +
518B PHE* 4.0 16.9 - - + -
528B ILE* 3.3 27.3 - - - +
529B SER* 3.1 28.0 + - - +
530B LEU 5.1 0.6 + - - -
531B LEU 4.5 1.8 - - - +
533B ARG 5.7 0.2 - - - -
536B GLU* 4.7 5.9 - - - +
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Residues in contact with ARG 533 (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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531A LEU 3.9 0.2 + - - -
532A ASN* 1.3 83.3 + - - +
534A ASN* 1.3 71.6 + - - +
535A VAL 3.3 0.9 + - - -
536A GLU* 3.6 23.8 + - - +
380B LEU 5.3 5.7 + - - -
381B ASN* 5.9 1.8 - - - +
383B PHE* 3.3 34.5 - - - +
531B LEU 5.1 0.6 + - - -
533B ARG* 3.9 58.5 + - + +
536B GLU* 3.2 38.1 + - - +
542B TYR* 4.8 6.1 + - - -
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Residues in contact with ASN 534 (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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532A ASN* 3.2 24.1 - - - +
533A ARG* 1.3 90.0 - - - +
535A VAL* 1.3 67.8 + - + +
536A GLU 3.7 0.4 - - - -
366B LEU* 5.9 4.6 - - - +
528B ILE* 5.4 1.4 - - - +
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Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.5 24.3 - - + +
532A ASN* 3.7 31.2 - - + +
533A ARG 3.2 0.4 - - - -
534A ASN* 1.3 88.8 - - + +
536A GLU* 1.3 62.5 + - - +
537A ALA 3.2 4.5 + - - +
538A PHE* 3.5 22.7 + - + +
518B PHE* 3.7 26.2 - - + -
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Residues in contact with GLU 536 (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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383A PHE* 5.1 2.8 - - - +
529A SER* 3.5 32.1 + - - +
531A LEU* 4.9 0.9 - - - +
532A ASN 3.3 15.9 + - - +
533A ARG* 3.6 8.8 + - - +
534A ASN 3.7 1.4 - - - -
535A VAL* 1.3 76.9 - - - +
537A ALA* 1.3 57.7 + - - +
538A PHE 3.1 5.8 + - - -
539A ASP* 3.2 21.5 + - - +
542A TYR* 3.3 35.1 + - + -
532B ASN* 4.7 3.5 - - - +
533B ARG* 3.2 50.0 + - - +
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Residues in contact with ALA 537 (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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535A VAL* 3.2 3.0 - - - +
536A GLU* 1.3 77.7 - - - +
538A PHE* 1.3 71.4 + - + +
539A ASP 3.5 2.0 - - - -
542A TYR* 5.6 2.7 - - - -
543A ARG* 3.9 27.0 - - - +
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Residues in contact with PHE 538 (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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531A LEU* 4.4 8.7 - - + -
535A VAL* 3.5 24.1 + - + +
536A GLU 3.1 1.6 + - - -
537A ALA* 1.3 88.8 - - + +
539A ASP* 1.3 64.5 + - - +
540A PRO* 3.2 10.8 - - - +
543A ARG* 5.9 0.7 - - - -
510B TRP* 4.6 8.3 + - - -
514B ILE* 4.7 8.8 - - + +
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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