Contacts of the helix formed by residues 532 - 541 (chain A) in PDB entry 2MYS
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 ILE 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LEU* 4.4 18.6 - - + -
525A LEU* 3.1 22.4 + - + +
526A ILE* 4.4 11.0 - - + +
531A GLY* 1.3 69.3 - - - +
533A PHE* 1.3 60.1 + - + +
535A ILE* 3.4 2.1 + - - +
536A LEU* 2.7 31.3 + - + +
550A PHE* 4.4 7.2 - - + -
554A LEU* 4.1 23.6 - - + -
558A HIS* 4.1 6.4 + - + -
565A PHE* 4.1 20.0 - - + -
579A PHE* 3.7 38.4 - - + -
581A LEU* 4.2 14.1 - - + -
595A TRP* 5.3 1.8 - - + -
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Residues in contact with PHE 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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475A PHE* 4.3 12.3 - + - -
478A LEU* 3.5 36.8 - - + -
479A CYS* 4.3 16.4 - - - -
482A PHE* 4.0 18.8 - + - -
526A ILE* 3.4 36.5 + - + +
527A GLU* 5.1 0.2 - - - -
531A GLY 3.0 1.6 + - - -
532A ILE* 1.3 78.5 - - + +
534A SER* 1.3 51.6 + - - +
536A LEU* 2.8 13.3 + - + +
537A GLU* 2.5 42.8 + - - +
650A SER* 4.1 21.1 - - - -
653A PHE* 4.8 4.7 - + - -
654A ARG* 3.5 42.0 - - + +
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Residues in contact with SER 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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526A ILE 4.8 0.4 + - - -
528A MLY 4.4 3.3 + - - -
529A PRO* 2.8 35.0 + - - +
530A MET* 4.7 4.3 - - - +
531A GLY 2.8 11.4 + - - -
533A PHE* 1.3 72.1 - - - +
535A ILE* 1.3 52.9 + - - -
537A GLU* 2.7 13.0 + - - +
538A GLU* 2.7 40.2 + - - +
654A ARG* 4.9 8.4 + - - +
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Residues in contact with ILE 535 (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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530A MET* 3.1 40.8 - - + +
531A GLY 3.2 3.1 + - - +
532A ILE 3.9 2.5 - - - +
534A SER* 1.3 77.6 - - - +
536A LEU* 1.3 63.4 + - - +
538A GLU* 4.0 9.4 - - - +
539A GLU* 3.4 23.3 + - - +
550A PHE* 3.9 12.1 - - + -
553A MLY 3.9 37.5 - - + +
554A LEU* 3.4 31.4 - - + +
557A GLU* 4.2 8.3 - - + -
558A HIS* 3.8 15.3 - - + +
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Residues in contact with LEU 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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475A PHE* 4.2 16.8 - - + -
532A ILE* 2.7 17.0 + - + +
533A PHE* 2.8 23.7 + - + +
535A ILE* 1.3 80.4 - - - +
537A GLU* 1.3 57.8 + - - +
538A GLU 3.3 1.0 + - - -
539A GLU* 4.3 1.2 - - - +
540A CYS* 3.3 18.7 + - - -
550A PHE* 3.2 33.2 - - + -
595A TRP* 3.9 33.7 - - + -
596A LEU* 3.8 17.0 - - + +
599A ASN* 3.6 22.2 - - - +
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Residues in contact with GLU 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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533A PHE* 2.5 38.0 + - - +
534A SER* 2.7 9.1 + - - +
536A LEU* 1.3 73.2 - - - +
538A GLU* 1.3 62.6 + - - +
540A CYS* 3.8 14.7 - - - +
541A MET* 4.3 10.4 + - - +
599A ASN* 4.4 0.7 - - - +
648A THR* 3.5 29.0 - - + +
650A SER* 2.6 33.3 + - - +
651A ALA* 3.5 7.6 + - - +
654A ARG* 2.9 36.7 + - - -
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Residues in contact with GLU 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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530A MET* 4.7 16.5 - - - +
534A SER* 2.7 21.8 + - - +
535A ILE* 4.0 10.4 - - - +
536A LEU 3.2 0.2 - - - -
537A GLU* 1.3 72.0 - - - +
539A GLU* 1.3 57.3 + - - +
540A CYS 2.8 3.4 - - - -
541A MET* 2.4 56.4 + - + +
542A PHE* 3.9 10.7 + - + -
553A MLY 4.3 25.6 - - - +
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Residues in contact with GLU 539 (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 ILE* 3.4 15.8 + - - +
536A LEU 4.3 2.9 - - - +
538A GLU* 1.3 82.2 - - - +
540A CYS* 1.3 56.7 + - - +
541A MET 2.8 5.3 + - - -
542A PHE* 3.0 29.7 + - - +
545A ALA* 3.5 19.8 - - + +
549A SER* 2.8 31.3 + - - +
550A PHE* 4.1 13.9 - - + -
553A MLY 3.0 57.5 + - - +
596A LEU* 4.6 12.1 - - + +
600A MLY 3.8 1.4 - - - -
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Residues in contact with CYS 540 (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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536A LEU* 3.3 19.0 + - - -
537A GLU* 3.8 13.9 - - - +
538A GLU 2.7 0.6 + - - -
539A GLU* 1.3 78.0 - - - +
541A MET* 1.3 57.3 + - + +
542A PHE 3.4 0.2 - - - -
596A LEU* 3.8 32.3 - - - -
599A ASN* 4.0 21.8 - - - -
600A MLY 3.3 38.2 - - + +
648A THR* 4.4 9.0 - - - +
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Residues in contact with MET 541 (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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537A GLU 4.3 10.1 - - - +
538A GLU* 2.4 42.3 + - + +
540A CYS* 1.3 74.6 - - + +
542A PHE* 1.3 66.0 + - + +
543A PRO* 3.2 12.5 - - - +
600A MLY 4.7 0.2 - - - -
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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