Contacts of the helix formed by residues 533 - 544 (chain A) in PDB entry 5I35
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 ASP 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A ALA* 2.8 16.6 + - + +
531A ASP* 4.0 9.2 - - + +
532A ARG* 1.3 72.9 - - - +
534A ARG* 1.3 61.3 + - - +
535A GLU* 3.3 9.7 + - - +
536A THR* 2.4 41.3 + - - +
537A VAL* 3.1 23.6 + - - +
564A LEU* 4.8 0.6 - - - +
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Residues in contact with ARG 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 ARG 3.6 5.8 + - - +
533A ASP* 1.3 72.0 + - - +
535A GLU* 1.3 69.4 + - + +
537A VAL* 3.3 8.6 + - - +
538A ARG* 3.0 27.9 + - + +
557A ASP* 2.8 35.6 + - - +
560A LEU* 3.6 30.4 - - + +
561A ASP* 2.4 32.5 + - - +
564A LEU* 3.7 33.3 - - + +
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Residues in contact with GLU 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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533A ASP* 3.2 6.9 + - - +
534A ARG* 1.3 88.9 - - + +
536A THR* 1.3 64.3 - - - +
538A ARG* 4.0 21.9 + - - +
539A ALA* 3.2 24.6 + - - +
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Residues in contact with THR 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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524A GLN* 4.8 4.7 - - + +
528A ALA* 3.6 18.4 - - + -
533A ASP* 2.4 38.9 + - - -
535A GLU* 1.3 69.6 - - - +
537A VAL* 1.3 65.0 + - - +
539A ALA* 3.2 5.0 + - + +
540A LYS* 3.0 39.6 + - + +
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Residues in contact with VAL 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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525A ILE* 3.5 32.9 - - + +
528A ALA* 3.6 3.4 - - + -
529A ALA* 3.5 21.5 - - + +
533A ASP 3.1 15.2 + - - +
534A ARG* 3.6 11.4 - - - +
535A GLU 3.3 0.4 - - - -
536A THR* 1.3 74.1 - - - +
538A ARG* 1.3 54.2 - - - +
540A LYS* 4.0 0.5 - - - -
541A SER* 2.7 36.3 + - - -
560A LEU* 3.8 20.4 - - + +
563A ILE* 4.0 30.1 - - + -
564A LEU* 4.8 5.4 - - + -
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Residues in contact with ARG 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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534A ARG* 3.0 16.4 + - - +
535A GLU* 4.0 23.5 + - - +
537A VAL* 1.3 78.6 - - - +
539A ALA* 1.3 58.4 + - - +
541A SER* 3.3 5.2 + - - -
542A ILE* 3.0 55.6 + - + +
547A LEU* 4.4 3.4 - - + +
549A GLY* 3.5 20.8 + - - -
556A GLU* 3.0 42.6 + - - -
560A LEU* 3.8 23.8 - - + -
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Residues in contact with ALA 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 GLU 3.2 19.2 + - - +
536A THR* 3.2 5.6 + - + +
538A ARG* 1.3 80.2 - - - +
540A LYS* 1.3 61.4 + - + +
542A ILE* 3.3 13.1 + - - +
543A GLU* 2.9 27.4 + - - +
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Residues in contact with LYS 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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521A LEU* 3.8 15.4 - - + +
524A GLN* 2.7 49.0 + - + +
525A ILE* 3.8 22.3 - - + +
536A THR* 3.0 28.8 + - + +
539A ALA* 1.3 76.5 - - + +
541A SER* 1.3 55.7 + - - +
543A GLU* 3.0 28.8 + - - +
544A MSE 2.8 36.7 + - - +
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Residues in contact with SER 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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525A ILE* 3.8 18.0 - - - +
537A VAL* 2.7 25.8 + - - +
538A ARG* 3.3 7.2 + - - -
540A LYS* 1.3 77.3 - - - +
542A ILE* 1.4 58.1 + - - +
544A MSE 3.7 3.4 + - - +
545A LYS 3.3 2.4 + - - -
546A PHE* 3.1 31.9 + - - +
547A LEU* 3.3 25.2 + - - -
559A HIS* 4.5 5.2 + - - -
560A LEU* 5.0 0.8 - - - +
563A ILE* 4.2 17.0 - - - +
610A HIS* 5.3 1.0 + - - -
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Residues in contact with ILE 542 (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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538A ARG* 3.0 57.8 + - + +
539A ALA* 3.5 9.4 - - - +
541A SER* 1.4 74.8 - - - +
543A GLU* 1.3 62.1 + - - +
545A LYS* 2.9 23.9 + - - +
547A LEU* 3.3 29.5 - - + +
548A THR* 4.2 12.3 - - - +
549A GLY* 3.7 17.3 - - - +
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Residues in contact with GLU 543 (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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521A LEU* 3.5 25.7 - - + +
539A ALA 2.9 16.7 + - - +
540A LYS* 3.0 38.8 + - + +
542A ILE* 1.3 78.8 - - - +
544A MSE 1.3 57.9 + - - +
545A LYS* 3.2 12.0 + - - +
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Residues in contact with MSE 544 (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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518A PHE* 3.7 33.5 - - + +
521A LEU* 3.9 22.6 - - + +
522A TYR* 4.1 22.4 - - + -
525A ILE* 3.7 27.8 - - + -
540A LYS 2.8 20.4 + - - +
541A SER* 3.9 3.6 - - - +
542A ILE 3.2 0.2 - - - -
543A GLU* 1.3 71.1 - - - +
545A LYS* 1.3 68.1 + - - +
546A PHE* 3.5 14.5 + - + -
603A PRO* 4.0 5.2 - - - +
606A THR* 3.7 41.0 - - + +
609A LEU* 4.5 5.2 - - - -
610A HIS* 4.3 10.5 - - + +
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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