Contacts of the helix formed by residues 537 - 552 (chain V) in PDB entry 5IJO
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 SER 537 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468V LEU 4.2 0.7 - - - -
469V ASP* 3.0 24.5 - - - -
536V TYR* 1.4 74.1 - - - +
538V SER* 1.3 61.5 + - - +
539V TRP* 4.5 1.8 - - - -
540V THR* 3.8 23.6 - - - -
541V LEU* 2.9 30.9 + - - +
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Residues in contact with SER 538 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468V LEU* 2.6 32.2 + - - -
471V MET* 4.8 9.7 - - - +
536V TYR 3.8 2.8 + - - -
537V SER* 1.3 70.6 - - - +
539V TRP* 1.3 57.6 + - - +
541V LEU* 3.2 5.9 + - - +
542V PHE* 2.8 30.9 + - - +
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Residues in contact with TRP 539 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468V LEU* 4.0 11.0 + - + +
469V ASP* 6.2 1.1 - - - -
537V SER* 3.3 2.1 - - - -
538V SER* 1.3 80.0 - - - +
540V THR* 1.3 57.3 + - - +
542V PHE* 3.3 5.0 + - - +
543V THR* 2.8 31.2 + - - -
586V LEU 5.2 8.5 - - - +
588V PRO* 4.0 10.7 - - + +
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Residues in contact with THR 540 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537V SER* 3.5 22.0 + - - -
538V SER 3.3 0.2 - - - -
539V TRP* 1.3 77.4 - - - +
541V LEU* 1.3 61.4 + - - +
543V THR* 3.3 10.6 + - - -
544V CYS* 3.3 12.8 + - - +
588V PRO* 4.3 12.5 - - - +
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Residues in contact with LEU 541 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536V TYR* 5.4 7.2 - - + -
537V SER 2.9 19.8 + - - +
538V SER* 3.5 6.7 - - - +
540V THR* 1.3 74.7 - - - +
542V PHE* 1.3 61.6 + - - +
544V CYS* 2.9 22.2 + - - +
545V GLU* 3.1 12.1 + - - +
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Residues in contact with PHE 542 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538V SER 2.8 19.3 + - - +
539V TRP* 4.0 4.5 - - - +
541V LEU* 1.3 68.2 - - - +
543V THR* 1.3 58.5 + - - +
544V CYS 2.8 11.1 + - - -
545V GLU* 3.1 16.2 + - - +
546V ILE* 3.1 16.5 + - - +
568V ILE* 5.4 13.0 - - + +
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Residues in contact with THR 543 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539V TRP 2.8 10.5 + - - -
540V THR* 3.5 6.3 - - - -
541V LEU 3.1 0.4 - - - -
542V PHE* 1.3 74.6 - - - +
544V CYS* 1.3 56.8 + - - +
546V ILE* 4.7 2.0 - - - +
547V GLU* 4.6 9.7 - - - +
588V PRO* 3.3 47.3 - - - +
589V ILE* 4.4 9.6 - - - -
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Residues in contact with CYS 544 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540V THR 3.3 7.2 + - - +
541V LEU* 2.9 11.1 + - - +
542V PHE 2.8 0.6 - - - -
543V THR* 1.3 80.7 - - - +
545V GLU* 1.3 68.9 + - - +
546V ILE 3.3 0.8 + - - -
547V GLU* 3.4 7.3 + - - +
548V MET* 3.3 19.6 + - - +
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Residues in contact with GLU 545 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541V LEU 3.1 7.4 + - - +
542V PHE* 3.1 11.8 + - - +
544V CYS* 1.3 81.5 - - - +
546V ILE* 1.3 65.1 + - - +
548V MET* 3.2 16.8 + - - +
549V LEU* 3.4 7.3 + - - +
558V VAL* 5.3 13.9 - - + -
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Residues in contact with ILE 546 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542V PHE 3.1 11.6 + - - +
543V THR* 5.9 0.9 - - - -
544V CYS 3.3 0.4 - - - +
545V GLU* 1.3 81.3 - - + +
547V GLU* 1.3 53.1 + - - +
549V LEU* 2.8 34.1 + - + +
550V LEU* 3.5 2.4 + - - +
592V ARG* 6.1 1.6 - - + -
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Residues in contact with GLU 547 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543V THR 4.6 8.6 + - - +
544V CYS* 3.6 12.5 - - - +
546V ILE* 1.3 71.0 - - - +
548V MET* 1.3 68.1 + - - +
549V LEU 3.0 1.6 - - - -
550V LEU* 2.9 22.3 + - - +
551V HIS* 3.5 5.0 + - - +
592V ARG* 4.9 19.8 - - + +
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Residues in contact with MET 548 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544V CYS 3.3 8.7 + - - +
545V GLU* 3.2 12.9 + - - +
546V ILE 3.2 0.4 - - - -
547V GLU* 1.3 80.3 - - - +
549V LEU* 1.3 64.5 + - - +
550V LEU 3.1 0.2 + - - -
551V HIS* 3.2 3.3 + - - +
552V VAL* 2.9 26.2 + - - -
553V VAL 4.8 0.2 + - - -
554V SER* 4.5 24.6 - - - +
556V ALA* 5.0 15.9 - - + -
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Residues in contact with LEU 549 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545V GLU 3.4 5.1 + - - +
546V ILE* 2.8 21.6 + - + +
548V MET* 1.3 81.4 - - - +
550V LEU* 1.3 65.3 + - - +
552V VAL* 3.9 6.8 + - - +
560V GLN* 5.6 8.3 - - + -
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Residues in contact with LEU 550 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546V ILE 3.5 1.6 + - - +
547V GLU* 2.9 15.4 + - - +
549V LEU* 1.3 84.3 - - - +
551V HIS* 1.4 64.9 + - + +
552V VAL* 4.4 1.7 - - - +
595V MET* 6.1 4.7 - - + -
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Residues in contact with HIS 551 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547V GLU 3.5 5.0 + - - +
548V MET* 3.2 6.9 + - - +
550V LEU* 1.4 80.8 - - - +
552V VAL* 1.3 67.0 + - - +
553V VAL* 2.8 28.6 + - + +
554V SER* 4.6 2.9 - - - +
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Residues in contact with VAL 552 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215Q ILE* 6.3 2.9 - - + -
548V MET 2.9 16.7 + - - -
549V LEU 4.5 4.7 - - - +
550V LEU 3.5 4.2 - - - +
551V HIS* 1.3 77.6 - - - +
553V VAL* 1.4 63.9 + - - +
554V SER 3.0 12.7 - - - +
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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