Contacts of the helix formed by residues 529 - 537 (chain V) in PDB entry 5IY8
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 LYS 529 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525V ILE* 4.6 18.6 - - + -
527V THR* 3.3 12.7 + - - +
528V LYS* 1.3 77.6 - - - +
530V ARG* 1.3 53.4 + - - +
531V ILE 3.1 0.7 - - - -
532V LEU* 2.9 36.1 + - + +
533V LEU* 3.7 6.6 + - + +
566V PHE* 6.1 2.6 - - - -
716V VAL* 2.8 30.7 + - + +
717V LEU* 3.3 24.0 - - + +
718V ALA 3.6 20.3 - - - -
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Residues in contact with ARG 530 (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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621 ASP* 4.6 7.5 - - - +
522V TYR* 2.7 61.9 + - + +
523V VAL* 3.8 5.1 + - - +
525V ILE* 2.8 33.8 + - + +
526V LYS* 3.6 42.9 + - - +
527V THR 3.0 15.6 + - - +
529V LYS* 1.3 68.9 - - - +
531V ILE* 1.4 68.4 + - + +
532V LEU 3.2 0.2 - - - -
533V LEU* 3.4 19.4 + - - +
534V TYR* 3.3 17.4 + - + -
668V GLN* 3.0 31.1 + - - +
79X A 6.0 0.4 - - - -
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Residues in contact with ILE 531 (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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528V LYS* 3.5 40.8 - - + +
530V ARG* 1.4 82.5 - - + +
532V LEU* 1.3 56.5 + - - +
534V TYR* 3.6 37.1 - - + +
535V THR* 3.0 36.4 + - - +
564V ASN* 5.1 13.2 - - + +
627V SER* 6.4 0.4 - - - -
668V GLN* 5.4 3.1 - - - +
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Residues in contact with LEU 532 (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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528V LYS 4.4 0.6 + - - +
529V LYS* 2.9 22.1 + - + +
531V ILE* 1.3 77.7 - - - +
533V LEU* 1.4 56.6 + - - +
535V THR* 4.5 3.8 - - - +
536V MET* 3.1 59.6 + - + +
564V ASN* 5.2 9.4 - - - +
566V PHE* 3.7 50.0 - - + -
567V ALA* 4.5 14.4 - - + +
716V VAL* 3.8 28.8 - - + +
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Residues in contact with LEU 533 (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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514V MET* 4.2 4.4 - - - +
518V PHE* 3.7 37.5 - - + +
521V GLU* 3.7 15.3 - - + +
522V TYR* 3.5 35.0 - - + +
525V ILE* 4.4 12.6 - - + -
529V LYS* 3.7 6.7 + - + +
530V ARG* 3.4 16.5 + - - +
532V LEU* 1.4 76.0 - - - +
534V TYR* 1.3 59.4 + - - +
537V ASN* 3.2 26.7 + - - +
713V LEU* 4.0 17.0 - - + -
716V VAL* 3.7 24.9 - - + -
717V LEU* 5.0 5.4 - - + -
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Residues in contact with TYR 534 (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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514V MET* 3.8 4.5 - - + -
522V TYR* 4.0 15.0 - + + -
530V ARG 3.3 18.4 + - - +
531V ILE* 3.6 42.1 - - + +
533V LEU* 1.3 79.0 - - - +
535V THR* 1.3 68.8 + - - +
537V ASN* 4.0 1.0 - - - +
540V LYS* 2.9 12.5 + - - +
627V SER* 4.8 3.1 - - - -
628V SER 5.4 0.4 - - - -
629V HIS* 5.4 6.7 + - - -
664V SER* 2.7 25.9 + - - -
667V THR* 3.8 25.6 - - + +
668V GLN* 3.9 26.2 - - + +
669V GLU* 3.1 50.7 - - + +
672V TYR* 4.8 11.1 + - - -
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Residues in contact with THR 535 (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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531V ILE* 3.0 24.6 + - - +
532V LEU* 3.5 5.4 + - - -
533V LEU 3.5 0.2 - - - -
534V TYR* 1.3 83.7 - - - +
536V MET* 1.3 60.9 + - - +
537V ASN 3.4 0.4 + - - -
540V LYS* 3.6 14.0 - - - +
567V ALA* 4.2 15.3 - - + -
571V TYR* 2.9 24.8 + - + -
626V ILE* 3.6 41.5 - - + +
627V SER* 3.8 17.4 - - - +
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Residues in contact with MET 536 (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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518V PHE* 4.3 5.6 - - + -
532V LEU* 3.1 46.6 + - + +
535V THR* 1.3 74.0 - - - +
537V ASN* 1.4 68.0 + - - +
538V PRO* 3.1 9.8 - - - +
541V PHE* 4.4 15.5 - - + +
567V ALA* 4.4 7.4 - - - -
570V GLU* 3.4 37.0 - - + -
571V TYR* 3.7 31.9 - - + -
574V ARG* 4.5 2.5 - - - +
712V LEU* 3.9 34.9 - - + +
716V VAL* 4.4 13.0 - - + -
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Residues in contact with ASN 537 (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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161 MET* 5.0 0.6 - - - +
512V CYS 4.3 1.2 + - - -
513V PRO 2.8 16.8 + - - +
514V MET* 2.8 37.6 - - - +
515V SER* 3.7 3.3 + - - -
518V PHE* 4.1 4.6 - - + +
533V LEU 3.2 17.4 + - - +
534V TYR 4.0 2.0 - - - +
535V THR 3.4 0.8 - - - -
536V MET* 1.4 72.8 - - - +
538V PRO* 1.3 71.4 - - - +
539V ASN* 2.8 29.7 + - - -
540V LYS* 3.1 20.1 + - + +
541V PHE 3.0 17.0 + - - -
664V SER* 3.2 17.5 + - - +
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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