Contacts of the helix formed by residues 476 - 484 (chain V) in PDB entry 5IY9
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 476 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447V PRO* 4.0 33.8 - - + +
448V ALA* 4.6 13.9 - - - +
449V LYS* 5.1 4.0 - - - +
452V ARG* 4.3 13.0 - - - +
471V VAL* 3.7 11.1 - - + +
472V ARG* 5.4 1.6 - - - +
474V ASP* 2.8 41.1 + - - +
475V ASP* 1.3 72.5 - - - +
477V ILE* 1.3 56.5 + - - +
478V VAL* 3.2 4.2 - - - +
479V ASP* 2.9 29.2 + - + +
480V LEU 4.1 0.7 + - - -
76X C 5.6 1.8 - - - -
77X C 3.1 31.5 + - - -
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Residues in contact with ILE 477 (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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337V VAL* 6.2 0.2 - - + -
447V PRO* 6.6 0.2 - - - -
470V LEU* 3.7 28.5 - - + -
471V VAL* 3.4 23.3 - - + +
475V ASP* 3.3 15.5 + - + +
476V LYS* 1.3 74.0 - - - +
478V VAL* 1.3 68.3 + - + +
479V ASP 3.2 0.2 - - - -
480V LEU* 3.0 46.9 + - + +
481V ASN* 3.8 4.0 + - - +
487V LYS* 6.5 1.6 - - + -
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Residues in contact with VAL 478 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475V ASP 5.9 0.7 - - - +
476V LYS 4.4 2.2 - - - +
477V ILE* 1.3 80.9 - - + +
479V ASP* 1.3 64.5 + - - +
480V LEU 3.4 0.3 + - - -
481V ASN* 3.5 20.0 + - - +
482V PHE* 4.1 4.3 + - - +
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Residues in contact with ASP 479 (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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282V LYS* 4.7 11.9 + - - -
447V PRO* 4.8 7.4 - - + -
452V ARG* 3.3 51.9 + - - +
476V LYS* 2.9 13.8 + - + +
478V VAL* 1.3 83.1 - - - +
480V LEU* 1.4 62.5 + - - +
482V PHE* 3.2 11.0 + - - +
483V LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 480 (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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337V VAL* 4.0 24.5 - - + -
443V VAL* 4.1 35.2 - - + +
444V HIS* 5.3 1.1 - - - +
446V ILE* 4.6 3.4 - - + -
447V PRO* 4.2 26.5 - - + +
470V LEU* 3.9 19.3 - - + +
476V LYS 4.1 0.8 + - - -
477V ILE* 3.0 39.7 + - + +
479V ASP* 1.4 76.8 - - - +
481V ASN* 1.4 54.1 + - - +
483V LEU* 4.2 6.3 - - + -
484V ILE* 3.1 33.3 + - + -
485V GLY 3.4 8.4 - - - +
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Residues in contact with ASN 481 (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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285V ILE* 4.0 3.5 - - - +
286V HIS* 5.5 4.0 + - - -
477V ILE 3.8 3.6 + - - +
478V VAL* 3.5 15.6 + - - +
479V ASP 3.3 0.2 - - - -
480V LEU* 1.4 71.1 - - - +
482V PHE* 1.3 68.2 + - - +
485V GLY* 3.1 31.9 + - - -
486V PRO* 3.8 25.5 - - + +
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Residues in contact with PHE 482 (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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280V LEU* 6.0 4.3 - - + -
282V LYS* 3.5 43.7 - - + +
283V ARG* 4.2 23.1 - - + -
285V ILE* 3.6 22.8 - - + +
286V HIS* 3.3 39.0 - + - -
463V LYS* 4.7 0.2 + - - -
478V VAL 4.1 3.5 + - - +
479V ASP* 3.2 13.1 + - - +
481V ASN* 1.3 85.1 + - - +
483V LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 483 (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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282V LYS* 3.6 27.3 - - + +
446V ILE* 4.3 11.9 - - + -
447V PRO* 4.0 24.7 - - + -
452V ARG* 3.9 27.6 - - + +
455V LEU* 3.6 29.8 - - + +
456V THR* 3.7 19.5 - - - +
463V LYS* 2.9 23.7 + - - +
479V ASP* 3.0 18.5 + - - +
480V LEU* 3.4 6.9 + - + +
482V PHE* 1.3 77.6 - - + +
484V ILE* 1.3 66.9 + - + +
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Residues in contact with ILE 484 (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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285V ILE* 3.4 6.7 - - - +
332V ARG* 3.0 24.4 + - - -
336V GLY 3.2 21.5 - - - +
337V VAL* 4.0 7.9 - - + -
440V LEU* 3.9 17.9 - - + -
443V VAL* 3.8 22.0 - - + -
446V ILE* 4.2 6.3 - - + -
455V LEU* 3.4 36.1 - - + -
463V LYS* 3.5 23.8 - - + +
464V LEU 4.0 1.8 - - - -
465V GLY* 3.7 14.8 - - - +
480V LEU* 3.1 18.9 + - + +
483V LEU* 1.3 75.8 - - + +
485V GLY* 1.3 53.0 + - - +
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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