Contacts of the helix formed by residues 451 - 457 (chain V) in PDB entry 5IY6
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 PHE 451 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410V TYR* 3.8 34.3 - - + -
411V SER* 4.7 7.4 - - - -
412V MET* 4.7 2.2 - - + -
420V SER* 4.4 7.2 - - - -
445V THR* 4.4 9.4 - - + +
446V ILE* 3.3 36.6 - - + +
448V ALA* 3.3 12.0 + - + +
450V MET* 1.3 76.0 - - + +
452V ARG* 1.4 65.2 + - - +
454V VAL* 3.0 26.3 + - - +
57X C 3.2 52.9 - - - -
58X T 3.4 16.4 - - - -
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Residues in contact with ARG 452 (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* 5.8 3.4 - - - +
446V ILE* 3.2 8.9 + - - +
447V PRO* 2.9 28.9 + - - +
448V ALA 2.9 16.7 + - - +
449V LYS* 4.1 13.1 - - - +
450V MET 3.2 0.2 + - - -
451V PHE* 1.4 76.8 - - - +
453V ARG* 1.4 59.5 + - - +
454V VAL 3.3 0.9 + - - -
455V LEU* 3.4 8.1 + - - +
456V THR* 3.0 32.8 + - - +
476V LYS* 4.3 16.4 - - - +
479V ASP* 3.3 37.4 + - - +
483V LEU* 3.9 19.0 - - + +
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Residues in contact with ARG 453 (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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255V MET* 5.2 7.2 - - - -
412V MET* 4.5 19.4 - - - +
420V SER* 4.9 10.1 + - - -
423V ALA* 6.2 1.7 - - - +
424V GLU* 5.3 5.5 + - - +
449V LYS 4.6 2.8 + - - +
450V MET 3.2 14.2 + - - +
451V PHE 3.0 0.8 - - - -
452V ARG* 1.4 77.8 - - - +
454V VAL* 1.3 64.6 + - + +
456V THR* 3.9 8.7 - - - -
457V ILE* 3.1 62.4 + - + +
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Residues in contact with VAL 454 (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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364V LEU* 4.8 9.9 - - + -
410V TYR* 5.0 1.1 - - + +
419V ARG* 4.6 21.1 - - + +
420V SER* 3.4 35.9 - - - +
423V ALA* 4.5 14.4 - - + +
427V MET* 4.7 7.1 - - + +
438V MET* 5.9 0.2 - - - +
446V ILE* 4.2 12.1 - - + -
450V MET 5.2 0.9 - - - +
451V PHE* 3.0 18.7 + - - +
453V ARG* 1.3 79.2 - - + +
455V LEU* 1.3 73.3 + - + +
457V ILE* 3.9 5.6 - - - +
458V VAL* 3.5 16.6 - - - +
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Residues in contact with LEU 455 (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* 4.8 2.8 - - - +
364V LEU* 4.5 5.8 - - + -
438V MET* 4.1 17.0 - - - -
440V LEU* 4.4 11.7 - - + -
446V ILE* 3.7 21.8 - - + -
452V ARG 3.4 3.7 + - - +
453V ARG 3.3 0.2 - - - -
454V VAL* 1.3 93.2 - - + +
456V THR* 1.3 63.8 + - - +
457V ILE 3.4 0.2 - - - -
458V VAL* 3.6 18.9 - - - +
460V ALA* 5.1 1.2 - - + +
463V LYS* 3.7 29.6 + - + -
483V LEU* 3.6 28.1 - - + +
484V ILE* 3.4 31.6 - - + -
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Residues in contact with THR 456 (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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255V MET* 3.6 33.2 - - + +
280V LEU* 5.6 6.3 - - + -
281V GLN* 4.2 1.7 + - - +
282V LYS* 4.1 34.1 + - + +
452V ARG* 3.0 28.0 + - - +
453V ARG* 3.2 8.1 + - - -
455V LEU* 1.3 76.9 - - - +
457V ILE* 1.3 58.0 + - - +
458V VAL 3.1 11.4 + - - +
483V LEU* 3.7 14.2 - - - +
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Residues in contact with ILE 457 (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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252V TYR* 5.1 5.5 + - - +
254V GLN 4.0 22.4 - - - +
255V MET* 4.0 20.6 - - + -
281V GLN* 3.5 10.1 - - - +
423V ALA* 4.6 21.5 - - + +
424V GLU* 5.2 19.2 - - + +
453V ARG* 3.1 54.5 + - + +
454V VAL* 3.9 8.1 - - - +
455V LEU 3.4 0.4 - - - -
456V THR* 1.3 72.9 - - - +
458V VAL* 1.3 62.5 + - - +
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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