Contacts of the helix formed by residues 417 - 423 (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 THR 417 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411V SER* 3.2 36.6 - - - +
412V MET* 3.4 1.9 - - - -
413V LEU* 3.0 36.3 + - + +
414V GLY 2.6 21.2 + - - +
416V THR* 1.4 71.1 - - - +
418V LYS* 1.3 62.7 + - - +
421V TRP* 3.3 17.8 + - - +
22Y G 3.8 3.8 - - - +
23Y T 3.6 38.1 - - - +
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Residues in contact with LYS 418 (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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392V PHE* 4.0 26.9 - - + +
393V THR* 3.8 33.3 + - - +
397V LYS* 4.4 17.2 - - - +
408V SER* 3.3 33.0 - - - +
409V THR 4.0 5.8 + - - +
411V SER* 3.8 5.7 + - - -
415V HIS 5.1 0.4 + - - -
416V THR* 3.3 16.3 + - - +
417V THR* 1.3 70.6 - - - +
419V ARG* 1.4 69.7 + - - +
421V TRP* 3.4 20.1 + - + +
422V GLU* 3.0 40.8 + - + +
23Y T 4.7 1.6 + - - -
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Residues in contact with ARG 419 (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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362V LEU* 3.6 37.7 - - - +
363V VAL 5.6 0.4 - - - -
364V LEU* 3.7 34.3 - - + -
392V PHE* 5.7 0.8 - - - -
406V ALA 5.8 0.6 + - - -
408V SER* 3.7 32.6 + - - -
409V THR 3.0 24.3 + - - +
410V TYR* 4.4 7.0 - - - +
417V THR 3.9 0.2 - - - -
418V LYS* 1.4 73.2 - - - +
420V SER* 1.3 61.5 + - - +
422V GLU* 2.8 43.3 + - - +
423V ALA* 3.1 26.6 + - - +
426V VAL* 3.8 14.1 - - - +
427V MET* 4.2 18.3 - - - +
435V TRP* 4.9 4.8 - - - -
454V VAL* 4.6 9.5 - - + +
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Residues in contact with SER 420 (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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410V TYR 2.8 22.7 + - - -
411V SER 3.3 15.8 + - - -
412V MET* 3.8 27.9 - - - +
418V LYS 3.4 0.4 - - - -
419V ARG* 1.3 78.2 - - - +
421V TRP* 1.3 64.7 + - - +
422V GLU 3.5 0.2 + - - -
423V ALA* 3.5 13.0 + - - +
451V PHE* 4.4 4.3 - - - -
453V ARG* 4.9 10.3 + - - -
454V VAL* 3.4 26.2 - - - +
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Residues in contact with TRP 421 (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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412V MET* 4.5 10.0 - - + -
414V GLY 4.0 6.7 - - - +
415V HIS* 3.0 54.2 - + + +
417V THR 3.3 20.1 + - - +
418V LYS* 3.4 18.5 + - - +
419V ARG 3.3 0.4 - - - -
420V SER* 1.3 81.9 - - - +
422V GLU* 1.3 82.4 + - + +
423V ALA 3.6 0.7 + - - -
424V GLU 5.1 0.5 + - - -
425V ARG* 5.1 9.4 - - + -
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Residues in contact with GLU 422 (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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392V PHE* 3.9 14.9 - - - -
397V LYS* 5.2 3.1 - - - +
418V LYS* 3.0 31.0 + - + +
419V ARG* 2.8 36.3 + - - +
421V TRP* 1.3 91.1 - - + +
423V ALA* 1.4 51.0 + - - +
424V GLU 2.7 19.2 + - - -
425V ARG* 2.7 69.6 + - + +
426V VAL* 3.7 3.5 - - + +
427V MET* 4.1 4.3 - - - +
435V TRP* 5.1 1.6 - - - -
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Residues in contact with ALA 423 (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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419V ARG 3.1 16.0 + - - +
420V SER 3.6 11.7 - - - +
421V TRP 3.4 3.0 + - - -
422V GLU* 1.4 72.9 - - - +
424V GLU* 1.3 61.0 + - + +
427V MET* 3.3 34.5 - - + +
453V ARG* 6.2 2.0 - - - +
454V VAL* 4.5 20.6 - - + +
457V ILE* 4.6 16.9 - - + +
458V VAL* 4.6 8.7 - - - +
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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