Contacts of the helix formed by residues 467 - 475 (chain D) in PDB entry 5I94
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 467 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D MET* 2.9 13.9 + - + +
466D ASP* 1.3 77.0 - - - +
468D SER* 1.3 58.6 + - - +
469D GLY 3.3 2.2 - - - -
470D GLN* 3.1 43.7 + - + -
471D PHE* 2.9 56.7 + + + +
474D HIS* 5.6 0.2 - + - -
505D ASP* 6.1 0.9 - - - -
507D MET* 3.7 29.9 - - + +
509D ASN* 3.4 21.8 - - - +
514D ILE* 4.5 13.9 - - + -
518D HIS* 4.1 27.8 - + - -
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Residues in contact with SER 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D HIS 4.4 3.2 - - - +
461D SER* 3.4 25.5 - - - +
462D CYS* 3.2 5.1 - - - -
463D GLY 3.2 10.8 + - - +
464D MET* 3.1 28.8 + - - +
465D TYR 2.8 20.7 + - - -
466D ASP 3.2 1.3 - - - -
467D PHE* 1.3 76.2 - - - +
469D GLY* 1.3 61.9 + - - +
471D PHE* 3.9 2.2 - - - +
472D ALA* 3.0 26.7 + - - +
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Residues in contact with GLY 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C LYS 4.2 4.8 - - - +
311C GLU* 3.6 33.3 + - - -
312C PRO* 5.4 4.7 - - - -
461D SER 5.1 0.2 + - - -
466D ASP 4.5 1.8 + - - -
467D PHE 3.3 1.0 + - - -
468D SER* 1.3 78.1 - - - +
470D GLN* 1.3 61.5 + - - +
472D ALA* 3.8 5.5 - - - +
473D PHE* 3.1 23.7 + - - +
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Residues in contact with GLN 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C LYS* 3.2 33.8 - - - +
311C GLU* 3.6 16.3 + - + +
466D ASP 5.6 0.4 - - - +
467D PHE* 3.1 43.4 + - + +
469D GLY* 1.3 73.6 - - - +
471D PHE* 1.3 61.4 + - - +
473D PHE* 3.5 3.4 + - - +
474D HIS* 3.0 52.4 + - - +
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Residues in contact with PHE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D MET 6.1 0.9 - - - -
460D HIS 5.7 2.0 - - - -
464D MET* 3.8 37.9 - - + -
467D PHE* 2.9 28.6 + + + +
468D SER 3.9 3.8 - - - +
470D GLN* 1.3 76.8 - - - +
472D ALA* 1.3 60.2 + - + +
474D HIS* 5.1 0.4 - - - -
475D VAL* 2.6 70.6 + - + +
476D GLY 3.0 5.4 + - - -
477D LEU 3.0 28.3 - - - -
479D ALA* 3.6 24.2 - - + -
489D LEU* 4.3 3.4 - - + -
514D ILE* 4.1 11.7 - - + -
517D CYS* 3.9 22.0 - - + -
518D HIS* 5.1 0.2 - + - -
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Residues in contact with ALA 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C SER* 4.6 3.7 + - - -
460D HIS* 3.5 40.1 - - + +
461D SER* 5.2 2.0 - - - -
468D SER 3.0 19.0 + - - +
469D GLY* 3.8 5.6 - - - +
471D PHE* 1.3 80.5 - - - +
473D PHE* 1.3 60.7 + - - +
476D GLY* 3.2 25.1 - - - +
477D LEU 5.4 0.9 - - - +
527D HIS* 3.8 4.9 + - - -
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Residues in contact with PHE 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C TYR* 3.7 2.7 - - - -
301C THR* 4.0 9.4 - - + -
305C HIS* 3.6 14.4 - + - -
310C LYS* 3.6 36.3 - - + +
453C ARG* 5.4 2.9 + - - +
454C ASN* 3.0 46.2 + - - -
457C SER* 4.2 14.1 + - - -
458C LEU* 3.8 38.1 - - + -
469D GLY 3.1 16.5 + - - +
470D GLN 3.8 3.8 - - - +
472D ALA* 1.3 78.1 - - - +
474D HIS* 1.3 77.8 + + - +
527D HIS* 3.0 20.0 + - - -
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Residues in contact with HIS 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C THR* 4.8 8.7 - - + +
310C LYS* 3.0 35.1 + - - -
453C ARG* 5.7 0.7 + - - -
467D PHE* 5.6 0.2 - + - -
470D GLN* 3.0 42.3 + - - +
471D PHE 4.5 0.2 - - - +
473D PHE* 1.3 95.1 - + - +
475D VAL* 1.3 64.2 + - - +
518D HIS* 3.8 30.2 - + + +
521D VAL* 4.4 7.1 - - - +
527D HIS* 3.5 11.3 - - - -
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Residues in contact with VAL 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D PHE* 2.6 61.7 + - + +
474D HIS* 1.3 75.8 - - - +
476D GLY* 1.3 60.2 + - - +
477D LEU* 3.2 14.4 + - + +
489D LEU* 5.0 0.2 - - + -
517D CYS* 4.0 17.3 - - + +
518D HIS* 3.9 29.4 - - + +
521D VAL* 3.6 31.9 - - + +
527D HIS* 3.2 14.7 - - - -
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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