Contacts of the helix formed by residues 464 - 469 (chain D) in PDB entry 6E7P
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 LEU 464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D TYR* 4.2 9.0 - - + -
439D TYR* 4.2 10.8 - - + +
440D CYS* 3.8 17.0 - - - -
454D PHE* 4.6 13.9 - - + -
460D VAL* 2.9 38.8 + - + +
463D CYS* 1.3 80.6 - - - +
465D PHE* 1.3 64.0 + - - +
466D SER 3.3 0.2 - - - -
467D LEU* 3.1 18.9 + - + +
468D ILE* 3.3 18.5 + - - +
497D TYR* 3.9 30.3 - - + +
498D LEU* 5.1 2.7 - - + -
501D PHE* 3.7 32.3 - - + -
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Residues in contact with PHE 465 (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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473C MET* 5.0 1.3 - - - -
477C PHE* 4.9 7.2 - + - -
499C TYR* 3.7 28.3 - + + -
502C ILE* 3.5 33.0 - - + -
503C SER* 4.2 20.6 - - - -
507C TYR* 4.5 18.2 - + - -
436D TYR* 3.4 19.3 + + - +
461D SER 3.3 20.4 - - - +
462D GLU 3.4 3.5 + - - +
464D LEU* 1.3 80.6 - - - +
466D SER* 1.3 62.2 + - - +
467D LEU 3.1 1.1 + - - -
468D ILE* 3.6 21.8 - - + +
469D ASN* 3.2 27.7 + - - -
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Residues in contact with SER 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C MET* 3.7 24.2 - - - +
474C PHE* 3.5 35.1 - - - +
477C PHE* 5.1 3.6 - - - -
462D GLU 2.9 23.2 + - - -
463D CYS* 3.7 8.3 + - - -
465D PHE* 1.3 77.4 - - - +
467D LEU* 1.3 59.7 + - - +
469D ASN* 4.1 3.6 + - - +
470D GLY 3.9 2.4 + - - -
471D ASP* 2.9 34.2 + - - +
472D ASP* 5.2 0.7 + - - +
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Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D PHE* 5.6 1.1 - - + -
463D CYS* 3.2 22.9 - - - +
464D LEU* 3.1 14.4 + - + +
466D SER* 1.3 78.1 + - - +
468D ILE* 1.3 60.6 + - - +
469D ASN 3.2 1.8 - - - -
470D GLY 3.1 14.0 + - - -
471D ASP 3.9 6.5 - - - +
472D ASP 4.3 9.4 - - - +
473D MET* 3.4 23.9 - - + +
476D THR* 4.0 24.9 - - + +
477D PHE* 5.9 2.7 - - + -
498D LEU* 4.7 19.1 - - + +
501D PHE* 4.6 12.3 - - + -
502D ILE* 3.2 43.1 - - + +
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Residues in contact with ILE 468 (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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507C TYR* 3.6 21.3 - - - +
436D TYR* 5.9 1.8 - - + -
464D LEU 3.3 12.0 + - - +
465D PHE* 3.6 27.6 - - + +
467D LEU* 1.3 75.7 - - - +
469D ASN* 1.3 68.6 + - - +
470D GLY 3.2 0.4 + - - -
501D PHE* 3.7 18.2 - - + +
502D ILE* 3.7 12.3 - - + -
505D PHE* 3.6 48.2 - - + -
506D ILE* 3.6 22.2 - - + +
510D LEU* 5.9 1.6 - - - +
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Residues in contact with ASN 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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469A ASN 4.7 4.0 - - - +
469C ASN 4.8 2.8 - - - +
470C GLY* 4.3 12.1 - - - +
473C MET* 3.2 43.4 - - + +
502C ILE* 4.0 9.1 - - - +
506C ILE* 3.5 27.3 - - + +
507C TYR* 3.7 17.8 + - - -
465D PHE* 3.2 24.5 + - - -
466D SER 4.4 2.2 - - - +
467D LEU 3.2 0.8 - - - -
468D ILE* 1.3 78.9 - - - +
470D GLY* 1.3 61.6 + - - +
506D ILE* 5.8 0.9 - - - -
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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