Contacts of the helix formed by residues 470 - 475 (chain C) in PDB entry 1DE4
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 TYR 470 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ASP* 2.5 44.0 + - - -
316C PHE* 3.6 22.9 - + - -
466C TRP* 2.7 43.5 + + - +
467C LEU 3.9 2.0 - - - -
469C GLY* 1.3 75.3 - - - -
471C LEU* 1.3 65.8 + - - +
472C SER* 3.3 3.8 - - - -
473C SER* 2.9 17.5 + - - +
474C LEU* 2.9 30.3 - - + +
740F TRP* 5.1 2.6 - + - -
747F ASN* 4.1 14.8 - - + -
753F VAL* 4.0 10.3 - - + -
756F ILE* 4.1 30.9 - - + +
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Residues in contact with LEU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C LEU 3.1 16.6 + - - +
468C GLU 4.1 9.6 - - - +
469C GLY 3.4 3.2 + - - +
470C TYR* 1.3 77.2 - - - +
472C SER* 1.3 69.1 + - - +
474C LEU* 3.0 14.6 + - - +
475C HIS* 3.1 17.2 + - + +
547C TYR* 4.0 26.2 - - + +
548C SER* 5.8 8.5 - - - +
698C ARG* 6.1 3.1 - - - +
688F PRO* 3.8 33.9 - - + -
689F TYR* 5.6 3.4 - - + +
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Residues in contact with SER 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C GLY 5.3 1.0 + - - -
470C TYR* 4.7 2.9 + - - -
471C LEU* 1.3 84.7 + - - +
473C SER* 1.3 61.2 + - - +
474C LEU 3.4 0.4 + - - -
475C HIS* 4.1 4.9 + - - +
680F ARG* 3.8 12.8 + - - -
684F HIS* 3.4 45.1 + - - -
744F GLY* 3.2 30.8 + - - -
747F ASN* 5.5 0.5 - - - +
748F ALA* 3.8 11.0 - - - +
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Residues in contact with SER 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C TYR* 3.5 9.9 + - - -
470C TYR* 2.9 12.1 + - - +
472C SER* 1.3 79.9 + - - +
474C LEU* 1.3 62.7 + - - +
477C LYS* 3.6 17.4 - - - +
747F ASN* 3.5 24.9 + - - +
748F ALA* 3.8 9.5 - - - +
751F GLY 6.1 0.2 - - - -
752F ASP* 6.1 1.0 - - - -
753F VAL* 3.3 35.3 + - - +
756F ILE* 4.2 5.4 - - - +
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Residues in contact with LEU 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TYR* 3.8 12.1 - - - +
466C TRP* 3.7 25.8 - - + -
467C LEU* 3.5 40.8 - - + +
470C TYR* 2.9 37.2 - - + +
471C LEU* 3.0 6.8 + - - +
473C SER* 1.3 83.2 - - - +
475C HIS* 1.3 54.4 + - - +
476C LEU 2.9 1.4 + - - -
477C LYS 2.7 26.6 + - - -
478C ALA* 3.0 22.7 + - + +
548C SER* 5.2 1.1 - - - +
550C ILE* 4.5 12.1 - - + +
753F VAL* 3.7 13.2 - - + -
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Residues in contact with HIS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C LEU* 3.1 19.0 + - + +
472C SER* 4.1 6.7 - - - +
473C SER 3.5 0.8 - - - -
474C LEU* 1.3 73.8 - - - +
476C LEU* 1.3 85.2 + - + +
477C LYS* 3.1 2.4 + - - +
548C SER 5.9 0.8 + - - -
683C TYR* 3.4 42.8 - + - -
475F HIS* 2.8 28.2 + + - -
476F LEU* 4.5 1.6 - - + -
680F ARG* 2.8 46.0 + - - +
683F TYR* 3.8 23.9 + + + -
684F HIS* 5.2 1.1 - - + -
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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