Contacts of the strand formed by residues 468 - 473 (chain C) in PDB entry 1Y9D
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 ILE 468 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383C ILE* 4.3 10.3 - - + -
440C GLN* 3.7 34.5 - - + +
441C VAL 2.8 11.7 + - - +
442C PHE* 3.3 34.9 - - + -
443C ASN 2.9 22.5 + - - +
466C PRO 4.8 0.2 - - - +
467C VAL* 1.3 72.3 - - - +
469C ASN* 1.3 62.3 + - - +
470C VAL* 3.7 11.6 + - + -
526C PHE* 5.5 0.7 - - + -
529C ALA* 4.5 11.9 - - + +
530C LYS* 4.5 7.6 - - - -
533C ALA* 3.4 31.9 - - + -
538C VAL* 3.9 13.2 - - + -
540C ILE* 4.8 3.4 - - + -
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Residues in contact with ASN 469 (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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443C ASN* 3.0 26.9 + - - +
457C LEU* 3.8 8.6 - - - +
460C GLN* 2.7 42.7 + - - -
467C VAL* 3.5 13.3 + - - +
468C ILE* 1.3 72.6 - - - +
470C VAL* 1.3 57.2 + - - +
471C VAL* 4.2 1.6 - - + -
511C MET* 3.6 10.7 - - - -
538C VAL 3.0 24.2 + - - +
539C LEU* 3.3 20.3 - - + -
540C ILE* 2.7 31.8 + - - +
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Residues in contact with VAL 470 (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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376C VAL* 3.5 30.7 - - + -
380C VAL* 4.3 4.3 - - + -
442C PHE* 4.6 0.7 - - + -
443C ASN* 2.8 11.7 + - - +
444C LEU* 3.5 23.5 - - + -
445C ALA* 3.0 24.8 + - - +
468C ILE* 4.2 15.5 - - + +
469C ASN* 1.3 78.7 - - - +
471C VAL* 1.3 65.4 + - - +
472C PHE* 3.6 13.5 - - + -
526C PHE* 4.2 24.0 - - + -
540C ILE* 3.4 11.2 - - + +
542C ALA* 4.7 3.8 - - + -
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Residues in contact with VAL 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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443C ASN* 5.7 2.7 - - - +
445C ALA* 3.4 7.0 - - + +
446C GLY 4.3 0.7 - - - +
447C ASP* 3.9 18.6 - - - +
450C ALA* 3.9 20.6 - - + -
469C ASN* 5.4 1.8 - - + -
470C VAL* 1.3 76.2 - - - +
472C PHE* 1.3 63.8 + - - +
473C THR* 3.3 22.0 + - - +
502C PHE* 3.7 28.3 - - + -
539C LEU* 4.2 20.0 - - + -
540C ILE 2.9 11.3 + - - +
541C ASP* 4.0 5.4 - - - +
542C ALA* 2.9 28.9 + - - +
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Residues in contact with PHE 472 (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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373C ALA* 4.0 31.9 - - + -
376C VAL* 3.6 35.4 - - + -
377C LEU* 4.2 15.7 - - + -
380C VAL* 5.5 0.2 - - + -
397C ILE* 3.6 35.9 - - + -
400C ASN* 5.7 0.7 - - - -
444C LEU* 4.2 7.9 - - + -
445C ALA 2.7 22.9 + - - +
446C GLY* 3.8 7.0 - - - -
447C ASP* 3.4 18.8 + - - +
470C VAL* 3.6 25.1 - - + -
471C VAL* 1.3 74.4 - - - +
473C THR* 1.3 57.9 + - - +
474C ASN* 3.4 11.3 + - - +
542C ALA* 3.8 4.9 - - + -
544C ILE* 4.1 16.8 - - + -
2801C MG 4.0 0.7 - - - -
2802C TPP 4.8 4.4 + - - +
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Residues in contact with THR 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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447C ASP* 3.5 20.3 - - + +
471C VAL* 3.3 13.3 - - - +
472C PHE* 1.3 67.9 - - - +
474C ASN* 1.3 57.4 + - - +
475C CYS* 4.1 10.6 - - - +
499C ASP* 3.8 22.4 - - - +
500C ILE 4.3 6.5 - - - +
502C PHE* 4.1 2.1 - - - -
515C ARG* 4.3 5.4 - - - +
541C ASP* 2.5 29.5 + - - +
542C ALA 2.9 11.1 + - - -
543C VAL* 3.4 12.4 - - + +
544C ILE* 3.1 24.3 + - - +
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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