Contacts of the strand formed by residues 464 - 467 (chain A) in PDB entry 1YY9
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 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A VAL* 3.5 9.4 - - + +
453A TRP* 3.6 30.6 - - + +
454A LYS* 3.4 23.6 + - - +
457A PHE* 4.0 5.9 - - - -
463A LYS* 1.3 79.9 + - - +
465A LYS* 1.3 70.4 + - - +
466A ILE* 3.5 32.3 - - + +
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PHE* 5.8 5.1 - - + -
437A VAL 2.9 11.7 + - - +
438A ILE* 3.4 26.5 - - + +
439A ILE 2.8 28.4 + - - +
463A LYS* 6.0 2.5 - - + -
464A THR* 1.3 78.0 - - - +
466A ILE* 1.3 62.5 + - - +
467A ILE* 3.8 9.6 + - + +
49C LYS* 5.3 1.6 - - - +
50C TYR* 3.7 21.1 + - + +
100D THR* 2.9 37.0 + - - +
101D TYR 4.8 1.0 + - - -
103D ASP* 2.9 22.1 + - - +
105D GLU* 4.2 2.0 + - - -
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Residues in contact with ILE 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 5.7 0.9 - - + -
439A ILE* 3.3 20.9 - - + +
448A ALA* 4.0 24.2 - - + +
449A ASN* 3.7 30.0 - - - +
453A TRP* 3.5 29.4 - - + +
464A THR* 3.5 26.1 - - + +
465A LYS* 1.3 75.8 - - - +
467A ILE* 1.3 63.2 + - - +
469A ASN* 3.4 19.1 - - + +
32C ASN* 4.1 12.1 + - - -
92C ASN* 5.0 4.5 + - - +
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Residues in contact with ILE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A ILE* 4.6 3.1 - - + -
439A ILE 3.0 7.3 + - - +
440A SER* 3.2 19.0 - - - +
441A GLY 3.1 15.8 + - - -
465A LYS* 4.1 16.2 - - + +
466A ILE* 1.3 87.1 - - - +
468A SER* 1.3 68.1 - - - +
469A ASN* 3.4 4.1 + - - +
32C ASN* 4.1 12.8 - - - +
50C TYR* 3.8 7.4 - - + +
91C ASN* 3.4 26.5 - - - +
92C ASN* 4.6 2.0 - - - +
102D TYR 3.9 13.7 - - - +
103D ASP* 3.4 35.7 - - - +
104D TYR* 3.9 6.1 - - + -
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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