Contacts of the strand formed by residues 66 - 71 (chain U) in PDB entry 1Y69
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 LYS 66 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28U GLY* 4.4 18.8 - - - +
29U GLU 3.6 6.7 - - - +
30U VAL* 4.9 8.3 - - + +
65U GLY* 1.3 72.8 - - - +
67U VAL* 1.3 71.1 + - - +
68U VAL* 3.3 21.7 - - - +
81U ILE* 3.1 10.1 - - - +
82U GLU* 2.8 59.8 + - + +
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Residues in contact with VAL 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U LYS* 4.5 3.6 - - + +
26U PHE 3.7 12.8 - - - +
27U GLY* 3.4 2.4 - - - -
28U GLY* 3.0 27.5 + - - -
29U GLU* 2.8 30.2 + - + +
31U VAL* 3.2 29.6 - - + -
37U LEU* 3.6 26.5 - - + -
66U LYS* 1.3 71.0 - - - +
68U VAL* 1.3 63.9 + - - +
69U PHE* 4.4 9.2 - - + -
79U ILE* 4.0 19.7 - - + -
80U SER 4.2 2.2 - - - +
81U ILE* 4.3 4.9 - - + -
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Residues in contact with VAL 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8690 C 6.5 0.4 - - - -
27U GLY* 4.8 1.3 - - - -
66U LYS* 3.3 29.4 - - - +
67U VAL* 1.3 82.1 - - - +
69U PHE* 1.3 76.2 + - - +
70U ILE* 4.9 7.0 - - + -
79U ILE* 3.2 5.9 - - - +
80U SER* 2.9 45.6 + - - +
82U GLU* 3.9 28.0 - - + +
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Residues in contact with PHE 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8690 C 2.9 55.1 + - - +
8700 C 2.8 43.1 - - - +
23U VAL* 4.3 3.4 - - + -
25U LYS 3.5 18.2 - - - -
26U PHE* 3.6 6.5 - - - -
27U GLY* 3.4 18.4 - - - -
38U VAL* 4.2 7.6 - - + -
45U PHE* 3.9 8.7 - + - -
67U VAL* 4.4 8.1 - - + -
68U VAL* 1.3 84.3 - - - +
70U ILE* 1.3 68.9 + - - +
71U ASN* 5.5 0.3 - - - +
77U ARG* 6.2 0.4 - - + -
78U PHE 4.1 2.5 - - - -
79U ILE* 3.2 35.2 - - + -
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Residues in contact with ILE 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8700 C 5.7 1.1 - - - -
68U VAL* 4.8 7.0 - - + +
69U PHE* 1.3 82.6 - - - +
71U ASN* 1.3 69.2 + - - +
72U LYS* 4.8 17.0 - - + +
77U ARG* 3.5 6.8 - - - +
78U PHE* 3.0 43.8 + - + +
80U SER* 3.2 28.3 - - - +
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Residues in contact with ASN 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8700 C 5.5 6.5 - - - +
149 C 5.6 0.2 + - - -
70U ILE* 1.3 79.9 - - - +
72U LYS* 1.3 63.7 + - - +
73U GLY* 4.0 14.3 - - - +
74U LYS* 5.2 7.0 - - - +
76U ALA 4.6 1.8 - - - -
77U ARG* 4.1 25.9 - - + +
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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