Contacts of the strand formed by residues 65 - 71 (chain A) in PDB entry 1DKT
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 HIS 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A MET* 4.4 15.4 - - + +
24A LEU* 2.8 67.7 + - + +
26A LYS* 3.8 39.7 - - + +
29A ALA* 4.0 24.7 - - + +
63A GLU* 3.0 36.9 + - + +
64A PRO* 1.3 82.2 - - + +
66A ILE* 1.3 70.6 + - + +
67A LEU* 3.7 3.6 + - - -
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Residues in contact with ILE 66 (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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21A HIS* 3.9 23.1 - - + +
22A VAL 3.1 11.9 - - - +
23A MET* 4.3 20.4 - - + -
60A HIS* 3.3 34.7 + - + +
63A GLU* 2.9 36.0 + - + +
64A PRO 4.5 2.2 - - - +
65A HIS* 1.3 98.7 - - + +
67A LEU* 1.3 61.9 + - - +
68A LEU* 3.7 17.6 + - + -
7B TYR* 5.6 0.2 - - - +
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Residues in contact with LEU 67 (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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21A HIS* 3.2 7.8 - - - +
22A VAL* 2.8 37.8 + - + +
24A LEU* 3.7 41.7 - - + -
32A VAL* 4.1 14.6 - - + -
38A MET* 3.7 33.0 - - + -
43A TRP* 4.8 1.6 - - + -
46A LEU* 4.6 3.4 - - + -
48A VAL* 4.1 9.9 - - + -
56A HIS* 4.6 8.1 - - - +
59A ILE* 6.3 0.4 - - + -
64A PRO 4.2 7.0 - - - +
66A ILE* 1.3 74.1 - - - +
68A LEU* 1.3 60.9 + - - +
69A PHE* 3.7 29.4 + - + -
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Residues in contact with LEU 68 (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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12A TYR* 5.7 2.0 - - - +
20A ARG 4.5 1.1 - - - -
21A HIS* 3.9 9.4 - - + -
56A HIS* 3.3 10.0 - - - -
57A TYR* 3.2 43.8 + - + +
58A MET* 3.5 40.6 + - - +
60A HIS* 3.7 34.7 - - + +
66A ILE* 3.5 24.0 + - + +
67A LEU* 1.3 79.3 - - - +
69A PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 69 (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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19A TYR* 3.7 2.8 - - - +
20A ARG* 3.1 33.6 + - + +
22A VAL* 3.7 24.0 - - + -
43A TRP* 3.2 48.9 - + + -
48A VAL* 4.3 3.4 - - + -
50A GLN* 3.3 29.6 - - - +
54A TRP* 3.9 14.6 - - + -
55A VAL 3.5 9.4 - - - -
56A HIS* 3.5 25.8 - + + -
57A TYR* 3.4 8.3 - - - -
67A LEU* 3.7 31.6 - - + -
68A LEU* 1.3 75.2 - - - +
70A ARG* 1.3 65.9 + - - +
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Residues in contact with ARG 70 (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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17A PHE* 3.6 48.6 - - + -
18A GLU 3.2 10.3 - - - +
19A TYR* 3.4 33.5 + - + -
54A TRP* 3.5 5.1 - - - -
55A VAL* 2.9 34.8 + - + +
57A TYR* 3.7 47.0 - - + +
69A PHE* 1.3 79.2 - - - +
71A ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 71 (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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11A LYS* 3.9 1.8 - - - +
17A PHE* 3.6 8.0 - - - -
18A GLU* 2.7 72.0 + - + +
51A SER* 3.3 14.3 + - - -
53A GLY* 3.2 27.4 - - - +
54A TRP* 3.3 37.0 - - + +
55A VAL* 5.7 0.2 - - - -
70A ARG* 1.3 74.9 - - - +
72A PRO* 1.3 73.8 - - + +
100A V7O 3.0 55.4 + - - -
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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