Contacts of the strand formed by residues 60 - 68 (chain J) in PDB entry 3DXA
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 ALA 60 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F LYS 6.0 0.2 - - - +
72F GLN* 4.0 19.3 - - + +
56J PHE* 3.2 6.8 - - - -
57J GLN 2.9 32.7 + - - +
58J ASN 3.6 0.2 - - - -
59J GLU* 1.3 85.4 - - - +
61J GLN* 1.3 59.1 + - - +
66J LEU* 3.1 16.0 - - + +
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Residues in contact with GLN 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F LYS* 4.8 9.5 + - - +
54J THR* 2.8 32.8 + - - +
55J TYR 3.8 2.9 - - - +
56J PHE* 3.5 26.1 - - + -
60J ALA* 1.3 69.9 - - - +
66J LEU* 1.3 63.7 + - - +
67J GLU 4.2 4.7 - - - +
68J LYS* 3.0 39.6 + - + +
72J LEU* 4.2 4.8 - - - +
78J ALA* 3.9 19.9 - - - +
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Residues in contact with LEU 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLN* 3.8 20.3 - - + +
68F LYS* 4.2 30.0 + - + +
69F THR* 3.1 45.5 - - - +
72F GLN* 4.8 1.8 - - + -
55J TYR* 3.1 26.5 + - + +
57J GLN* 3.5 32.1 - - + +
60J ALA* 3.1 33.7 - - + +
61J GLN* 1.3 73.0 - - - +
67J GLU* 1.3 59.6 + - - +
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Residues in contact with GLU 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLN* 3.2 39.5 + - - +
111I GLN* 4.0 5.4 - - - +
112I LYS* 3.3 51.3 + - - +
52J PHE* 4.1 11.9 - - + -
54J THR* 3.1 19.8 + - - -
55J TYR* 3.2 28.5 + - + +
61J GLN* 4.2 1.5 - - - +
66J LEU* 1.3 78.7 - - - +
68J LYS* 1.3 69.6 + - - +
69J SER* 5.9 0.4 - - - -
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Residues in contact with LYS 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J PHE* 4.1 2.2 - - - -
53J LEU 3.6 6.3 - - - -
54J THR* 3.7 2.7 - - - +
61J GLN* 3.0 32.8 + - + +
67J GLU* 1.3 82.5 - - - +
69J SER* 1.3 63.0 + - - +
70J ARG* 5.8 0.2 - - - -
72J LEU* 3.5 26.5 - - + -
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Residues in contact with SER 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I LYS* 4.6 15.7 - - - -
52J PHE* 2.9 38.4 + - - -
53J LEU* 3.3 9.9 + - - -
67J GLU* 5.9 0.2 - - - -
68J LYS* 1.3 76.5 - - - +
70J ARG* 1.3 69.0 + - - +
71J LEU* 3.0 13.2 - - - +
72J LEU* 3.1 25.6 + - - +
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Residues in contact with ARG 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I LYS* 4.1 20.4 - - - +
68J LYS 5.8 0.2 - - - -
69J SER* 1.3 78.9 - - - +
71J LEU* 1.3 62.3 + - - +
72J LEU* 3.3 7.3 - - - +
73J SER* 5.4 0.5 - - - -
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Residues in contact with LEU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ARG* 3.3 40.4 - - + +
51J GLU* 3.5 23.8 - - + +
52J PHE 3.7 17.5 - - - +
53J LEU* 4.1 9.0 - - + -
69J SER* 3.0 12.9 + - - +
70J ARG* 1.3 76.6 - - - +
72J LEU* 1.3 59.7 + - - +
73J SER* 2.9 10.0 + - - -
76J PHE* 3.9 12.8 - - + -
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J LEU* 3.6 40.6 - - + +
54J THR* 3.9 14.1 - - - +
61J GLN* 4.2 6.3 - - - +
68J LYS* 3.5 34.1 - - + -
69J SER* 3.1 12.9 + - - +
70J ARG* 4.3 5.7 - - - +
71J LEU* 1.3 73.5 - - - +
73J SER* 1.3 67.6 + - - +
74J ASP* 3.9 1.7 + - - +
76J PHE* 3.3 33.0 - - + +
77J SER* 6.4 0.2 - - - -
78J ALA* 5.7 4.5 - - + +
89J LEU* 5.1 7.6 - - + -
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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