Contacts of the strand formed by residues 45 - 51 (chain J) in PDB entry 4ADV
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 ARG 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253A G 5.2 12.3 + - - -
1254A A 4.2 29.1 + - - +
1255A G 3.7 19.8 + - - -
1279A G 2.9 40.8 + - + -
1280A A 5.0 11.0 + - - +
1282A C 5.5 0.2 - - - +
43J PRO* 3.8 7.6 + - - +
44J THR* 1.3 76.5 - - - +
46J LYS* 1.3 56.0 + - - +
47J GLU* 2.6 33.9 + - - +
67J ILE 3.9 1.4 - - - +
69J THR* 3.5 36.6 + - + +
71J LEU* 5.4 4.9 - - + +
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Residues in contact with LYS 46 (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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1151A A 3.4 27.3 + - - -
1253A G 3.1 43.0 + - - +
1254A A 3.3 15.3 + - - -
44J THR* 3.4 25.6 + - + +
45J ARG* 1.3 68.9 - - - +
47J GLU* 1.3 62.4 + - - +
48J ARG* 3.3 25.3 + - - +
66J GLU* 4.9 6.7 - - - +
67J ILE 4.8 2.0 - - - -
68J ARG* 4.2 23.6 - - + +
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Residues in contact with GLU 47 (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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1254A A 3.0 47.2 + - - +
1255A G 4.4 7.1 + - - +
45J ARG* 2.6 46.1 + - - +
46J LYS* 1.3 70.4 - - - +
48J ARG* 1.3 61.4 + - - +
49J PHE* 3.0 32.7 - - + -
66J GLU* 4.2 1.9 - - - +
67J ILE* 3.1 27.9 + - + +
69J THR* 4.8 3.2 + - - -
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Residues in contact with ARG 48 (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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1252A A 3.1 40.4 + - - -
1253A G 3.4 22.4 + - - -
1254A A 4.6 3.1 + - - -
1368A A 5.3 3.8 + - - -
1369A C 5.5 2.2 - - - -
46J LYS* 3.3 28.8 + - - +
47J GLU* 1.3 71.7 - - - +
49J PHE* 1.3 74.9 + - - +
64J GLN* 5.9 1.1 - - + -
65J TYR 3.0 18.4 - - - +
66J GLU* 3.6 21.5 - - + +
98N ALA* 4.3 5.2 - - + -
100N TRP* 4.6 37.5 - - + +
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Residues in contact with PHE 49 (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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1254A A 5.9 0.4 - - - -
1357A A 5.9 8.7 - - - -
47J GLU* 3.0 37.5 - - + -
48J ARG* 1.3 84.3 - - - +
50J THR* 1.3 63.9 + - - +
51J VAL* 4.1 9.4 + - + -
63J ASP 3.5 1.0 - - - +
64J GLN* 3.2 3.7 - - - -
65J TYR* 2.7 56.5 + - + +
66J GLU* 4.5 0.7 - - - -
67J ILE* 4.4 17.7 - - + -
73N LEU* 5.1 12.1 - - + -
75N LYS* 4.7 22.7 - - + -
76N PHE* 4.1 31.0 - + + -
95N LEU* 4.8 0.7 - - + -
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Residues in contact with THR 50 (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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975A A 2.6 52.6 + - - +
1367A C 3.8 33.0 + - - +
1368A A 5.9 0.2 - - - -
115I VAL* 5.8 1.6 - - + -
49J PHE* 1.3 75.3 - - - +
51J VAL* 1.3 63.1 + - - +
52J LEU* 5.3 2.1 - - - +
62J ARG* 4.9 11.9 - - + -
63J ASP 3.2 4.3 - - - +
64J GLN* 3.7 28.9 - - + +
73N LEU* 5.6 2.1 - - - +
100N TRP* 6.4 0.4 - - + -
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Residues in contact with VAL 51 (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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49J PHE* 5.0 3.6 - - + -
50J THR* 1.3 80.4 - - - +
52J LEU* 1.3 72.9 + - - +
53J ILE* 3.1 1.3 + - - -
62J ARG* 3.9 2.2 - - - -
63J ASP* 2.6 44.8 + - + +
65J TYR* 4.2 28.3 - - + +
73N LEU* 4.4 22.2 - - + -
76N PHE* 6.1 0.2 - - + -
80N ARG* 3.5 39.9 - - + +
83N VAL* 4.9 8.5 - - + -
84N ARG* 5.2 4.7 - - + -
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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