Contacts of the strand formed by residues 56 - 62 (chain F) in PDB entry 3TNP
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 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F THR* 4.8 5.4 + - + +
50F GLY 2.9 15.7 - - - +
51F THR* 3.5 21.0 - - + +
55F GLY* 1.3 75.6 - - - -
57F VAL* 1.3 79.9 + - - +
58F MET* 3.6 24.8 - - + +
72F LYS* 3.4 6.3 - - - +
73F ILE* 3.2 49.6 + - + +
333F GLU* 2.9 48.3 + - - +
334F GLU 3.3 17.8 + - - -
335F ILE* 4.1 7.3 - - - +
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Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F THR* 3.5 6.1 - - - +
49F LEU* 2.7 39.3 + - + -
50F GLY* 2.7 23.0 + - - +
56F ARG* 1.3 83.4 - - - +
58F MET* 1.3 59.4 + - - +
70F ALA* 3.8 29.2 - - + +
71F MET 3.4 11.2 - - - +
72F LYS* 4.2 16.8 - - + +
120F MET* 6.3 0.7 - - + -
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Residues in contact with MET 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ARG* 4.5 16.2 - - + -
46F ILE 5.6 0.2 - - - -
47F LYS* 3.5 4.3 - - - -
48F THR* 3.5 35.0 - - - +
49F LEU* 4.0 2.9 - - - -
56F ARG* 3.6 35.7 - - + +
57F VAL* 1.3 74.9 - - - +
59F LEU* 1.3 71.7 + - - +
60F VAL* 3.4 13.4 + - + -
70F ALA* 3.5 0.7 - - - -
71F MET* 2.7 41.7 + - - +
73F ILE* 3.9 14.4 - - + -
332F GLU* 4.4 4.0 - - - +
333F GLU 4.1 7.0 - - - +
335F ILE* 3.9 21.3 - - + -
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ILE* 2.8 46.1 + - + -
47F LYS* 2.6 24.2 + - + +
49F LEU* 3.5 16.9 - - + +
58F MET* 1.3 72.5 - - - +
60F VAL* 1.3 60.0 + - - +
68F HIS* 4.1 13.0 - - + +
69F TYR 3.5 16.2 - - - +
122F TYR* 3.8 34.8 - - + -
322F GLY* 3.6 21.5 - - - +
324F THR* 3.4 29.4 - - + -
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Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F PHE* 3.6 30.1 - - + -
44F ASP 3.1 13.7 - - - +
45F ARG* 4.1 8.3 - - + -
46F ILE* 3.3 5.8 - - - -
58F MET* 3.8 9.4 - - + +
59F LEU* 1.3 79.1 - - - +
61F LYS* 1.3 59.3 + - - +
68F HIS* 3.3 7.3 + - - +
69F TYR* 2.8 54.5 + - + +
71F MET* 3.3 41.5 - - + -
119F VAL* 4.8 0.2 - - + -
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Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F PHE* 3.3 4.5 - - - -
44F ASP* 2.8 49.0 + - + +
46F ILE* 3.4 19.1 - - + -
60F VAL* 1.3 72.1 - - - +
62F HIS* 1.3 71.5 + - - +
63F LYS* 3.1 5.4 + - - -
66F GLY* 3.7 26.7 + - - +
67F ASN 3.5 2.7 - - - -
68F HIS* 3.7 31.3 + - + +
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Residues in contact with HIS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLN* 3.7 33.1 + - + +
43F PHE* 3.7 29.1 - + + -
60F VAL 4.2 0.2 - - - -
61F LYS* 1.3 71.9 - - - +
63F LYS* 1.3 66.7 + - - +
64F GLU* 3.2 26.7 - - + +
65F SER* 2.7 41.5 + - - +
66F GLY* 2.8 25.8 + - - -
67F ASN 2.7 16.1 + - - +
69F TYR* 4.0 14.5 + + + -
108F PHE* 5.1 9.9 - + - -
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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