Contacts of the strand formed by residues 81 - 87 (chain C) in PDB entry 5TF6
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 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ASN 3.5 6.1 + - - -
48C LEU* 3.0 39.7 + - + +
49C PRO 3.7 13.0 - - - +
50C LYS* 3.3 25.8 + - - -
51C SER 4.8 0.8 - - - -
52C TYR* 2.5 39.3 + - + -
53C ASN* 3.9 11.1 - - - +
72C VAL* 3.5 28.2 + - + +
73C ALA* 3.4 7.8 - - - +
74C ASP* 2.8 37.5 + - - +
80C PHE* 1.3 79.9 - - - +
82C PHE* 1.3 60.2 + - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.0 11.4 - - + -
45C VAL 3.2 14.8 - - - +
46C LYS* 3.8 33.2 - - + -
48C LEU* 4.5 1.1 - - - -
72C VAL* 3.3 8.1 - - - +
73C ALA 2.6 38.7 + - - +
75C SER* 4.1 18.4 - - - -
80C PHE* 3.7 24.9 - + - -
81C ARG* 1.3 75.1 - - - +
83C ALA* 1.3 59.9 + - - +
143C VAL* 4.5 13.5 - - + -
145C LEU* 3.8 17.2 - - + +
166C THR* 3.8 42.0 - - + -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL 3.7 0.2 - - - +
44C LEU* 3.5 8.0 - - - +
45C VAL* 2.9 41.7 + - + +
48C LEU* 3.6 23.1 - - + +
57C VAL* 4.2 24.0 - - + -
71C ASP 3.2 10.5 - - - +
72C VAL* 4.4 2.5 - - + -
82C PHE* 1.3 74.6 - - - +
84C ARG* 1.3 58.6 + - - +
85C ILE* 4.1 2.0 - - + -
145C LEU* 4.6 4.0 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 4.3 19.0 - - - +
42C THR* 3.6 32.1 + - + +
43C VAL 3.4 4.3 - - - +
69C HIS* 3.9 9.7 - - - +
70C VAL* 3.3 5.0 - - - -
71C ASP* 2.8 51.5 + - + +
83C ALA* 1.3 73.0 - - - +
85C ILE* 1.3 62.5 + - - +
86C GLU* 4.3 19.2 + - - +
114C LEU* 3.7 12.4 - - + +
145C LEU* 4.1 19.9 - - + +
146C SER* 3.8 20.8 + - - -
148C ARG* 3.2 30.4 - - - +
164C ASP* 2.7 22.2 + - - -
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR 3.6 1.2 - - - +
42C THR* 3.3 4.6 - - - -
43C VAL* 2.9 45.8 + - + +
45C VAL* 4.0 16.2 - - + -
57C VAL* 3.7 19.3 - - + -
61C PHE* 3.6 39.9 - - + -
67C ILE* 4.0 28.7 - - + -
69C HIS 3.4 3.4 - - - +
70C VAL* 4.3 3.8 - - + -
83C ALA* 4.7 0.2 - - + -
84C ARG* 1.3 81.0 - - - +
86C GLU* 1.3 61.0 + - - +
87C PHE* 3.6 22.4 + - + -
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 4.6 5.9 + - - -
36C ARG* 2.8 32.8 + - - -
38C ARG* 3.9 13.6 + - - -
41C THR* 3.7 8.0 + - - +
42C THR* 4.0 17.6 - - - +
67C ILE* 3.7 4.9 - - - +
68C ILE* 2.8 55.8 + - + +
69C HIS* 2.9 20.4 + - + +
84C ARG* 4.3 16.3 + - - +
85C ILE* 1.3 71.4 - - - +
87C PHE* 1.3 69.2 + - - +
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Residues in contact with PHE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 4.8 0.3 + - - -
41C THR* 2.8 32.8 + - - +
43C VAL* 4.0 10.5 - - + -
61C PHE* 4.0 20.6 - - + -
64C CYS* 4.1 5.6 - - + -
65C GLY 3.5 26.7 - - - -
66C PRO 3.6 4.9 - - - +
67C ILE* 3.5 11.4 - - + -
68C ILE* 3.9 1.9 - - - +
85C ILE* 3.6 26.0 - - + -
86C GLU* 1.3 82.1 - - - +
88C ALA* 1.3 64.9 + - - +
89C ARG 3.3 17.6 + - - +
92C GLY* 3.5 17.9 - - - -
93C ALA* 3.6 14.8 - - + +
96C ALA* 3.5 32.8 - - + -
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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