Contacts of the strand formed by residues 81 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL 3.9 0.7 - - - +
47A ASN 3.4 8.5 + - - -
48A LEU* 2.7 47.3 + - + +
49A PRO 4.2 3.1 - - - +
50A LYS* 3.6 28.7 + - + +
51A SER 4.5 1.6 + - - -
52A TYR 2.9 33.5 + - - +
53A ASN* 3.8 11.9 - - - +
72A VAL* 3.4 24.7 + - + +
73A ALA* 3.4 7.4 - - - +
74A ASP* 2.8 30.1 + - - +
80A PHE* 1.3 84.2 - - - +
82A PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 82 (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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44A LEU* 4.0 12.6 - - + -
45A VAL 3.2 13.7 - - - -
46A LYS* 3.4 34.8 - - + -
48A LEU* 4.8 0.4 - - - -
72A VAL* 3.4 6.2 - - - +
73A ALA 2.7 37.8 + - - +
75A SER* 4.2 16.2 - - - -
80A PHE* 3.7 26.0 - + - -
81A ARG* 1.3 76.4 - - - +
83A ALA* 1.3 63.0 + - - +
143A VAL* 4.3 16.2 - - + -
145A LEU* 3.7 18.1 - - + +
166A THR* 3.9 39.3 - - + -
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Residues in contact with ALA 83 (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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43A VAL 3.7 0.3 - - - +
44A LEU* 3.4 10.2 - - - +
45A VAL* 2.8 40.7 + - + +
48A LEU* 3.7 23.3 - - + +
57A VAL* 4.0 16.6 - - + -
71A ASP 3.2 10.5 - - - +
72A VAL* 3.9 10.3 - - + -
82A PHE* 1.3 76.2 - - - +
84A ARG* 1.3 60.9 + - - +
85A ILE* 4.1 1.3 - - + -
145A LEU* 4.9 1.8 - - - -
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Residues in contact with ARG 84 (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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38A ARG* 4.4 18.6 - - - +
42A THR* 3.7 33.5 + - + +
43A VAL 3.3 4.0 - - - +
44A LEU* 4.9 0.4 - - - +
69A HIS* 4.0 10.6 - - - +
70A VAL* 3.3 3.8 - - - -
71A ASP* 2.8 61.5 + - + +
83A ALA* 1.3 75.0 - - - +
85A ILE* 1.3 62.5 + - - +
86A GLU* 4.2 16.5 + - - +
114A LEU* 3.7 11.6 - - + +
145A LEU* 4.2 20.2 - - + +
146A SER* 3.8 14.1 + - - -
148A ARG* 3.3 29.9 - - - +
164A ASP* 2.9 22.1 + - - -
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Residues in contact with ILE 85 (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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41A THR 3.6 1.7 - - - +
42A THR* 3.2 6.0 - - - -
43A VAL* 2.8 47.6 + - + +
45A VAL* 4.0 18.6 - - + -
57A VAL* 3.7 20.9 - - + -
61A PHE* 3.7 39.9 - - + -
67A ILE* 4.0 25.8 - - + -
69A HIS 3.6 3.8 - - - +
70A VAL* 4.4 4.0 - - + -
84A ARG* 1.3 81.0 - - - +
86A GLU* 1.3 60.4 - - - +
87A PHE* 3.5 23.6 + - + -
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Residues in contact with GLU 86 (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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36A ARG* 3.0 30.5 + - - -
38A ARG* 4.1 11.9 + - - +
41A THR* 3.7 7.7 + - - +
42A THR* 4.0 16.5 + - - +
67A ILE* 3.7 2.6 - - - +
68A ILE* 2.8 59.4 + - + +
69A HIS* 2.9 26.4 + - + +
84A ARG* 4.2 15.3 + - - +
85A ILE* 1.3 71.6 - - - +
87A PHE* 1.3 63.2 + - - +
89C ARG* 4.1 8.0 + - - -
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Residues in contact with PHE 87 (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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41A THR* 2.8 33.7 + - - +
43A VAL* 3.9 9.6 - - + -
61A PHE* 3.9 17.9 - - + -
64A CYS* 4.1 4.0 - - + -
65A GLY 3.8 10.3 - - - -
66A PRO 3.6 9.9 - - - +
67A ILE* 3.3 28.0 - - + -
68A ILE* 4.1 2.0 - - - +
85A ILE* 3.5 25.6 - - + -
86A GLU* 1.3 81.1 - - - +
88A ALA* 1.3 66.0 + - - +
89A ARG 3.2 17.6 + - - +
92A GLY* 3.8 14.1 - - - -
93A ALA* 3.5 18.4 - - + +
96A ALA* 3.7 32.3 - - + -
89C ARG* 4.9 0.3 + - - -
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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