Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 3TKR
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 TYR 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B TYR* 5.4 0.3 - - - -
72B LYS* 1.3 79.3 - - - +
74B LEU* 1.3 58.8 + - - +
105B ASN* 3.2 7.8 + - - +
106B THR* 3.4 25.5 - - + +
107B GLU* 3.0 23.4 + - - +
167B ILE* 3.9 22.7 - - + -
168B ILE 3.4 12.8 - - - -
169B ASP* 3.2 24.9 - - + +
170B ASP* 3.7 17.0 - - + +
175B ARG* 3.4 5.3 + - + -
195B VAL* 4.2 9.4 - - + -
198B PHE* 3.4 32.5 - - + +
199B GLN* 3.7 29.6 - - + +
202B ASP* 2.5 29.9 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TRP* 4.3 7.9 - - + -
66B LEU* 3.6 30.3 - - + -
69B TYR* 3.9 34.3 - - + -
72B LYS 3.8 1.5 + - - +
73B TYR* 1.3 76.3 - - - +
75B VAL* 1.3 72.9 + - - +
76B PHE* 3.7 16.6 + - + +
106B THR* 4.5 0.2 - - - -
107B GLU 3.4 23.3 - - - +
109B VAL* 3.8 22.4 - - + -
166B PHE 3.6 2.8 - - - +
167B ILE* 3.6 2.5 - - - +
168B ILE* 2.8 47.2 + - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 1.3 75.2 - - - +
76B PHE* 1.3 59.0 + - - +
77B PHE* 4.4 8.1 - - + -
94B PHE* 4.3 9.6 - - + -
101B PHE* 4.2 6.7 - - + -
106B THR* 4.0 10.8 - - + -
107B GLU 2.8 11.8 + - - +
108B VAL* 3.3 8.7 - - + +
109B VAL 2.9 27.2 + - - +
165B LEU* 3.8 33.0 - - + -
166B PHE 3.6 3.1 - - - -
167B ILE* 4.5 4.9 - - + -
191B THR* 3.8 23.1 - - + -
195B VAL* 3.9 20.9 - - + -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TRP* 3.4 48.9 - + - -
74B LEU* 3.7 15.6 - - + -
75B VAL* 1.3 71.1 - - - +
77B PHE* 1.3 60.4 + - - +
78B PHE* 3.5 34.5 - + - -
109B VAL* 3.5 23.1 - - + -
111B CYS* 4.1 10.8 - - + -
140B LEU* 4.0 15.3 - - + -
147B ILE* 4.1 8.1 - - + -
151B TYR* 3.8 24.7 - + - -
166B PHE* 2.8 43.0 + + + +
168B ILE* 4.1 8.3 - - + -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.4 9.4 - - + -
76B PHE* 1.3 76.4 - - - +
78B PHE* 1.3 64.1 + - - +
79B TYR* 4.4 5.6 - + + -
90B GLU* 4.6 9.2 - - + -
91B ILE* 4.2 24.9 - - + -
94B PHE* 3.8 28.5 - + + -
108B VAL* 3.8 27.4 - - + -
109B VAL 2.9 14.7 + - - -
110B ALA* 3.2 31.1 - - + -
111B CYS* 2.9 25.3 + - - +
137B ILE* 5.0 2.5 - - + -
164B GLY 3.4 9.6 - - - +
165B LEU* 3.8 16.2 - - + -
186B ARG* 3.7 30.5 - - - +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.5 31.4 - + - -
77B PHE* 1.3 77.6 - - - +
79B TYR* 1.3 59.4 + - - +
111B CYS* 3.1 37.7 - - + +
112B SER* 5.3 0.2 - - - -
147B ILE* 3.8 9.9 - - + -
148B SER* 3.7 29.6 - - - -
151B TYR* 3.6 21.8 - + + -
153B VAL* 3.7 11.7 - - + -
161B THR* 3.5 19.1 - - + +
162B LEU 4.1 3.4 - - - +
163B ARG* 3.8 0.3 - - - -
164B GLY 2.8 15.1 + - - +
166B PHE* 3.6 33.0 - + - -
186B ARG* 2.8 27.1 + - - -
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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