Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 1TK0
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 GLU 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B PHE* 4.2 5.0 - - - -
82B LYS* 2.9 32.9 + - - +
83B ASN* 2.9 14.1 + - - +
84B GLY* 1.3 86.4 - - - +
86B VAL* 1.3 65.7 + - - +
87B ALA 3.1 0.7 + - - -
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Residues in contact with VAL 86 (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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70B TYR* 3.9 22.4 - - + -
79B LEU* 4.1 12.8 - - + -
80B LEU 3.9 5.2 - - - +
81B PHE* 3.9 27.3 - - + -
85B GLU* 1.3 71.8 - - - +
87B ALA* 1.3 62.4 + - - +
88B ALA 3.7 25.6 - - - +
89B THR* 4.1 14.8 - - + -
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Residues in contact with ALA 87 (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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80B LEU* 2.8 23.2 + - + +
82B LYS* 3.8 25.4 - - + -
85B GLU 3.1 1.6 + - - -
86B VAL* 1.3 73.1 - - - +
88B ALA* 1.3 65.2 + - + +
106B ASN* 4.6 8.7 - - + +
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Residues in contact with ALA 88 (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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78B LEU 3.9 0.3 - - - +
79B LEU* 3.7 1.2 - - - -
80B LEU* 2.9 33.6 + - + +
86B VAL* 3.5 5.9 - - - +
87B ALA* 1.3 83.3 - - - +
89B THR* 1.3 65.7 + - - +
102B PHE* 3.5 26.6 - - + -
106B ASN* 3.7 21.8 - - + +
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Residues in contact with THR 89 (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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317A THR 5.1 2.1 - - - +
318A ARG 4.1 1.0 - - - +
319A GLU* 3.8 32.3 + - + +
77B THR* 4.9 0.7 - - - +
78B LEU 3.4 7.6 - - - -
79B LEU* 4.1 18.3 - - - +
86B VAL* 4.1 12.3 - - + -
88B ALA* 1.3 80.2 - - - +
90B LYS* 1.3 81.1 + - - +
91B VAL* 4.6 3.1 - - - +
102B PHE* 4.5 1.1 - - - -
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Residues in contact with LYS 90 (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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296A GLY 4.6 7.0 + - - -
297A ILE* 5.0 5.5 + - - +
316A ASP 3.2 16.4 + - - -
317A THR 4.6 0.8 - - - -
318A ARG 2.6 29.5 + - - +
319A GLU 3.5 9.9 - - - +
320A TYR 4.1 0.4 - - - +
321A VAL* 3.7 24.0 - - + -
78B LEU* 2.9 42.3 + - + +
89B THR* 1.3 81.3 + - - +
91B VAL* 1.3 63.6 + - - +
92B GLY 5.5 0.2 - - - -
94B LEU* 3.9 29.6 - - + -
102B PHE* 3.6 39.3 - - + -
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Residues in contact with VAL 91 (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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292A PRO* 5.7 0.3 - - - +
319A GLU* 2.8 45.4 + - + +
320A TYR* 3.8 27.5 - - + -
321A VAL 4.6 2.4 + - - -
324A ALA* 4.6 2.4 - - - +
326A TYR* 3.9 23.6 - - + -
73B ARG 6.3 0.2 - - - +
74B GLY* 3.7 26.5 - - - +
76B PRO 3.6 12.8 - - - +
77B THR* 3.9 19.7 - - + +
89B THR* 4.6 2.0 - - - +
90B LYS* 1.3 75.9 - - - +
92B GLY* 1.3 59.4 + - - +
94B LEU* 4.9 3.8 - - - +
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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