Contacts of the strand formed by residues 106 - 112 (chain F) 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 THR 106 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73F TYR* 3.3 22.2 - - + +
75F VAL* 4.0 12.1 - - + -
98F LEU* 5.3 0.2 - - - +
101F PHE* 3.0 52.5 + - + +
102F ARG* 3.3 12.0 + - - +
104F ILE* 3.0 17.1 + - - +
105F ASN* 1.3 76.9 - - - +
107F GLU* 1.3 76.4 + - - +
195F VAL* 3.4 12.0 - - + +
199F GLN* 3.3 12.8 + - - -
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Residues in contact with GLU 107 (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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69F TYR* 3.5 40.5 - - + -
72F LYS* 3.0 40.2 + - + +
73F TYR 3.0 8.3 + - - +
74F LEU* 3.5 5.1 - - + -
75F VAL 2.9 25.1 + - - -
98F LEU* 5.4 1.3 - - - +
102F ARG* 2.9 48.7 + - - +
105F ASN* 5.5 0.3 - - - -
106F THR* 1.3 78.4 + - - +
108F VAL* 1.3 69.4 + - - +
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Residues in contact with VAL 108 (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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69F TYR* 5.1 0.2 + - - -
75F VAL* 3.3 18.4 - - + +
77F PHE* 3.8 22.2 - - + -
94F PHE* 4.3 12.6 - - + -
98F LEU* 3.8 28.5 - - + +
101F PHE* 4.0 26.2 - - + -
107F GLU* 1.3 84.1 + - - +
109F VAL* 1.3 65.8 + - - +
137F ILE* 3.4 25.4 - - + +
138F PRO* 3.3 23.0 - - - +
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Residues in contact with VAL 109 (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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51F TRP* 4.3 12.8 - - + -
64F LEU* 4.3 8.1 - - + -
69F TYR* 3.2 41.5 - - + +
74F LEU* 3.7 10.8 - - + -
75F VAL 2.9 7.2 + - - +
76F PHE* 3.4 28.7 - - + -
77F PHE* 2.9 29.2 + - - +
108F VAL* 1.3 79.9 - - - +
110F ALA* 1.3 71.6 + - - +
137F ILE* 4.3 1.1 - - - -
138F PRO* 4.0 13.0 - - + +
140F LEU* 4.3 5.8 - - + -
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Residues in contact with ALA 110 (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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77F PHE* 3.2 37.0 - - + -
79F TYR* 3.9 15.0 - - + -
91F ILE* 4.5 2.2 - - + -
109F VAL* 1.3 74.7 - - - +
111F CYS* 1.3 56.1 + - - +
137F ILE* 3.8 4.6 - - + +
138F PRO 3.2 8.3 + - - +
139F LEU* 3.5 16.9 - - + -
140F LEU* 2.7 35.0 + - - +
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Residues in contact with CYS 111 (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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76F PHE* 4.1 13.0 - - + -
77F PHE 2.8 8.5 + - - +
78F PHE* 3.1 36.0 - - + +
79F TYR* 3.0 30.3 + - - -
110F ALA* 1.3 76.8 - - - +
112F SER* 1.3 65.1 + - - +
140F LEU* 3.4 33.0 - - + -
142F ASP* 3.8 23.8 - - - -
147F ILE* 4.6 3.4 - - - -
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Residues in contact with SER 112 (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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78F PHE* 5.3 2.9 - - - -
79F TYR* 3.2 38.2 + - - -
80F PRO 4.2 1.3 - - - -
111F CYS* 1.3 73.6 - - - +
113F VAL* 1.3 60.4 + - - +
114F ASP* 2.6 35.0 + - - +
119F HIS* 3.1 14.6 - - - -
140F LEU 3.2 8.3 + - - +
142F ASP* 2.8 28.2 + - - +
148F SER* 5.3 0.4 - - - -
161F THR* 5.3 1.6 - - - -
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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