Contacts of the strand formed by residues 106 - 112 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C TYR* 3.4 23.0 - - + +
75C VAL* 4.0 11.4 - - + -
101C PHE* 2.9 52.7 + - + +
102C ARG* 3.3 12.3 + - - +
104C ILE* 2.9 15.0 + - - +
105C ASN* 1.3 76.1 - - - +
107C GLU* 1.3 79.2 + - - +
195C VAL* 3.4 12.3 - - + +
199C GLN* 3.3 13.7 + - - -
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Residues in contact with GLU 107 (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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69C TYR* 3.6 37.1 - - + -
72C LYS* 3.4 37.5 + - + +
73C TYR 3.0 8.6 + - - +
74C LEU* 3.5 5.3 - - + -
75C VAL 2.8 25.1 + - - -
98C LEU* 4.7 2.2 - - - +
101C PHE* 5.2 0.2 - - - -
102C ARG* 3.0 49.8 + - - +
106C THR* 1.3 78.7 - - - +
108C VAL* 1.3 72.9 + - - +
138C PRO* 5.8 1.6 - - - +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.3 18.2 - - + +
77C PHE* 3.6 29.8 - - + -
94C PHE* 4.1 20.4 - - + +
98C LEU* 4.0 13.0 - - + +
101C PHE* 3.8 31.6 - - + -
107C GLU* 1.3 87.9 + - - +
109C VAL* 1.3 66.3 + - - +
137C ILE* 3.6 21.4 - - + +
138C PRO* 3.4 20.3 - - - +
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Residues in contact with VAL 109 (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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51C TRP* 4.3 5.6 - - + -
64C LEU* 4.2 15.9 - - + -
69C TYR* 3.3 41.7 - - + +
74C LEU* 3.8 9.6 - - + +
75C VAL 2.9 8.4 + - - +
76C PHE* 3.5 27.4 - - + -
77C PHE* 3.0 31.1 + - - +
108C VAL* 1.3 79.3 - - - +
110C ALA* 1.3 71.4 + - - +
137C ILE* 5.1 0.2 - - - -
138C PRO* 4.0 13.9 - - + +
140C LEU* 4.3 5.6 - - + -
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Residues in contact with ALA 110 (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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77C PHE* 3.2 34.8 - - + -
79C TYR* 3.9 16.4 - - + -
91C ILE* 4.5 1.6 - - + -
109C VAL* 1.3 74.0 - - - +
111C CYS* 1.3 54.9 + - - +
137C ILE* 4.1 7.2 - - + +
138C PRO 3.2 8.8 + - - +
139C LEU* 3.6 16.5 - - + -
140C LEU* 2.7 35.3 + - - +
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Residues in contact with CYS 111 (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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76C PHE* 4.0 14.1 - - + -
77C PHE 2.8 11.0 + - - +
78C PHE* 3.1 37.6 - - + +
79C TYR* 2.9 28.6 + - - -
110C ALA* 1.3 77.9 - - - +
112C SER* 1.3 64.5 + - - +
140C LEU* 3.4 32.3 - - + +
142C ASP* 3.8 24.5 - - - -
147C ILE* 4.7 1.8 - - - -
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Residues in contact with SER 112 (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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78C PHE* 5.3 2.5 - - - -
79C TYR* 3.1 37.5 + - - -
80C PRO 4.1 2.0 - - - -
111C CYS* 1.3 73.4 - - - +
113C VAL* 1.3 59.9 + - - +
114C ASP* 2.6 35.2 + - - +
119C HIS* 3.2 14.2 + - - -
140C LEU 3.2 8.1 + - - +
141C SER 3.7 0.2 - - - -
142C ASP* 2.9 27.9 + - - +
148C SER* 5.4 0.4 - - - -
161C 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