Contacts of the strand formed by residues 73 - 78 (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 TYR 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C TYR* 5.5 0.3 - - - -
72C LYS* 1.3 80.3 - - - +
74C LEU* 1.3 58.2 + - - +
105C ASN* 3.2 7.5 + - - +
106C THR* 3.4 25.0 - - + +
107C GLU* 3.0 22.7 + - - +
167C ILE* 4.0 22.0 - - + -
168C ILE 3.4 15.3 - - - -
169C ASP* 3.3 25.7 - - + +
170C ASP* 3.6 17.9 - - + +
175C ARG* 3.5 5.5 + - + -
195C VAL* 4.4 10.3 - - + -
198C PHE* 3.3 30.7 - - + +
199C GLN* 3.7 30.3 - - + +
202C ASP* 2.6 30.1 + - - -
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Residues in contact with LEU 74 (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* 4.2 8.3 - - + -
66C LEU* 3.6 30.7 - - + -
69C TYR* 3.9 34.3 - - + -
72C LYS 4.7 1.6 - - - +
73C TYR* 1.3 76.4 - - - +
75C VAL* 1.3 71.7 + - - +
76C PHE* 4.1 15.0 - - + -
106C THR* 4.6 0.2 - - - -
107C GLU 3.5 19.5 - - - +
109C VAL* 3.8 24.7 - - + -
166C PHE 3.5 3.3 - - - +
167C ILE* 3.6 2.6 - - - +
168C ILE* 2.8 46.5 + - + +
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Residues in contact with VAL 75 (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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74C LEU* 1.3 74.0 - - - +
76C PHE* 1.3 58.6 - - - +
77C PHE* 4.4 3.4 - - + -
94C PHE* 4.2 10.3 - - + -
101C PHE* 3.9 17.7 - - + -
106C THR* 4.0 7.9 - - + -
107C GLU 2.8 13.3 + - - +
108C VAL* 3.3 12.7 - - + +
109C VAL 2.9 27.4 + - - +
165C LEU* 3.8 33.4 - - + -
166C PHE 3.6 3.1 - - - -
167C ILE* 4.7 3.4 - - + +
191C THR* 3.8 23.6 - - + -
195C VAL* 4.0 15.5 - - + -
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Residues in contact with PHE 76 (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* 3.4 55.2 - + - -
74C LEU* 3.7 14.6 + - + -
75C VAL* 1.3 71.6 - - - +
77C PHE* 1.3 61.1 + - - +
78C PHE* 3.5 35.4 - + - -
109C VAL* 3.5 20.4 - - + -
111C CYS* 4.0 13.2 - - + -
140C LEU* 4.0 12.1 - - + -
147C ILE* 4.1 8.3 - - + -
151C TYR* 3.8 24.0 - + - -
166C PHE* 2.8 43.4 + + + +
168C ILE* 4.1 8.3 - - + -
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Residues in contact with PHE 77 (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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75C VAL* 4.4 6.7 - - + -
76C PHE* 1.3 77.0 - - - +
78C PHE* 1.3 66.7 + - - +
79C TYR* 4.4 4.9 - + + -
90C GLU* 4.6 8.1 - - + -
91C ILE* 4.2 24.0 - - + -
94C PHE* 3.7 28.0 - + - -
108C VAL* 3.6 29.2 - - + -
109C VAL 3.0 14.2 + - - +
110C ALA* 3.2 34.8 - - + -
111C CYS* 2.8 25.4 + - - +
137C ILE* 4.3 3.4 - - + -
164C GLY 3.3 9.2 - - - +
165C LEU* 3.8 15.9 - - + -
186C ARG* 3.7 28.5 - - - +
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Residues in contact with PHE 78 (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* 3.5 30.3 - + - -
77C PHE* 1.3 77.2 - - - +
79C TYR* 1.3 60.8 + - - +
111C CYS* 3.1 37.7 - - + +
147C ILE* 3.8 7.9 - - + -
148C SER* 3.7 29.8 - - - -
151C TYR* 3.5 33.4 - + + -
153C VAL* 3.7 12.6 - - + -
161C THR* 3.6 19.3 - - + +
162C LEU 3.8 3.9 - - - +
164C GLY 2.8 22.3 + - - +
166C PHE* 3.6 13.9 - + - -
186C ARG* 2.8 26.2 + - - -
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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