Contacts of the strand formed by residues 73 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TYR* 5.2 0.3 - - - +
72A LYS* 1.3 80.9 - - - +
74A LEU* 1.3 59.1 + - - +
105A ASN* 3.2 7.7 + - - +
106A THR* 3.3 27.5 - - + +
107A GLU* 3.1 21.8 + - - +
167A ILE* 3.9 21.5 - - + -
168A ILE 3.3 13.0 - - - -
169A ASP* 3.2 27.8 - - + +
170A ASP* 3.7 16.4 - - + +
175A ARG* 3.5 4.4 + - + -
195A VAL* 4.3 10.5 - - + -
198A PHE* 3.3 33.1 + - + +
199A GLN* 3.7 29.6 - - + +
202A ASP* 2.6 29.8 + - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 4.3 7.6 - - + -
66A LEU* 3.6 30.5 - - + -
69A TYR* 4.0 32.5 - - + -
72A LYS 4.8 1.1 - - - +
73A TYR* 1.3 76.7 - - - +
75A VAL* 1.3 74.0 + - - +
76A PHE* 3.7 16.1 + - + +
106A THR* 4.7 0.2 - - - -
107A GLU 3.5 20.0 - - - +
109A VAL* 3.8 24.2 - - + -
166A PHE 3.5 3.5 - - - +
167A ILE* 3.6 2.3 - - - +
168A ILE* 2.7 50.4 + - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 1.3 75.2 - - - +
76A PHE* 1.3 57.2 + - - +
77A PHE* 4.5 4.0 - - + -
94A PHE* 4.3 9.9 - - + -
101A PHE* 4.1 7.6 - - + -
106A THR* 4.0 10.8 - - + -
107A GLU 2.8 12.7 + - - +
108A VAL* 3.3 14.0 - - + +
109A VAL 2.9 26.5 + - - +
165A LEU* 3.8 33.0 - - + -
166A PHE 3.6 3.4 - - - -
167A ILE* 4.6 4.9 - - + -
191A THR* 3.8 16.4 - - + -
195A VAL* 3.8 29.2 - - + -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TRP* 3.4 50.9 - + - -
74A LEU* 3.7 16.1 + - + -
75A VAL* 1.3 71.4 - - - +
77A PHE* 1.3 61.5 + - - +
78A PHE* 3.4 35.7 - + - -
109A VAL* 3.4 22.0 - - + -
111A CYS* 4.0 18.8 - - + -
140A LEU* 4.0 9.4 - - + -
147A ILE* 4.0 8.7 - - + -
151A TYR* 3.8 24.9 - + - -
166A PHE* 2.9 39.2 + + + +
168A ILE* 4.0 10.1 - - + -
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.5 7.4 - - + -
76A PHE* 1.3 75.9 - - - +
78A PHE* 1.3 64.8 + - - +
79A TYR* 4.3 5.8 - + + -
90A GLU* 4.6 8.5 - - + -
91A ILE* 4.2 26.2 - - + -
94A PHE* 3.9 27.6 - + + -
108A VAL* 3.8 26.7 - - + -
109A VAL 2.9 14.7 + - - -
110A ALA* 3.2 32.2 - - + -
111A CYS* 2.8 25.5 + - - +
137A ILE* 5.1 2.0 - - + -
164A GLY 3.4 9.6 - - - +
165A LEU* 3.8 15.3 - - + -
186A ARG* 3.6 31.9 - - - +
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.4 31.9 - + - -
77A PHE* 1.3 76.8 - - - +
79A TYR* 1.3 60.6 + - - +
111A CYS* 3.1 35.4 - - + +
112A SER* 5.3 0.2 - - - -
147A ILE* 3.8 9.2 - - + -
148A SER* 3.7 29.6 - - - -
151A TYR* 3.6 21.1 - + + -
153A VAL* 3.7 12.3 - - + -
161A THR* 3.6 19.7 - - + +
162A LEU 3.8 3.0 - - - +
164A GLY 2.8 14.4 + - - +
166A PHE* 3.6 32.8 - + - -
186A ARG* 2.9 25.9 + - - -
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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