Contacts of the strand formed by residues 73 - 78 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69H TYR* 5.5 0.5 - - - -
72H LYS* 1.3 79.0 - - - +
74H LEU* 1.3 59.8 + - - +
105H ASN* 3.1 8.3 + - - +
106H THR* 3.2 25.7 - - + +
107H GLU* 3.0 23.4 + - - +
167H ILE* 4.0 21.8 - - + -
168H ILE 3.4 12.3 - - - -
169H ASP* 3.3 20.9 - - + +
170H ASP* 3.5 28.0 - - + -
175H ARG* 3.5 4.4 + - + -
195H VAL* 4.2 11.4 - - + -
198H PHE* 3.3 29.9 - - + +
199H GLN* 3.6 29.8 - - + -
202H ASP* 2.6 25.5 + - - -
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H TRP* 4.2 7.9 - - + -
66H LEU* 3.6 30.3 - - + -
69H TYR* 4.1 33.9 - - + -
72H LYS 3.8 1.3 + - - +
73H TYR* 1.3 75.4 - - - +
75H VAL* 1.3 74.3 + - - +
76H PHE* 3.7 16.3 + - + -
106H THR* 4.6 0.2 - - - -
107H GLU 3.6 22.2 - - - +
109H VAL* 4.0 20.9 - - + -
166H PHE 3.5 3.1 - - - +
167H ILE* 3.6 2.1 - - - +
168H ILE* 2.7 50.5 + - + +
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Residues in contact with VAL 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H LEU* 1.3 72.2 - - - +
76H PHE* 1.3 59.3 - - - +
77H PHE* 4.5 7.4 - - + -
94H PHE* 4.3 9.9 - - + -
101H PHE* 3.9 12.1 - - + -
106H THR* 4.0 7.0 - - + -
107H GLU 2.9 11.6 + - - +
108H VAL* 3.3 10.5 - - + +
109H VAL 3.0 26.2 + - - +
165H LEU* 3.8 33.0 - - + -
166H PHE 3.5 3.6 - - - -
167H ILE* 4.7 4.5 - - + -
191H THR* 3.7 24.5 - - + -
195H VAL* 3.9 20.4 - - + -
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Residues in contact with PHE 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H TRP* 3.4 52.7 - + - -
74H LEU* 3.7 8.0 + - + -
75H VAL* 1.3 72.7 - - - +
77H PHE* 1.3 61.2 + - - +
78H PHE* 3.5 35.4 - + - -
109H VAL* 3.4 23.8 - - + -
111H CYS* 4.1 10.3 - - + -
140H LEU* 4.0 15.0 - - + -
147H ILE* 4.0 8.5 - - + -
151H TYR* 3.7 23.6 - + - -
166H PHE* 2.8 39.4 + + + +
168H ILE* 4.0 18.4 - - + -
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Residues in contact with PHE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H VAL* 4.5 8.1 - - + -
76H PHE* 1.3 76.5 - - - +
78H PHE* 1.3 64.1 + - - +
79H TYR* 4.4 5.4 - + + -
90H GLU* 4.5 10.1 - - + -
91H ILE* 4.2 25.6 - - + -
94H PHE* 4.0 25.4 - + + -
108H VAL* 3.7 27.8 - - + -
109H VAL 2.9 14.9 + - - -
110H ALA* 3.2 34.1 - - + -
111H CYS* 2.8 25.3 + - - +
137H ILE* 4.4 2.5 - - + -
164H GLY 3.4 10.1 - - - +
165H LEU* 3.8 15.7 - - + -
186H ARG* 3.7 30.1 - - - +
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Residues in contact with PHE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H PHE* 3.5 29.2 - + - -
77H PHE* 1.3 77.1 - - - +
79H TYR* 1.3 55.6 + - - +
111H CYS* 3.0 33.7 - - + -
112H SER* 5.3 0.7 - - - -
147H ILE* 4.0 7.2 - - + -
148H SER* 3.8 30.1 - - - -
151H TYR* 3.6 32.1 - + + -
153H VAL* 3.6 18.2 - - + -
161H THR* 3.4 20.2 - - + +
162H LEU 3.9 2.1 - - - +
164H GLY 2.8 20.6 + - - +
166H PHE* 3.6 14.1 - + - -
186H ARG* 2.8 33.3 + - - -
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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