Contacts of the strand formed by residues 73 - 78 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69G TYR* 5.5 0.2 - - - -
72G LYS* 1.3 78.7 - - - +
74G LEU* 1.3 58.4 + - - +
105G ASN* 3.1 8.3 + - - +
106G THR* 3.3 25.1 - - + +
107G GLU* 2.9 23.7 + - - +
167G ILE* 4.0 22.9 - - + -
168G ILE 3.4 13.0 - - - -
169G ASP* 3.2 26.0 - - + +
170G ASP* 3.6 17.2 - - + +
175G ARG* 3.5 4.9 + - + -
195G VAL* 4.1 11.0 - - + -
198G PHE* 3.3 30.8 - - + +
199G GLN* 3.7 29.6 - - + +
202G ASP* 2.6 29.0 + - - -
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G TRP* 4.3 7.9 - - + -
66G LEU* 3.6 31.0 - - + -
69G TYR* 4.1 32.5 - - + -
72G LYS 3.7 1.3 + - - +
73G TYR* 1.3 75.6 - - - +
75G VAL* 1.3 75.3 + - - +
76G PHE* 4.1 15.0 - - + -
106G THR* 4.6 0.4 - - - -
107G GLU 3.5 19.5 - - - +
109G VAL* 3.8 24.9 - - + -
166G PHE 3.6 3.3 - - - +
167G ILE* 3.6 3.1 - - - +
168G ILE* 2.7 48.8 + - + +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G LEU* 1.3 76.2 - - - +
76G PHE* 1.3 58.0 + - - +
77G PHE* 4.5 7.4 - - + -
94G PHE* 4.3 9.4 - - + -
101G PHE* 4.0 7.9 - - + -
106G THR* 4.0 10.7 - - + +
107G GLU 2.9 12.7 + - - +
108G VAL* 3.3 11.1 - - + +
109G VAL 3.0 25.6 + - - +
165G LEU* 3.8 34.3 - - + -
166G PHE 3.5 3.1 - - - -
167G ILE* 4.6 4.0 - - + -
191G THR* 3.8 24.0 - - + -
195G VAL* 3.8 21.8 - - + -
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Residues in contact with PHE 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G TRP* 3.4 52.0 - + - -
74G LEU* 3.7 8.2 + - + -
75G VAL* 1.3 71.4 - - - +
77G PHE* 1.3 60.9 + - - +
78G PHE* 3.5 33.7 - + - -
109G VAL* 3.5 23.8 - - + -
111G CYS* 4.1 10.5 - - + -
140G LEU* 3.9 15.3 - - + -
147G ILE* 4.0 9.9 - - + -
151G TYR* 3.7 25.4 - + - -
166G PHE* 2.8 40.8 + + + +
168G ILE* 4.0 18.2 - - + -
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Residues in contact with PHE 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G VAL* 4.5 7.2 - - + -
76G PHE* 1.3 77.8 - - - +
78G PHE* 1.3 64.8 + - - +
79G TYR* 4.5 5.4 - + + -
90G GLU* 4.5 9.2 - - + -
91G ILE* 4.2 25.4 - - + -
94G PHE* 3.8 28.3 - + + -
108G VAL* 3.8 26.7 - - + -
109G VAL 2.9 16.2 + - - -
110G ALA* 3.2 31.2 - - + -
111G CYS* 2.8 25.9 + - - +
137G ILE* 5.1 1.8 - - + -
164G GLY 3.4 9.2 - - - +
165G LEU* 3.8 16.4 - - + -
186G ARG* 3.7 30.7 - - - +
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Residues in contact with PHE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G PHE* 3.5 30.3 - + - -
77G PHE* 1.3 76.3 - - - +
79G TYR* 1.3 56.8 + - - +
111G CYS* 3.1 34.5 - - + +
147G ILE* 3.9 7.4 - - + -
148G SER* 3.7 30.5 - - - -
151G TYR* 3.6 22.4 - + + -
153G VAL* 3.6 15.0 - - + -
161G THR* 3.5 19.5 - - + +
162G LEU 3.9 3.2 - - - +
164G GLY 2.8 21.2 + - - +
166G PHE* 3.6 25.8 - + - -
186G ARG* 2.8 32.3 + - - -
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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