Contacts of the helix formed by residues 73 - 81 (chain A) in PDB entry 3TR6
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 GLY 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.1 1.6 - - - -
70A THR* 2.6 31.3 + - - -
71A PHE 3.2 1.4 + - - -
72A THR* 1.3 73.8 - - - +
74A TYR* 1.3 62.5 + - - +
75A SER 3.5 2.0 - - - -
76A ALA* 3.8 8.2 - - - +
77A ILE* 3.0 32.0 + - - +
102A ALA* 3.9 12.1 - - - -
106A TRP* 5.2 0.7 - - - -
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Residues in contact with TYR 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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23A GLU* 2.8 31.6 + - - +
27A LEU* 3.5 52.0 - - + +
30A LEU* 3.8 8.7 - - + -
31A ARG* 4.4 6.7 - - + -
44A GLN* 3.5 35.2 - - + +
45A THR* 3.9 14.4 - - - -
47A PRO* 3.5 24.8 + - + +
50A ALA* 3.5 29.6 - - + -
72A THR 3.6 2.0 - - - -
73A GLY* 1.3 77.5 - - - +
75A SER* 1.3 59.7 + - - +
77A ILE 3.8 0.2 - - - -
78A ALA* 2.9 29.8 + - - +
224A SAH 3.5 14.3 + - - +
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Residues in contact with SER 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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45A THR* 3.7 7.0 - - - -
50A ALA* 4.9 1.1 - - - -
53A LEU* 4.4 6.3 - - - -
67A ASP* 2.7 22.5 + - - -
70A THR 5.2 0.3 + - - -
74A TYR* 1.3 75.9 - - - +
76A ALA* 1.3 65.0 + - - +
78A ALA* 3.7 6.9 - - - +
79A MSE 3.0 34.7 + - - +
142A TYR* 3.5 24.4 - - - -
224A SAH 2.8 30.6 + - - -
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Residues in contact with ALA 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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67A ASP* 3.5 24.2 - - - +
70A THR* 4.9 0.2 - - + -
73A GLY* 3.6 16.1 + - - +
74A TYR 3.3 0.2 - - - -
75A SER* 1.3 81.5 + - - +
77A ILE* 1.3 57.9 + - + +
80A GLY* 2.8 25.5 + - - -
89A LEU* 3.6 14.7 - - + +
91A THR* 4.0 19.5 - - + +
106A TRP* 4.9 2.5 - - + -
115A ILE* 3.5 15.2 - - + +
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Residues in contact with ILE 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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26A LEU* 4.5 11.0 - - + -
27A LEU* 3.8 16.2 - - + -
30A LEU* 3.9 13.0 - - + -
72A THR 4.8 0.4 - - - +
73A GLY* 3.0 20.4 + - - +
74A TYR 3.8 2.7 - - - +
76A ALA* 1.3 76.8 - - - +
78A ALA* 1.3 64.7 + - - +
80A GLY 4.2 0.4 - - - +
81A LEU* 2.9 41.4 + - + +
102A ALA 4.4 3.6 - - - +
105A TYR* 3.8 30.5 - - + +
106A TRP* 3.7 30.5 - - + +
109A ALA* 4.6 3.1 - - + -
111A LEU* 4.2 7.4 - - + -
115A ILE* 4.3 5.2 - - + -
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Residues in contact with ALA 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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27A LEU* 4.0 19.5 - - + +
50A ALA* 3.8 35.4 - - + +
51A GLN* 5.9 0.2 - - - -
53A LEU* 5.8 0.2 - - + -
54A ALA* 3.7 18.4 - - + +
74A TYR 2.9 18.5 + - - +
75A SER* 3.7 4.7 - - - +
77A ILE* 1.3 78.5 - - - +
79A MSE 1.3 61.8 + - + +
81A LEU* 3.6 10.0 + - - +
82A ALA* 3.8 4.3 + - - +
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Residues in contact with MSE 79 (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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53A LEU* 3.8 28.9 - - + -
54A ALA* 4.7 1.3 - - - +
57A VAL* 3.9 19.2 - - + +
65A VAL* 4.0 18.2 - - + -
67A ASP* 3.3 35.4 - - + +
75A SER* 3.0 24.2 + - - +
78A ALA* 1.3 75.7 - - + +
80A GLY* 1.3 66.9 + - - +
82A ALA* 3.0 16.0 + - - +
83A LEU* 3.2 13.4 + - - +
89A LEU* 3.7 15.3 - - + -
140A LEU* 4.1 16.6 - - - -
142A TYR* 3.8 27.8 - - + -
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Residues in contact with GLY 80 (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 ALA 2.8 20.1 + - - -
77A ILE 3.3 1.8 + - - -
79A MSE 1.3 76.9 - - - +
81A LEU* 1.3 60.9 + - - +
83A LEU* 3.2 35.5 + - - +
89A LEU* 4.1 2.1 - - - +
111A LEU* 3.7 24.2 - - - +
114A LYS* 4.4 2.3 + - - +
115A ILE* 4.5 5.6 - - - -
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Residues in contact with LEU 81 (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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24A PRO* 4.5 16.8 - - + -
26A LEU* 5.9 3.4 - - + -
27A LEU* 4.4 16.2 - - + -
58A LYS* 4.5 5.6 + - - -
77A ILE* 2.9 34.7 + - + +
78A ALA* 3.9 5.8 - - - +
79A MSE 3.2 0.2 - - - -
80A GLY* 1.3 75.6 - - - +
82A ALA* 1.3 59.3 + - - +
83A LEU 4.4 3.6 - - - +
109A ALA* 4.5 16.6 - - + +
111A LEU* 4.0 24.7 - - + -
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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