Contacts of the helix formed by residues 71 - 81 (chain A) in PDB entry 2B3O
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 THR 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.4 13.0 - - + +
69A PHE* 3.6 2.3 - - - +
70A ALA* 1.3 87.5 - - + +
72A LEU* 1.3 59.8 + - - +
73A THR* 3.7 5.3 + - - -
74A GLU* 2.9 34.9 + - - +
75A LEU* 2.8 27.4 + - - +
255A GLU* 3.8 25.4 - - + +
259A LEU* 5.4 0.2 - - - +
492A ARG* 6.6 0.4 - - - -
496A SER* 4.5 0.9 - - - -
497A GLY* 3.6 25.6 - - - +
500A GLN* 5.0 0.2 - - - +
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Residues in contact with LEU 72 (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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4A TRP* 3.8 17.7 - - + -
5A PHE* 4.0 15.7 - - + -
29A ALA* 4.6 7.6 - - + -
39A PHE* 4.0 28.5 - - + -
41A LEU* 6.2 1.3 - - + -
54A ILE* 4.3 22.4 - - + -
61A TYR* 3.3 41.7 - - + +
71A THR* 1.3 72.1 - - - +
73A THR* 1.3 58.5 + - - +
75A LEU* 3.1 10.8 + - + +
76A VAL* 2.9 33.7 + - + +
252A GLN* 3.8 23.3 - - + +
255A GLU* 4.1 5.1 + - - +
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Residues in contact with THR 73 (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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2A VAL* 3.4 21.8 - - - +
4A TRP* 3.7 15.6 - - + -
71A THR* 3.1 3.5 - - - -
72A LEU* 1.3 80.6 - - - +
74A GLU* 1.3 57.3 + - - +
76A VAL* 3.6 2.1 + - - +
77A GLU* 3.1 25.5 + - + +
255A GLU* 2.7 36.6 + - - +
256A VAL* 5.0 4.0 - - + -
259A LEU* 3.6 37.2 - - + -
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Residues in contact with GLU 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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69A PHE* 4.2 7.6 - - + -
70A ALA* 3.3 20.5 + - - +
71A THR* 2.9 32.6 + - - +
73A THR* 1.3 74.1 - - - +
75A LEU* 1.3 67.6 + - - +
77A GLU* 3.3 8.4 + - - +
78A TYR* 2.9 25.1 + - - +
258A ASN 5.1 1.6 - - - +
259A LEU* 3.9 21.3 - - + +
262A ARG* 3.7 37.9 + - - +
278A ASN 4.0 5.1 - - - +
279A ILE* 5.3 0.3 - - - -
280A LEU 5.5 0.2 + - - -
282A PHE* 4.5 4.2 - - - -
496A SER* 2.9 31.8 + - - -
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Residues in contact with LEU 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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41A LEU* 4.2 27.4 - - + -
54A ILE* 4.1 34.3 - - + -
61A TYR* 4.7 4.9 - - + -
63A LEU* 4.4 11.9 - - + +
69A PHE* 3.5 39.9 - - + -
71A THR 2.8 12.4 + - - +
72A LEU* 3.3 17.0 - - + +
74A GLU* 1.3 76.2 - - - +
76A VAL* 1.3 75.8 + - + +
78A TYR* 3.1 11.8 + - - +
79A TYR* 3.2 25.9 + - + -
96A LEU* 5.4 1.1 - - + -
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Residues in contact with VAL 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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4A TRP* 3.7 37.7 - - + +
27A PHE* 3.7 37.5 - - + -
41A LEU* 4.8 7.9 - - + -
72A LEU* 2.9 19.9 + - + +
73A THR 3.8 4.5 - - - +
75A LEU* 1.3 89.4 - - + +
77A GLU* 1.3 66.8 + - - +
79A TYR* 3.1 1.6 + - - +
80A THR* 2.8 31.7 + - + +
96A LEU* 4.5 6.5 - - + +
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Residues in contact with GLU 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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73A THR 3.1 15.3 + - - +
74A GLU* 3.6 6.2 - - - +
76A VAL* 1.3 81.5 - - - +
78A TYR* 1.3 64.6 + - - +
80A THR* 4.1 9.9 - - - -
81A GLN* 3.0 48.2 + - + +
259A LEU* 4.0 29.2 - - + +
262A ARG* 3.6 22.3 + - - -
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Residues in contact with TYR 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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67A GLU* 2.5 33.6 + - - -
69A PHE* 3.4 29.6 - + + -
74A GLU 2.9 10.8 + - - +
75A LEU 3.1 3.1 + - - +
76A VAL 3.0 0.2 + - - -
77A GLU* 1.3 81.7 - - - +
79A TYR* 1.3 94.7 + + - +
81A GLN* 3.4 1.8 + - - -
83A GLN* 3.0 65.8 + - + +
84A GLY* 3.8 9.4 - - - -
277A LYS* 3.1 17.4 + - - -
278A ASN* 3.1 26.0 - - + -
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Residues in contact with TYR 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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41A LEU* 5.7 0.2 - - + -
63A LEU* 3.1 29.4 - - + -
66A GLY* 3.3 10.1 - - - -
67A GLU* 3.2 33.1 + - - -
69A PHE* 3.7 16.1 - + - -
75A LEU* 3.2 22.6 + - + -
76A VAL 3.1 4.9 + - - +
78A TYR* 1.3 99.5 - + - +
80A THR* 1.3 60.8 + - - +
81A GLN 3.1 2.0 - - - -
82A GLN* 2.8 23.2 + - - +
84A GLY* 3.8 25.4 - - - +
85A VAL 4.2 1.9 + - - -
86A LEU* 4.1 28.5 - - + -
96A LEU* 4.1 27.7 + - + +
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Residues in contact with THR 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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27A PHE* 4.1 23.9 - - - -
76A VAL* 2.8 21.3 + - + +
77A GLU* 3.8 8.1 - - - +
79A TYR* 1.3 73.2 - - - +
81A GLN* 1.3 76.4 + - - +
82A GLN* 3.0 17.5 + - - +
96A LEU* 4.2 20.4 + - - +
97A LYS* 5.0 7.3 + - - -
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Residues in contact with GLN 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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77A GLU* 3.0 44.2 + - + +
78A TYR* 3.7 0.4 - - - +
79A TYR 3.1 0.4 - - - -
80A THR* 1.3 102.1 - - - +
82A GLN* 1.3 73.2 + - - +
83A GLN* 2.9 35.0 + - + +
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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