Contacts of the helix formed by residues 73 - 84 (chain A) in PDB entry 6B3I
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU* 1.3 78.7 - - - +
74A GLY* 1.3 74.9 + - - +
76A PHE* 3.5 6.7 + - - +
77A GLU* 3.2 21.0 + - - -
73B SER* 3.2 38.4 + - - -
74B GLY* 3.3 0.5 - - - -
75B ASN 4.1 0.3 + - - -
76B PHE* 4.7 0.9 + - - -
306B ASP* 4.3 16.6 + - - -
402B EDO 3.3 26.0 + - - -
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Residues in contact with GLY 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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73A SER* 1.3 84.6 + - - +
75A ASN* 1.3 62.2 + - - -
77A GLU* 3.7 7.0 + - - +
78A LYS* 3.3 21.7 + - - +
73B SER* 3.7 11.9 - - - -
74B GLY* 3.7 12.2 - - - -
402B EDO 4.9 1.0 + - - -
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Residues in contact with ASN 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 GLY* 1.3 71.5 - - - -
76A PHE* 1.3 60.1 + - - +
78A LYS* 3.5 28.1 + - - +
79A THR* 2.9 33.6 + - - -
265A GLU* 2.3 41.1 + - - +
266A GLU* 5.3 4.2 - - - +
269A ILE* 4.2 10.2 - - + +
307A PHE* 3.3 24.7 - - + +
73B SER* 4.8 1.6 - - - -
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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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34A GLU* 4.5 15.7 - - + -
37A ILE* 4.8 10.8 - - + -
38A ILE* 3.6 32.3 - - + -
41A LEU* 5.9 0.2 - - + -
72A LEU* 3.5 43.1 - - + -
73A SER 3.5 8.2 + - - +
74A GLY 3.3 0.4 - - - -
75A ASN* 1.3 77.2 - - - +
77A GLU* 1.3 57.5 + - - +
79A THR* 3.5 2.6 + - - -
80A ALA* 3.0 28.6 + - + +
306A ASP* 3.1 61.5 - - + +
307A PHE* 3.9 12.0 - - - +
310A LEU* 3.7 19.9 - - + +
73B SER* 4.4 2.2 + - - +
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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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68A LEU 4.6 4.0 - - - +
69A LYS* 3.3 33.7 - - - +
72A LEU* 3.6 23.5 - - + +
73A SER* 3.2 34.5 + - - +
74A GLY 3.7 5.8 + - - +
75A ASN 3.3 0.2 - - - -
76A PHE* 1.3 78.8 - - - +
78A LYS* 1.3 62.1 + - - +
80A ALA* 3.7 2.6 - - - +
81A LEU* 2.9 45.5 + - + +
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Residues in contact with LYS 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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74A GLY 3.3 12.8 + - - +
75A ASN* 3.5 27.9 + - - +
76A PHE 3.3 0.4 - - - -
77A GLU* 1.3 82.9 - - - +
79A THR* 1.3 57.2 + - - +
81A LEU* 4.0 4.8 - - - +
82A ALA* 3.0 28.4 + - - +
90A TYR* 4.8 6.9 - - + +
97A LYS* 3.0 17.8 - - - +
266A GLU* 2.3 40.0 + - - +
269A ILE* 4.3 11.5 - - + +
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Residues in contact with THR 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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75A ASN 2.9 19.3 + - - -
78A LYS* 1.3 73.1 - - - +
80A ALA* 1.3 66.6 + - - +
82A ALA* 3.2 1.6 + - - +
83A LEU* 3.0 31.1 + - + +
269A ILE* 3.3 23.1 - - + +
273A VAL* 4.6 2.5 - - + -
307A PHE* 3.2 19.9 - - - -
310A LEU* 3.7 24.2 - - + -
311A LEU* 4.5 8.7 - - + -
314A LEU* 4.1 24.7 - - + -
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Residues in contact with ALA 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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41A LEU* 3.7 28.3 - - + +
68A LEU* 4.3 6.5 - - + -
72A LEU* 3.7 22.9 - - + -
76A PHE* 3.0 20.3 + - + +
77A GLU 3.2 3.8 + - - +
79A THR* 1.3 77.5 - - - +
81A LEU* 1.3 64.1 + - + +
83A LEU* 3.4 4.7 + - - +
84A LEU* 3.3 26.5 + - - +
310A LEU* 4.1 4.4 - - + +
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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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65A GLU* 3.7 46.8 - - + +
68A LEU* 4.3 15.9 - - + -
69A LYS* 3.7 33.9 - - + -
77A GLU* 2.9 35.4 + - + +
78A LYS* 4.2 4.3 - - - +
80A ALA* 1.3 74.8 - - + +
82A ALA* 1.3 65.1 + - - +
84A LEU* 3.3 11.5 + - + +
85A ASP* 3.1 24.1 + - - +
90A TYR* 5.6 0.2 - - - -
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Residues in contact with ALA 82 (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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78A LYS 3.0 20.5 + - - +
79A THR* 3.2 7.4 + - - +
81A LEU* 1.3 77.9 - - - +
83A LEU* 1.3 60.3 + - - +
85A ASP* 3.4 20.4 + - - +
90A TYR* 3.5 46.2 - - + +
269A ILE* 4.4 0.4 - - + -
273A VAL* 3.7 25.4 - - + +
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Residues in contact with LEU 83 (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* 3.5 39.3 - - + +
46A SER* 5.2 0.2 + - - -
49A ARG* 2.6 54.3 + - - +
79A THR* 3.0 23.5 + - + +
80A ALA 3.8 5.2 - - - +
81A LEU 3.3 0.2 - - - -
82A ALA* 1.3 77.6 - - - +
84A LEU* 1.3 61.0 + - - +
85A ASP 3.3 2.9 + - - +
273A VAL* 3.8 29.2 - - + -
276A ALA* 6.0 3.4 - - + -
310A LEU* 4.3 9.0 - - + -
314A LEU* 3.9 32.8 - - + -
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Residues in contact with LEU 84 (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* 3.8 23.8 - - + -
49A ARG* 4.4 23.1 - - + +
50A GLN* 3.0 8.9 + - - -
53A LYS* 2.7 38.9 + - + -
64A LEU* 3.8 27.1 - - + -
65A GLU* 3.8 28.3 - - + +
68A LEU* 3.7 29.4 - - + -
80A ALA 3.3 13.0 + - - +
81A LEU* 3.3 7.7 + - + +
82A ALA 3.2 0.8 - - - -
83A LEU* 1.3 79.1 - - - +
85A ASP* 1.3 56.9 + - - +
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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