Contacts of the helix formed by residues 73 - 85 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A SER* 3.2 42.7 + - - -
74A GLY* 3.7 5.2 - - - -
75A ASN 4.8 1.6 - - - -
76A PHE* 4.4 2.9 + - - +
306A ASP* 3.2 22.1 + - - -
307A PHE* 5.8 1.0 - - - +
72B LEU* 1.3 83.5 + - - +
74B GLY* 1.3 68.9 + - - +
76B PHE* 3.5 5.5 + - - +
77B GLU* 3.1 18.9 + - - -
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Residues in contact with GLY 74 (chain B).
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* 3.3 11.2 - - - -
74A GLY* 3.7 12.4 - - - -
73B SER* 1.3 79.6 - - - +
75B ASN* 1.3 60.6 + - - -
77B GLU* 3.6 6.2 + - - +
78B LYS* 3.2 27.9 + - - +
402B EDO 3.6 4.5 - - - -
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLY* 1.3 70.8 - - - -
76B PHE* 1.3 60.4 + - - +
77B GLU 3.2 0.4 - - - -
78B LYS* 3.2 34.0 + - - +
79B THR* 2.8 34.5 + - - -
265B GLU* 2.2 40.3 + - - +
269B ILE* 4.0 7.1 - - + +
307B PHE* 3.3 22.7 - - + -
402B EDO 2.9 25.1 + - - +
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Residues in contact with PHE 76 (chain B).
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* 4.7 1.3 + - - +
34B GLU* 4.4 20.0 - - + -
37B ILE* 4.7 13.0 - - + -
38B ILE* 3.7 29.6 - - + -
72B LEU* 3.6 42.2 - - + -
73B SER 3.5 8.0 + - - +
74B GLY 3.3 1.0 - - - -
75B ASN* 1.3 78.7 - - - +
77B GLU* 1.3 59.2 + - - +
79B THR* 4.2 2.1 - - - -
80B ALA* 3.2 23.5 + - + +
306B ASP* 3.3 61.7 - - + +
307B PHE* 4.0 10.3 - - - +
310B LEU* 4.0 17.3 - - + +
402B EDO 4.6 0.6 + - - -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU 4.3 7.4 - - - +
69B LYS* 3.8 14.8 - - - +
72B LEU* 3.6 26.0 - - + +
73B SER* 3.1 32.7 + - - +
74B GLY 3.6 9.6 + - - +
75B ASN 3.2 0.2 - - - -
76B PHE* 1.3 77.3 - - - +
78B LYS* 1.3 69.1 + - - +
80B ALA* 3.4 3.1 + - - +
81B LEU* 3.0 50.5 + - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLY 3.2 14.8 + - - +
75B ASN* 3.2 31.3 + - - +
77B GLU* 1.3 84.6 - - - +
79B THR* 1.3 57.4 + - - +
81B LEU* 3.9 4.6 - - - +
82B ALA* 2.9 30.4 + - - +
90B TYR* 4.8 5.6 - - + +
97B LYS* 5.8 1.5 - - - +
266B GLU* 3.0 48.9 + - - +
269B ILE* 4.2 10.5 - - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN 2.8 19.2 + - - -
78B LYS* 1.3 73.2 - - - +
80B ALA* 1.3 61.2 + - - +
82B ALA* 3.2 1.4 + - - +
83B LEU* 2.9 31.2 + - + +
269B ILE* 3.2 22.5 - - + +
273B VAL* 4.4 5.2 - - + -
307B PHE* 3.2 19.0 - - - -
310B LEU* 3.6 25.1 - - + -
311B LEU* 4.2 9.4 - - + -
314B LEU* 4.0 22.2 - - + -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.7 29.0 - - + +
68B LEU* 4.4 7.9 - - + -
72B LEU* 4.0 20.2 - - + -
76B PHE* 3.2 19.1 + - + +
77B GLU 3.8 4.0 - - - +
79B THR* 1.3 79.6 - - - +
81B LEU* 1.3 63.6 + - + +
83B LEU* 3.4 4.1 + - - +
84B LEU* 3.2 27.3 + - - +
310B LEU* 4.2 3.3 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 3.7 43.6 - - + +
68B LEU* 4.3 14.1 - - + -
69B LYS* 3.7 24.9 - - + -
77B GLU* 3.0 44.8 + - + +
78B LYS* 4.1 4.3 - - - +
80B ALA* 1.3 75.5 - - - +
82B ALA* 1.3 65.1 + - - +
84B LEU* 3.2 15.9 + - + +
85B ASP* 3.2 20.8 + - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS 2.9 20.3 + - - +
79B THR* 3.5 7.0 - - - +
81B LEU* 1.3 76.5 - - - +
83B LEU* 1.3 59.7 + - - +
85B ASP* 3.3 20.1 + - - +
86B HIS 5.5 0.2 - - - -
90B TYR* 3.6 48.2 - - + +
269B ILE* 4.3 0.4 - - + -
273B VAL* 3.7 23.2 - - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.9 30.7 - - + +
49B ARG* 2.4 63.6 + - - +
50B GLN* 4.8 0.2 + - - -
79B THR* 2.9 24.4 + - + +
80B ALA* 3.8 5.2 - - - +
81B LEU 3.3 0.2 - - - -
82B ALA* 1.3 76.1 - - - +
84B LEU* 1.3 60.1 + - - +
85B ASP 3.6 2.7 + - - +
273B VAL* 4.0 30.1 - - + +
276B ALA* 5.9 3.6 - - + -
310B LEU* 4.5 5.2 - - + -
314B LEU* 3.8 39.0 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.0 21.5 - - + -
49B ARG* 4.6 19.1 - - + +
50B GLN* 2.9 10.6 + - - +
53B LYS* 2.6 39.6 + - + -
64B LEU* 3.9 24.5 - - + -
65B GLU* 3.6 35.0 - - + +
68B LEU* 3.7 29.6 - - + -
80B ALA 3.2 11.6 + - - +
81B LEU* 3.2 9.7 + - + +
83B LEU* 1.3 76.9 - - - +
85B ASP* 1.3 56.2 + - - +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.4 3.3 + - - -
49B ARG* 4.6 0.9 + - - -
50B GLN* 3.9 4.1 + - - -
53B LYS* 4.7 1.4 + - - -
65B GLU* 3.2 17.9 - - - +
81B LEU* 3.2 15.0 + - - +
82B ALA 3.3 16.7 + - - +
83B LEU 3.7 6.4 - - - +
84B LEU* 1.3 81.5 - - - +
86B HIS* 1.3 73.0 + - - +
87B PRO* 3.7 3.5 - - - +
89B GLU* 3.8 14.2 - - - +
90B TYR* 4.0 15.9 - - + +
93B ARG* 2.9 41.6 + - - -
273B VAL* 5.9 0.3 - - - +
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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