Contacts of the helix formed by residues 73 - 82 (chain N) in PDB entry 3BBX
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 ASN 73 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1453B A 5.9 14.6 - - + +
2701B U 4.4 0.4 + - - -
66N ALA* 3.4 25.2 + - - +
67N PHE* 3.0 45.7 - - - -
71N ARG 3.9 5.7 + - - -
72N ASP* 1.3 82.6 + - - +
74N GLU* 1.3 57.3 + - - +
76N VAL* 3.1 17.3 - - + -
77N ALA* 2.8 33.9 + - + +
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Residues in contact with GLU 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293B C 3.9 13.0 + - - +
30N ARG* 2.7 47.1 + - - +
72N ASP* 3.0 39.9 + - + +
73N ASN* 1.3 79.8 - - - +
75N ILE* 1.3 53.6 + - - +
77N ALA* 3.5 3.9 - - - +
78N LYS* 2.8 35.8 + - - +
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Residues in contact with ILE 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N GLY* 3.2 37.7 - - - +
29N VAL* 3.3 33.2 - - + +
30N ARG* 4.7 12.2 - - - +
51N LEU* 6.5 0.9 - - + -
69N ARG* 5.1 2.5 - - + +
70N THR* 3.3 34.3 + - + +
72N ASP 4.5 0.4 + - - -
74N GLU* 1.3 78.8 - - - +
76N VAL* 1.3 72.5 + - + +
78N LYS* 3.3 9.6 + - - +
79N LEU* 3.1 33.0 + - + +
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Residues in contact with VAL 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N ASN* 3.8 21.8 - - - +
63N ARG* 5.1 2.2 - - + -
65N LEU 3.6 23.6 - - - +
66N ALA* 3.7 20.9 - - + +
70N THR* 4.5 2.7 - - + -
73N ASN* 2.9 44.9 - - + +
75N ILE* 1.3 81.5 - - + +
77N ALA* 1.3 61.8 + - - +
79N LEU* 2.9 37.5 + - + +
80N PHE* 3.3 14.0 - - + -
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Residues in contact with ALA 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453B A 5.9 7.0 - - + -
73N ASN* 2.8 27.5 + - + +
74N GLU* 3.5 3.8 - - - +
76N VAL* 1.3 74.1 - - + +
78N LYS* 1.3 61.9 + - - +
79N LEU 3.2 0.7 + - - -
80N PHE* 3.5 19.4 + - + -
81N ASN* 2.8 37.8 + - - +
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Residues in contact with LYS 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N VAL* 3.4 33.0 - - + +
30N ARG* 5.4 7.1 + - - +
74N GLU 2.8 13.1 + - - +
75N ILE* 3.3 12.1 - - - +
77N ALA* 1.3 77.0 - - - +
79N LEU* 1.3 57.1 + - - +
81N ASN* 4.8 1.3 - - - -
82N GLU* 3.0 76.8 + - - +
83N LEU* 3.2 10.5 + - + -
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Residues in contact with LEU 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N VAL* 4.0 16.8 - - + -
51N LEU* 4.5 28.0 - - + +
52N ILE* 3.7 31.6 - - + +
62N ASN* 4.6 8.5 - - - +
65N LEU 5.9 0.2 - - - +
75N ILE* 3.1 34.0 + - + +
76N VAL* 2.9 24.8 + - + +
78N LYS* 1.3 74.8 - - - +
80N PHE* 1.3 58.9 + - - +
81N ASN 2.9 9.9 + - - -
82N GLU 3.2 4.2 + - - -
83N LEU* 4.0 8.1 - - + -
84N GLY* 2.6 30.3 + - - +
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Residues in contact with PHE 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453B A 5.8 3.6 - - - -
54N LEU 4.7 1.3 - - - +
55N ALA* 5.4 3.4 - - - +
58N ASP* 2.6 38.6 - - - +
62N ASN* 3.1 40.8 - - + +
63N ARG* 2.9 46.2 - - + +
76N VAL* 3.3 18.1 + - + -
77N ALA* 3.5 22.4 - - + -
79N LEU* 1.3 76.8 - - - +
81N ASN* 1.3 96.2 + - - +
84N GLY* 4.9 3.4 - - - +
85N PRO* 4.2 10.8 - - - +
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Residues in contact with ASN 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N ASP* 4.7 1.2 + - - -
77N ALA* 2.8 26.3 + - - +
78N LYS* 4.5 0.9 - - - +
79N LEU 2.9 1.0 - - - -
80N PHE* 1.3 115.0 + - - +
82N GLU* 1.3 67.4 + - + +
85N PRO* 3.4 14.5 - - - +
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Residues in contact with GLU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N LYS* 3.0 56.1 + - + +
81N ASN* 1.3 85.6 - - + +
83N LEU* 1.3 69.4 + - + +
84N GLY 3.2 1.1 - - - -
85N PRO* 2.9 7.0 - - - +
86N ARG* 2.9 44.6 + - + +
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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