Contacts of the helix formed by residues 75 - 87 (chain N) in PDB entry 2FBW
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 75 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67N ALA* 3.7 5.9 - - - +
74N ASP* 1.3 88.6 + - - +
76N TRP* 1.3 65.3 + - - +
77N ARG* 2.8 59.8 + - - +
78N TRP* 2.9 52.4 + - + +
79N HIS 3.4 3.5 + - - -
137N PHE* 5.9 0.8 - - - -
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Residues in contact with TRP 76 (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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67N ALA* 3.6 18.8 - - + +
75N ASN* 1.3 74.9 + - - +
77N ARG* 1.3 110.9 + - + +
79N HIS* 3.0 7.6 + - + +
80N PHE* 2.8 32.8 + + + -
97N HIS* 3.5 39.3 - + - -
100N THR* 3.5 34.5 + - - +
101N GLU* 3.3 43.2 + - + +
104N PRO* 5.0 8.7 - - + -
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Residues in contact with ARG 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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75N ASN* 2.8 36.3 + - - +
76N TRP* 1.3 131.2 - - + +
78N TRP* 1.3 57.0 + - - +
80N PHE* 3.3 10.0 - - + +
81N TYR 3.0 20.8 + - - -
101N GLU* 5.6 0.4 + - - -
137N PHE* 3.4 32.0 - - + -
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Residues in contact with TRP 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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73N ASP* 3.7 26.2 - - + -
74N ASP* 3.4 23.6 - - - -
75N ASN* 2.9 33.0 + - + +
77N ARG* 1.3 74.3 - - - +
79N HIS* 1.3 61.2 + - - +
81N TYR* 3.3 7.4 + - - +
82N ASP* 2.9 33.3 + - - +
134N SER 4.0 6.1 - - - +
135N LEU* 3.9 15.5 - - + -
136N GLN* 3.3 52.5 + - + +
137N PHE* 3.4 46.7 - + - +
145N ARG* 3.7 10.8 - - - +
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Residues in contact with HIS 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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65N ASN* 3.5 42.7 + - + +
66N ALA* 4.7 3.2 - - - -
67N ALA* 4.8 2.7 + - + +
75N ASN 3.4 2.0 + - - -
76N TRP* 3.0 15.4 + - - +
78N TRP* 1.3 76.7 - - - +
80N PHE* 1.3 62.5 + - - +
82N ASP* 3.3 4.2 + - + +
83N THR* 2.9 43.2 + - - -
99N MET* 5.2 7.9 - - + +
100N THR* 3.7 25.0 + - + +
103N ALA* 4.5 9.2 - - + +
133N GLN* 3.8 16.2 - - + -
145N ARG* 3.7 28.8 - - - +
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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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76N TRP* 2.8 17.6 + + + +
77N ARG* 3.3 18.8 - - + +
79N HIS* 1.3 71.9 - - - +
81N TYR* 1.3 72.4 + + + +
83N THR* 3.1 3.6 + - - -
84N VAL* 3.0 43.3 + - + +
93N GLN* 3.6 46.9 - - + -
96N ILE* 3.5 14.9 - - + +
97N HIS* 3.6 24.7 - + + -
100N THR* 3.4 18.9 + - - +
137N PHE* 5.7 2.5 - + - -
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Residues in contact with TYR 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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77N ARG 3.0 14.8 + - - +
78N TRP* 3.3 6.7 + - - +
80N PHE* 1.3 83.7 - + + +
82N ASP* 1.3 74.5 + - - +
84N VAL* 3.3 7.0 + - + +
85N LYS* 3.0 50.2 + - + +
89N TRP* 5.5 10.0 - + - -
137N PHE* 3.3 59.4 + + + -
138N GLY* 3.7 9.9 - - - -
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Residues in contact with ASP 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 TRP 2.9 16.1 + - - +
79N HIS* 3.7 7.2 - - + +
80N PHE 3.2 0.2 - - - -
81N TYR* 1.3 85.1 - - - +
83N THR* 1.3 58.5 + - - +
85N LYS* 3.9 4.3 - - - +
86N GLY* 2.8 26.5 + - - -
132N GLY 3.8 16.1 - - - +
133N GLN* 3.3 8.8 - - + -
134N SER* 2.7 52.2 + - - +
138N GLY* 4.8 0.2 - - - -
145N ARG* 2.8 21.4 + - - +
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Residues in contact with THR 83 (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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79N HIS* 2.9 33.5 + - - -
80N PHE 3.7 4.0 - - - -
82N ASP* 1.3 75.0 - - - +
84N VAL* 1.3 65.4 + - - +
86N GLY* 3.3 2.0 + - - +
87N SER* 3.0 24.8 + - - -
96N ILE* 3.7 28.7 - - + -
99N MET* 4.4 14.8 - - + +
100N THR* 3.9 3.5 - - - +
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Residues in contact with VAL 84 (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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80N PHE* 3.0 49.8 + - + +
81N TYR* 3.7 8.3 - - + +
83N THR* 1.3 74.0 - - - +
85N LYS* 1.3 63.0 + - - +
87N SER* 2.6 24.9 + - - +
88N ASP 3.4 3.8 + - - -
89N TRP* 3.5 34.2 + - + +
91N GLY 5.8 0.9 - - - +
93N GLN* 3.7 22.9 - - + +
96N ILE* 4.0 16.5 - - + +
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Residues in contact with LYS 85 (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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81N TYR* 3.0 42.9 + - + +
82N ASP* 4.0 4.3 - - - +
84N VAL* 1.3 76.6 - - - +
86N GLY* 1.3 66.5 + - - +
88N ASP* 2.8 16.8 + - - +
89N TRP* 3.9 31.4 - - + -
138N GLY* 6.0 3.4 - - - -
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Residues in contact with GLY 86 (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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82N ASP 2.8 19.5 + - - -
83N THR* 3.7 2.2 - - - -
84N VAL 3.3 0.4 - - - -
85N LYS* 1.3 79.4 - - - +
87N SER* 1.3 59.1 + - - +
88N ASP* 3.2 3.7 + - - +
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Residues in contact with SER 87 (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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83N THR* 3.0 15.1 + - - -
84N VAL* 2.6 21.5 + - - +
85N LYS 3.1 0.2 - - - -
86N GLY* 1.3 74.2 - - - +
88N ASP* 1.3 67.6 + - - +
89N TRP* 3.2 2.9 + - - -
90N LEU* 3.4 14.4 + - - +
91N GLY* 3.3 31.7 + - - -
96N ILE* 5.0 2.7 - - - -
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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