Contacts of the helix formed by residues 71 - 83 (chain E) in PDB entry 1F9N
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 71 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E GLN 4.4 0.4 + - - -
70E PHE* 1.3 110.9 - - + +
72E PRO* 1.3 63.5 - - - +
73E LEU 3.5 2.0 - - - -
74E SER* 2.9 25.6 + - - +
75E LYS* 2.8 36.7 + - + +
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Residues in contact with PRO 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLN 3.3 20.4 - - - +
69E ARG* 4.1 5.6 - - - +
70E PHE 2.9 24.7 - - - +
71E ASN* 1.3 75.6 - - - +
73E LEU* 1.3 58.1 + - - +
75E LYS* 3.8 0.7 - - - +
76E LEU* 2.8 33.3 + - - +
109E LEU* 4.1 19.1 - - + +
112E ASN* 3.6 24.9 - - + +
113E LEU* 3.7 19.7 - - + +
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASN 3.5 0.4 - - - -
72E PRO* 1.3 80.3 - - - +
74E SER* 1.3 58.4 + - - +
76E LEU* 3.3 3.0 + - + +
77E LYS* 2.9 30.7 + - + +
113E LEU* 3.6 19.6 - - + +
115E TRP* 4.3 19.1 - - + +
148E LEU* 4.6 24.0 - - + +
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Residues in contact with SER 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASN* 2.9 42.5 + - - +
73E LEU* 1.3 78.2 - - - +
75E LYS* 1.3 72.7 + - - +
77E LYS* 3.2 17.6 + - - +
78E ARG* 3.2 14.2 + - - +
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Residues in contact with LYS 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E PRO* 2.6 31.0 + - - -
66E ALA* 3.7 11.0 + - - +
67E ASP 3.1 19.6 + - - -
68E GLN* 4.6 1.2 - - - +
70E PHE* 3.9 10.7 - - - +
71E ASN* 2.8 33.7 + - + +
72E PRO 3.8 2.5 - - - +
74E SER* 1.3 85.3 + - - +
76E LEU* 1.3 62.5 + - - +
78E ARG* 3.4 5.2 + - - +
79E ALA* 3.0 23.2 + - - +
109E LEU* 3.8 26.9 - - + +
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E PRO 2.8 22.9 + - - +
73E LEU* 3.6 4.7 - - + +
75E LYS* 1.3 72.8 - - - +
77E LYS* 1.3 64.0 + - - +
79E ALA* 3.3 2.2 + - - +
80E LEU* 2.9 36.8 + - + +
106E ILE* 3.7 34.8 - - + +
109E LEU* 3.6 16.3 - - + +
110E MET* 3.8 15.3 - - + -
113E LEU* 3.4 36.3 - - + -
145E LEU* 4.3 9.4 - - + -
148E LEU* 4.3 17.3 - - + -
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Residues in contact with LYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E LEU* 2.9 14.0 + - + +
74E SER* 3.2 13.4 + - - +
76E LEU* 1.3 78.0 - - - +
78E ARG* 1.3 62.9 + - - +
80E LEU* 3.3 5.0 + - - +
81E MET* 3.0 43.4 + - + +
147E GLU 5.1 1.0 + - - -
148E LEU* 2.7 57.0 + - + +
149E LEU 5.1 0.8 + - - -
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E SER 3.2 7.8 + - - +
75E LYS* 3.8 8.1 - - - +
77E LYS* 1.3 81.1 - - - +
79E ALA* 1.3 63.5 + - - +
81E MET* 3.2 10.0 + - - +
82E ASP* 3.0 34.3 + - - +
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LYS 3.0 19.3 + - - +
76E LEU* 3.5 5.8 - - - +
78E ARG* 1.3 76.8 - - - +
80E LEU* 1.3 52.6 + - - +
82E ASP* 3.3 5.3 + - - +
83E ALA* 2.7 39.0 + - - +
105E ALA* 6.4 0.2 - - + -
106E ILE* 3.2 27.8 - - + -
109E LEU* 4.6 5.4 - - + -
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Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 2.9 28.6 + - + +
77E LYS* 3.7 4.0 - - - +
79E ALA* 1.3 73.6 - - - +
81E MET* 1.3 61.8 + - - +
83E ALA 4.9 0.2 - - - -
84E PHE* 2.6 64.8 + - + +
96E LEU* 4.0 20.6 - - + -
98E THR* 5.4 2.5 - - + -
106E ILE* 4.5 13.7 - - + -
110E MET* 6.3 0.2 - - - -
145E LEU* 3.8 41.1 - - + +
148E LEU* 3.9 20.9 - - + -
149E LEU* 5.2 7.0 - - + -
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Residues in contact with MET 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 2.9 33.3 + - - +
48B LEU 5.2 5.0 - - - +
49B HIS* 6.0 9.4 - - + -
64B LEU* 4.9 2.1 - - - +
65B PRO* 5.2 0.2 - - - +
77E LYS* 3.0 54.8 + - + +
78E ARG* 3.4 12.8 - - - +
80E LEU* 1.3 76.1 - - - +
82E ASP* 1.3 63.8 + - - +
148E LEU 3.1 14.8 - - - +
149E LEU* 4.1 18.1 - - - +
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Residues in contact with ASP 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 4.7 0.9 - - - -
49B HIS* 5.4 7.3 - - - -
64B LEU* 3.4 23.2 - - - +
65B PRO* 3.8 24.7 - - - +
66B ALA* 3.2 29.7 + - + +
78E ARG* 3.0 25.9 + - - +
79E ALA* 3.9 4.1 - - - +
81E MET* 1.3 85.1 - - - +
83E ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.4 1.6 - - - -
66B ALA* 3.6 16.8 - - + -
79E ALA 2.7 20.3 + - - +
80E LEU* 5.2 0.7 - - - -
82E ASP* 1.3 75.3 - - - +
84E PHE* 1.3 64.9 + - - +
85E VAL* 3.2 2.6 + - - +
98E THR* 3.2 10.4 - - + -
99E MET* 3.0 30.8 + - - +
102E ASN* 3.9 26.5 - - + -
106E ILE* 5.3 4.9 - - + -
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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