Contacts of the helix formed by residues 66 - 77 (chain E) in PDB entry 1YFL
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 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLU* 4.1 4.5 + - - -
141A ASN* 3.4 34.5 + - - -
145A GLN* 3.8 10.5 - - - +
65E VAL* 1.3 78.2 - - - +
67E TRP* 1.3 54.8 + - - +
68E ASP* 2.7 25.6 + - - +
69E ASP* 2.8 37.2 + - - +
70E VAL 3.6 2.3 + - - -
140E PHE* 3.6 5.2 - - - -
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Residues in contact with TRP 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 6.2 0.2 - - - -
145A GLN* 4.3 2.7 - - + +
66E SER* 1.3 70.4 - - - +
68E ASP* 1.3 64.7 + - - +
69E ASP 3.4 0.2 - - - -
70E VAL* 3.8 32.8 - - + -
71E LEU* 3.2 38.5 + - + +
104E TYR* 4.0 17.7 - - - -
108E PHE* 4.2 4.9 - + - -
132E ILE* 3.5 28.3 - - + -
133E ASN 5.7 0.2 - - - -
136E SER* 3.5 24.5 - - - -
137E GLU* 3.5 53.6 + - + +
140E PHE* 3.3 41.0 - + + -
141E ASN* 5.5 0.4 - - - +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 4.2 9.9 - - - -
67A TRP* 3.5 36.4 + - + +
68A ASP 5.0 0.2 + - - -
137A GLU* 4.7 5.4 - - - +
140A PHE* 4.3 6.9 - - - -
141A ASN* 3.2 22.3 + - - -
144A LYS* 5.6 2.8 - - - +
66E SER* 2.7 10.1 + - - +
67E TRP* 1.3 82.7 + - - +
69E ASP* 1.3 63.3 + - - +
70E VAL 3.0 1.8 - - - -
71E LEU* 3.0 14.4 + - - +
72E LYS* 2.8 30.5 + - - +
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Residues in contact with ASP 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 5.2 2.3 - - - +
61E ARG* 6.3 0.4 - - - +
65E VAL* 3.2 21.5 - - + +
66E SER* 2.8 37.5 + - - +
68E ASP* 1.3 80.5 - - - +
70E VAL* 1.3 60.1 + - - +
72E LYS* 3.8 8.1 - - - +
73E VAL* 3.2 29.8 + - - +
101E LEU* 4.5 9.0 - - + +
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Residues in contact with VAL 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 4.7 6.5 - - + -
66E SER 4.1 10.5 - - - +
67E TRP* 3.8 42.8 - - + +
68E ASP 3.0 0.4 - - - -
69E ASP* 1.3 78.9 - - - +
71E LEU* 1.3 56.8 + - - +
73E VAL* 3.5 5.9 + - - +
74E ILE* 3.0 44.2 + - + +
101E LEU* 4.4 11.7 - - + -
104E TYR* 3.8 31.9 - - + -
105E VAL* 4.5 10.8 - - + +
108E PHE* 4.6 5.8 - - + -
140E PHE* 4.7 1.8 - - + -
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Residues in contact with LEU 71 (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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66A SER* 5.6 6.7 - - - -
67E TRP* 3.2 46.6 + - + +
68E ASP* 3.0 16.5 + - - +
70E VAL* 1.3 77.7 - - - +
72E LYS* 1.3 55.3 + - - +
74E ILE* 3.0 10.2 + - + +
75E LYS* 2.7 37.1 + - - +
132E ILE* 4.3 20.6 - - + -
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Residues in contact with LYS 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 ASP 2.8 15.9 + - - +
69E ASP* 3.9 9.6 - - - +
70E VAL 3.4 0.2 - - - -
71E LEU* 1.3 76.1 - - - +
73E VAL* 1.3 59.0 + - + +
75E LYS* 3.7 5.4 - - - +
76E GLN* 2.9 34.1 + - - +
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Residues in contact with VAL 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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69E ASP 3.2 17.4 + - - +
70E VAL 3.8 4.3 - - - +
71E LEU 3.2 0.4 - - - -
72E LYS* 1.3 76.4 - - + +
74E ILE* 1.3 67.2 + - - +
76E GLN* 4.2 13.9 - - - +
77E TYR* 3.2 31.9 + - + +
79E LEU* 4.7 0.3 - - - +
90E LEU* 4.6 1.1 - - + -
101E LEU* 3.3 22.7 - - + -
102E LEU* 3.5 27.6 - - + -
105E VAL* 3.7 22.9 - - + -
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Residues in contact with ILE 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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70E VAL* 3.0 24.0 + - + +
71E LEU* 3.0 13.3 + - + +
73E VAL* 1.3 73.9 - - - +
75E LYS* 1.3 67.6 + - - +
77E TYR* 3.2 3.5 + - - +
78E LYS 2.9 16.5 + - - -
79E LEU* 3.3 39.7 + - + +
105E VAL* 3.9 17.0 - - + -
109E HIS* 4.6 9.2 - - + +
131E THR* 4.8 2.7 - - + +
132E ILE* 3.6 44.9 - - + -
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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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71E LEU 2.7 19.4 + - - +
72E LYS* 3.7 7.9 - - - +
74E ILE* 1.3 73.5 - - - +
76E GLN* 1.3 56.1 + - - +
78E LYS* 2.5 30.5 + - - +
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Residues in contact with GLN 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 LYS* 2.9 24.6 + - - +
73E VAL* 3.9 15.6 - - - +
75E LYS* 1.3 72.4 - - - +
77E TYR* 1.3 85.3 + - + +
78E LYS* 5.3 0.3 - - - +
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Residues in contact with TYR 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 VAL* 3.2 26.9 + - + +
74E ILE 3.2 1.8 + - - -
75E LYS 2.7 2.4 + - - -
76E GLN* 1.3 103.9 + - + +
78E LYS* 1.3 74.0 + - - +
79E LEU* 3.3 20.4 + - + -
86E GLU* 3.3 23.7 - - - +
89E LYS* 4.2 17.0 + - + -
90E LEU* 3.5 47.6 - - + +
93E ASP* 2.7 40.1 + - - +
102E LEU* 4.2 9.5 - - + +
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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