Contacts of the helix formed by residues 75 - 86 (chain E) in PDB entry 1S9D
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 ASP 75 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E LYS 2.9 8.2 + - - +
72E PHE 3.3 2.2 - - - -
74E MET* 1.3 81.4 - - + +
76E PRO* 1.3 71.1 - - - +
77E LYS* 3.2 22.6 + - - +
78E LYS* 3.1 38.2 + - + +
79E GLY 3.0 18.2 + - - -
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Residues in contact with PRO 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 PHE* 3.1 33.5 - - + +
73E ASN 4.6 0.7 - - - +
74E MET 4.1 3.4 - - - +
75E ASP* 1.3 84.0 - - - +
77E LYS* 1.3 64.4 + - - +
79E GLY 3.1 0.5 + - - -
80E ILE* 2.9 27.9 + - - +
110E ALA* 3.5 32.1 - - + +
113E ASP* 4.9 5.6 - - + +
114E TYR* 3.5 28.3 - - + +
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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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75E ASP* 3.2 12.9 + - - +
76E PRO* 1.3 75.9 - - - +
78E LYS* 1.3 57.7 + - + +
80E ILE* 3.3 4.9 + - - +
81E GLN* 2.8 57.8 + - - +
114E TYR* 4.2 14.3 - - + -
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Residues in contact with LYS 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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71E LYS* 4.8 7.2 - - + +
75E ASP* 3.1 35.8 + - + +
77E LYS* 1.3 82.7 - - + +
79E GLY* 1.3 58.9 + - - +
81E GLN* 3.3 16.9 - - + +
82E PHE* 3.0 27.4 + - - +
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Residues in contact with GLY 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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68E GLY 3.9 4.1 - - - +
71E LYS* 3.7 12.9 + - - -
72E PHE* 3.5 26.9 - - - -
75E ASP 3.0 10.5 + - - -
76E PRO 3.6 2.2 - - - -
78E LYS* 1.3 74.9 - - - +
80E ILE* 1.3 64.6 + - - +
82E PHE* 3.2 3.6 + - - +
83E LEU* 3.0 30.0 + - - +
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Residues in contact with ILE 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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72E PHE* 3.7 25.6 - - + -
76E PRO 2.9 16.6 + - - +
77E LYS* 3.6 8.1 - - - +
79E GLY* 1.3 75.4 - - - +
81E GLN* 1.3 56.8 - - - +
83E LEU* 3.1 6.0 + - + +
84E VAL* 2.9 40.3 + - + +
89E LEU* 4.1 16.8 - - + -
91E ASN* 4.9 2.0 - - - +
96E ILE* 4.1 36.8 - - + -
99E PHE* 4.3 14.4 - - + -
100E LEU* 4.9 0.7 - - + -
114E TYR* 4.0 20.4 - - + +
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Residues in contact with GLN 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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77E LYS* 2.8 44.7 + - - +
78E LYS* 3.3 18.8 - - + +
80E ILE* 1.3 77.7 - - - +
82E PHE* 1.3 55.2 + - - +
84E VAL* 3.1 12.3 - - + +
85E GLU* 3.1 53.5 + - + +
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Residues in contact with PHE 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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64E LYS* 3.3 37.9 - - + -
67E MET* 3.7 30.7 - - + -
68E GLY* 3.6 22.9 - - - -
71E LYS* 3.6 25.8 - - + -
78E LYS 3.0 14.1 + - - +
79E GLY* 3.5 7.4 - - - +
80E ILE 3.2 0.2 - - - -
81E GLN* 1.3 72.6 - - - +
83E LEU* 1.3 68.1 + - - +
85E GLU* 4.8 4.0 - - - -
86E ASN* 2.9 62.4 + - - +
88E LEU* 4.5 2.5 - - + -
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Residues in contact with LEU 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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65E MET* 4.0 20.6 - - + +
68E GLY* 3.9 25.6 - - - +
72E PHE* 5.6 0.7 - - + -
79E GLY 3.0 22.4 + - - +
80E ILE* 3.1 8.7 + - + +
82E PHE* 1.3 77.8 - - - +
84E VAL* 1.3 60.7 + - - +
86E ASN 3.3 1.2 + - - -
87E GLU 3.1 4.5 + - - -
88E LEU* 3.0 54.9 + - + +
89E LEU* 3.8 23.3 - - + -
99E PHE* 3.4 38.1 - - + -
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Residues in contact with VAL 84 (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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80E ILE* 2.9 29.6 + - + +
81E GLN* 3.1 26.7 - - + +
83E LEU* 1.3 76.6 - - - +
85E GLU* 1.3 65.3 + - + +
87E GLU* 3.2 15.4 + - - +
89E LEU* 3.5 29.2 - - + +
91E ASN* 3.8 42.4 - - + +
96E ILE* 5.4 0.2 - - + -
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Residues in contact with GLU 85 (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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81E GLN* 3.1 39.9 + - + +
82E PHE* 4.2 5.1 - - - +
84E VAL* 1.3 83.0 - - + +
86E ASN* 1.3 63.6 + - - +
87E GLU* 3.3 7.5 + - - +
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Residues in contact with ASN 86 (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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64E LYS* 3.6 24.8 + - + +
82E PHE* 2.9 60.1 + - - +
84E VAL 3.2 0.2 - - - -
85E GLU* 1.3 83.5 + - - +
87E GLU* 1.3 69.8 + - - +
88E LEU* 3.3 26.0 + - + +
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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