Contacts of the helix formed by residues 57 - 75 (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 LYS 57 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E THR* 1.3 63.9 + - - +
59E LEU* 3.7 3.8 - - - +
60E GLN* 3.6 48.5 + - - +
61E ARG* 3.2 26.0 + - - +
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Residues in contact with THR 58 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E LYS* 1.3 77.6 - - - +
59E LEU* 1.3 67.0 + - + +
60E GLN 3.2 1.3 - - - -
61E ARG* 3.4 4.4 + - - +
62E ASN* 3.0 46.2 + - - +
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Residues in contact with LEU 59 (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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57E LYS 4.5 1.9 - - - +
58E THR* 1.3 82.0 - - + +
60E GLN* 1.3 56.3 - - - +
62E ASN* 3.6 10.6 + - + +
63E ARG* 3.0 42.5 + - - +
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Residues in contact with GLN 60 (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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57E LYS* 3.6 53.9 + - + +
59E LEU* 1.3 76.5 - - - +
61E ARG* 1.3 63.6 + - - +
63E ARG* 3.3 10.1 + - - +
64E LYS* 3.1 46.8 + - + +
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Residues in contact with ARG 61 (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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57E LYS 3.2 17.7 + - - +
58E THR* 3.4 5.8 + - - +
60E GLN* 1.3 78.0 - - - +
62E ASN* 1.3 73.6 + - - +
64E LYS* 3.2 13.5 + - - +
65E MET* 2.9 52.7 + - - +
87E GLU 5.6 1.6 + - - -
88E LEU* 3.8 26.0 + - + +
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Residues in contact with ASN 62 (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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58E THR* 3.0 34.2 + - - +
59E LEU* 3.7 12.4 - - + +
61E ARG* 1.3 95.4 - - - +
63E ARG* 1.3 56.8 + - + +
65E MET* 3.5 8.0 + - - +
66E ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 63 (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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59E LEU* 3.0 30.4 + - - +
60E GLN* 3.7 8.3 - - - +
61E ARG 3.3 0.4 - - - -
62E ASN* 1.3 74.3 - - + +
64E LYS* 1.3 64.5 + - - +
66E ALA* 3.4 6.1 + - - +
67E MET* 3.0 26.8 + - - +
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Residues in contact with LYS 64 (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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60E GLN* 3.1 44.1 + - - +
61E ARG* 3.2 11.9 + - - +
63E ARG* 1.3 75.8 - - + +
65E MET* 1.3 57.7 + - - +
67E MET* 3.3 7.2 + - - -
68E GLY* 2.9 24.1 + - - -
82E PHE* 3.3 21.3 - - + -
86E ASN* 3.6 35.5 + - + +
88E LEU* 4.2 17.2 - - + +
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Residues in contact with MET 65 (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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61E ARG* 2.9 35.5 + - - +
62E ASN* 3.6 10.8 - - - +
63E ARG 3.2 0.2 - - - -
64E LYS* 1.3 75.2 - - - +
66E ALA* 1.3 63.6 + - - +
68E GLY* 3.1 10.6 + - - -
69E ARG* 3.1 48.7 + - - +
83E LEU* 4.0 15.7 - - + +
88E LEU* 3.2 48.9 - - + +
99E PHE* 4.2 13.5 - - - -
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Residues in contact with ALA 66 (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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62E ASN 3.0 17.6 + - - +
63E ARG* 3.7 7.0 - - - +
65E MET* 1.3 76.5 - - - +
67E MET* 1.3 61.7 + - - +
69E ARG* 3.4 12.5 + - - +
70E LYS* 3.1 27.2 + - + +
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Residues in contact with MET 67 (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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63E ARG 3.0 17.9 + - - +
64E LYS* 3.6 8.7 - - - +
66E ALA* 1.3 75.8 - - - +
68E GLY* 1.3 58.1 + - - +
70E LYS* 3.3 9.4 + - + +
71E LYS* 3.0 66.3 + - - +
82E PHE* 3.7 20.9 - - + -
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Residues in contact with GLY 68 (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 2.9 13.0 + - - -
65E MET 3.1 4.4 + - - -
67E MET* 1.3 75.1 - - - +
69E ARG* 1.3 52.8 + - - +
71E LYS* 3.3 4.3 + - - +
72E PHE* 2.7 34.5 + - - +
79E GLY* 3.9 5.6 - - - +
82E PHE* 3.6 23.1 - - - -
83E LEU* 3.9 18.8 - - - +
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Residues in contact with ARG 69 (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* 3.1 40.1 + - - +
66E ALA* 3.6 11.8 - - - +
67E MET 3.3 0.2 - - - -
68E GLY* 1.3 74.9 - - - +
70E LYS* 1.3 64.8 + - + +
72E PHE* 3.1 8.2 + - - +
73E ASN* 3.0 29.4 + - - -
83E LEU* 5.0 0.4 - - + +
99E PHE* 3.7 34.6 - - + -
103E GLY* 4.4 5.3 - - - -
104E GLU* 2.9 70.0 + - - +
105E GLY* 3.9 15.4 - - - +
106E LEU* 4.3 7.0 - - + +
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Residues in contact with LYS 70 (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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66E ALA* 3.1 20.4 + - + +
67E MET* 3.6 11.7 - - + +
69E ARG* 1.3 75.0 - - - +
71E LYS* 1.3 63.8 + - + +
73E ASN* 3.1 23.7 + - + +
74E MET* 3.3 18.3 + - + +
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Residues in contact with LYS 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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67E MET* 3.0 51.9 + - + +
68E GLY 3.6 4.5 - - - +
70E LYS* 1.3 73.4 - - + +
72E PHE* 1.3 66.0 + - - +
74E MET* 3.3 7.6 + - - +
75E ASP* 2.9 26.7 + - - +
78E LYS* 4.8 5.2 - - + +
79E GLY* 3.7 13.1 + - - +
82E PHE* 3.6 35.4 - - + -
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Residues in contact with PHE 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 GLY 2.7 18.5 + - - +
69E ARG* 3.1 8.2 + - - +
71E LYS* 1.3 73.1 - - - +
73E ASN* 1.3 71.5 + - - +
75E ASP 3.9 1.3 - - - -
76E PRO* 2.9 59.2 - - + +
79E GLY* 3.5 9.1 - - - -
80E ILE* 3.7 24.7 - - + -
83E LEU* 5.6 0.2 - - + -
99E PHE* 5.0 2.7 - + + -
100E LEU* 3.4 29.6 - - + -
106E LEU* 3.6 22.7 - - + -
107E ASN 4.7 0.2 - - - -
110E ALA* 3.7 26.9 - - + -
111E ILE* 3.9 18.8 - - + -
114E TYR* 4.1 10.8 - + + -
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Residues in contact with ASN 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 ARG 3.0 16.7 + - - -
70E LYS* 3.1 15.5 + - + +
72E PHE* 1.3 84.8 - - - +
74E MET* 1.3 76.5 + - + +
76E PRO* 4.6 1.2 - - - +
105E GLY 2.9 24.4 + - - -
106E LEU* 3.5 5.0 - - - -
107E ASN* 2.7 39.6 + - + +
110E ALA* 4.1 14.8 - - - +
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Residues in contact with MET 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 LYS* 3.5 14.6 - - + +
71E LYS* 3.7 9.2 - - - +
72E PHE 3.1 0.2 - - - -
73E ASN* 1.3 96.8 - - + +
75E ASP* 1.3 62.8 + - + +
76E PRO* 4.1 2.4 - - - +
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Residues in contact with ASP 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 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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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