Contacts of the helix formed by residues 67 - 81 (chain K) in PDB entry 2EHO
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 67 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148H ARG* 3.2 29.7 + - - -
64K GLU 4.6 3.1 - - - +
65K TRP 2.7 12.1 + - - +
66K MSE 1.3 74.4 - - - +
68K VAL* 1.3 71.4 + - - +
69K GLU* 3.7 10.1 + - - +
70K LYS* 3.0 34.9 + - + +
71K LEU* 2.8 27.1 + - - +
108K PRO* 6.0 3.1 - - + +
109K LYS* 6.2 0.7 - - - +
113K ILE* 4.1 1.6 - - - -
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Residues in contact with VAL 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ASP* 1.3 77.1 + - - +
69K GLU* 1.3 59.8 + - - +
71K LEU 3.1 0.2 + - - -
72K GLU* 2.8 48.5 + - - +
109K LYS* 4.1 25.8 - - + +
112K GLU* 3.0 40.8 - - + +
113K ILE* 3.5 23.2 - - + +
116K LEU* 3.4 18.1 - - + +
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Residues in contact with GLU 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ARG* 5.0 5.2 - - - -
148H ARG* 3.5 28.2 + - - +
151H ASP* 4.0 18.3 - - - +
67K ASP* 3.3 13.5 + - - +
68K VAL* 1.3 79.2 - - - +
70K LYS* 1.3 63.6 + - + +
72K GLU* 3.5 15.0 + - - +
73K LYS* 3.2 40.6 + - + +
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Residues in contact with LYS 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ALA 5.4 0.6 + - - -
103H ASP* 4.3 10.9 + - - +
105H ASN* 5.5 3.7 - - - +
148H ARG* 4.9 9.6 - - - +
64K GLU* 2.9 57.7 + - - +
65K TRP* 4.3 9.4 - - - +
67K ASP* 3.0 22.4 + - + +
69K GLU* 1.3 79.3 - - + +
71K LEU* 1.3 60.6 + - - +
73K LYS* 3.5 9.5 + - - +
74K MSE 2.9 33.9 + - + +
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K TRP* 3.6 33.2 - - + +
66K MSE 4.5 1.8 - - - -
67K ASP 2.8 30.2 + - - +
68K VAL 3.6 2.7 - - - +
70K LYS* 1.3 69.1 - - - +
72K GLU* 1.3 67.4 + - - +
74K MSE 2.9 19.6 + - + +
75K ARG* 2.8 23.6 + - - +
88K PRO* 5.2 1.3 - - + -
113K ILE* 3.5 33.7 - - + -
116K LEU* 3.9 21.8 - - + -
117K VAL* 3.9 17.7 - - + -
120K MSE 5.0 9.9 - - + +
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Residues in contact with GLU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL* 2.8 42.6 + - - +
69K GLU* 3.7 13.5 - - - +
71K LEU* 1.3 72.3 - - - +
73K LYS* 1.3 62.3 + - + +
75K ARG* 3.1 26.2 - - + +
76K ASP* 3.1 15.6 + - - +
112K GLU* 3.8 6.6 - - - +
116K LEU* 3.4 25.6 - - + +
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Residues in contact with LYS 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ARG* 4.9 15.2 - - - +
69K GLU* 3.2 29.4 + - + +
70K LYS* 3.8 11.7 - - + +
71K LEU 3.2 0.4 - - - -
72K GLU* 1.3 79.2 - - + +
74K MSE 1.3 58.7 + - + +
76K ASP* 3.7 6.9 + - - +
77K HIS* 3.0 28.1 + - - +
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Residues in contact with MSE 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K TRP* 5.2 5.4 - - + +
70K LYS* 2.9 27.1 - - - +
71K LEU* 2.9 20.5 + - + +
73K LYS* 1.3 76.0 - - + +
75K ARG* 1.3 67.0 + - - +
76K ASP 3.1 1.3 - - - -
77K HIS* 3.3 5.9 + - - +
78K GLU* 2.9 26.0 + - - +
85K THR* 5.0 1.0 + - - -
86K PRO 4.6 10.3 - - - +
87K MSE 5.2 0.2 - - - -
88K PRO* 3.2 46.0 - - + -
120K MSE 3.8 19.5 - - + +
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Residues in contact with ARG 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K LEU 2.8 14.4 + - - +
72K GLU* 3.1 18.4 - - - +
74K MSE 1.3 73.6 - - - +
76K ASP* 1.3 74.5 + - - +
78K GLU* 3.4 2.8 + - - +
79K ARG* 2.8 33.9 + - - +
115K THR* 5.6 1.4 - - - +
116K LEU* 4.4 24.6 + - + +
119K ASP* 2.7 57.8 + - - +
120K MSE 4.0 24.8 - - + +
123K THR* 3.5 20.4 + - - +
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Residues in contact with ASP 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K GLU* 3.1 22.4 + - - +
73K LYS* 3.9 6.4 - - - +
74K MSE 3.1 0.6 - - - -
75K ARG* 1.3 90.7 + - - +
77K HIS* 1.3 66.8 + - - +
78K GLU 3.0 1.3 - - - -
79K ARG* 2.8 15.7 + - - +
80K LYS* 2.6 24.7 + - - +
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Residues in contact with HIS 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K LYS 3.0 20.0 + - - +
74K MSE 3.7 6.3 - - - +
76K ASP* 1.3 74.6 - - - +
78K GLU* 1.3 56.9 + - - +
80K LYS* 3.0 33.6 + - - +
81K GLU* 2.9 51.0 + - + +
85K THR* 3.5 28.9 - - + +
86K PRO* 5.9 1.6 - - + +
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Residues in contact with GLU 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K MSE 2.9 16.9 + - - +
75K ARG 3.5 4.7 - - - +
77K HIS* 1.3 75.8 - - - +
79K ARG* 1.3 60.8 + - - +
80K LYS 3.0 5.8 + - - -
81K GLU 3.6 2.1 + - - +
84K PHE* 3.3 15.1 - - - +
85K THR* 2.4 43.5 + - - +
120K MSE 4.1 13.9 - - - +
123K THR* 4.3 7.0 - - - +
124K ARG* 3.3 37.5 + - + -
127K LYS* 2.7 58.4 + - + +
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Residues in contact with ARG 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K ARG* 2.8 23.2 + - - +
76K ASP* 3.4 15.2 + - - +
78K GLU* 1.3 75.8 - - - +
80K LYS* 1.3 64.2 + - - +
81K GLU 4.0 2.1 - - - +
123K THR* 5.0 21.3 + - + +
127K LYS* 5.5 2.7 - - - -
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Residues in contact with LYS 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K ASP 2.6 11.6 + - - +
77K HIS* 3.0 40.0 + - - +
78K GLU 3.0 0.6 - - - -
79K ARG* 1.3 77.9 - - - +
81K GLU* 1.3 83.8 + - - +
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Residues in contact with GLU 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K HIS* 2.9 29.6 + - + +
78K GLU 3.6 1.4 + - - +
79K ARG 4.0 2.4 - - - +
80K LYS* 1.3 103.0 + - + +
82K GLU* 1.3 59.8 + - - +
83K THR* 3.1 39.7 - - - +
85K THR* 3.7 22.9 - - + -
127K LYS* 3.3 17.4 + - - +
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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