Contacts of the helix formed by residues 80 - 94 (chain E) in PDB entry 1MDU
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 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E ARG* 5.5 2.4 - - - +
70E LYS* 4.8 10.3 - - - +
71E TYR 5.1 1.5 - - - +
72E PRO* 3.2 21.3 + - + +
78E ILE* 4.4 0.9 - - - -
79E THR* 1.3 79.9 - - - +
81E TRP* 1.3 56.6 + - - +
82E ASP* 3.3 8.5 + - - +
83E ASP* 2.7 40.7 + - - +
84E MET* 3.1 25.3 + - - +
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Residues in contact with TRP 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ILE* 3.6 41.5 + - + -
79E THR* 4.4 9.1 + - - +
80E ASN* 1.3 70.7 + - - +
82E ASP* 1.3 62.5 + - - +
84E MET* 3.6 4.0 - - + +
85E GLU* 3.0 27.8 + - - +
88E TRP* 4.0 9.6 - + - -
117E ASN* 3.5 48.1 - - + +
120E LYS* 3.7 46.6 - - + +
121E MET* 3.6 28.9 - - + -
124E ILE* 3.8 25.9 - - + +
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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
----------------------------------------------------------
80E ASN* 3.3 6.4 + - - +
81E TRP* 1.3 80.7 - - - +
83E ASP* 1.3 65.2 + - - +
85E GLU* 3.4 18.8 - - - +
86E LYS* 3.0 32.8 + - - +
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Residues in contact with ASP 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E VAL* 3.7 26.1 - - + +
39E ARG* 4.8 7.1 + - - -
70E LYS* 4.3 19.0 - - + +
72E PRO* 4.1 11.2 - - + +
80E ASN* 2.7 36.8 + - - +
82E ASP* 1.3 74.9 - - - +
84E MET* 1.3 65.8 + - - +
86E LYS* 2.7 43.1 + - - +
87E ILE* 2.9 24.1 + - - +
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Residues in contact with MET 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASN* 3.6 22.9 - - + +
19E VAL* 5.7 0.2 - - + -
35E SER* 6.1 0.4 - - - -
72E PRO* 3.8 11.8 - - + +
73E ILE* 3.7 30.3 - - + -
78E ILE* 3.8 20.6 - - + -
80E ASN 3.1 18.8 + - - +
81E TRP* 3.6 7.2 - - - +
82E ASP 3.2 0.2 - - - -
83E ASP* 1.3 77.8 - - - +
85E GLU* 1.3 56.0 + - - +
87E ILE* 2.9 26.6 + - + +
88E TRP* 2.9 80.6 + - + +
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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 TRP 3.0 13.2 + - - +
82E ASP* 3.4 23.4 - - - +
84E MET* 1.3 77.1 - - - +
86E LYS* 1.3 51.5 + - + +
88E TRP* 3.2 10.2 + - - -
89E HIS* 2.8 35.7 + - - +
124E ILE* 3.8 30.2 - - + +
128E THR* 3.5 34.7 + - + +
129E PHE* 3.4 9.1 - - + -
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Residues in contact with LYS 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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37E VAL* 4.1 12.4 - - + +
39E ARG* 5.6 8.7 - - - +
54E SER* 4.1 16.4 + - - +
56E VAL* 4.2 16.8 - - + +
82E ASP* 3.0 21.8 - - - +
83E ASP* 2.7 35.2 + - - +
85E GLU* 1.3 74.3 - - + +
87E ILE* 1.3 60.3 + - - +
89E HIS* 3.7 7.8 - - - +
90E HIS* 2.8 31.5 + - - +
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Residues in contact with ILE 87 (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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14E ASN* 4.2 1.6 - - - +
19E VAL* 3.7 25.4 - - + -
33E PHE* 4.3 4.1 - - + -
34E PRO 4.4 1.1 - - - +
35E SER* 3.9 7.0 - - - -
36E ILE 3.8 25.6 - - - +
37E VAL* 4.1 4.5 - - + -
56E VAL* 3.3 27.8 - - + -
72E PRO* 3.9 20.0 - - + -
83E ASP 2.9 16.4 + - - +
84E MET* 2.9 28.3 + - + +
86E LYS* 1.3 77.3 - - - +
88E TRP* 1.3 57.3 + - - +
90E HIS* 3.3 2.4 + - - +
91E THR* 2.8 36.6 + - - +
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Residues in contact with TRP 88 (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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12E CYS* 4.1 11.2 - - - -
14E ASN* 3.0 31.3 + - - -
78E ILE* 3.8 22.0 - - + -
81E TRP* 4.0 14.8 - + - -
84E MET* 2.9 55.2 + - + +
85E GLU* 3.6 6.5 - - - +
87E ILE* 1.3 78.3 - - + +
89E HIS* 1.3 62.8 + - - +
91E THR* 3.0 6.8 + - - -
92E PHE* 2.9 36.6 + + + -
107E LEU* 4.1 8.5 - - + +
121E MET* 4.4 22.0 - - + -
124E ILE* 4.1 28.9 - - + -
125E MET* 3.4 30.5 - - + -
129E PHE* 3.8 12.1 - - + -
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Residues in contact with HIS 89 (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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85E GLU 2.8 21.2 + - - +
86E LYS* 3.7 9.0 - - - +
88E TRP* 1.3 72.3 - - - +
90E HIS* 1.3 66.2 + - + +
92E PHE* 4.5 0.4 - - - -
93E TYR* 3.0 61.9 + + + +
94E ASN* 5.1 3.1 - - - -
129E PHE* 3.6 20.0 - - + -
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Residues in contact with HIS 90 (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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33E PHE* 3.8 19.8 - + - -
56E VAL* 3.7 47.2 + - + +
57E GLY* 4.9 1.2 - - - -
58E ASP 5.7 0.4 + - - -
59E GLU* 5.0 9.0 - - + -
86E LYS 2.8 18.5 + - - +
87E ILE 3.7 3.4 - - - +
89E HIS* 1.3 78.9 - - + +
91E THR* 1.3 62.1 + - - +
94E ASN* 2.9 58.0 + - + -
95E GLU* 3.3 29.9 + - + +
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Residues in contact with THR 91 (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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12E CYS* 4.5 13.5 - - + -
19E VAL* 3.9 6.6 - - + +
21E ALA* 3.6 31.4 - - + -
33E PHE* 3.2 25.4 - - + -
87E ILE* 2.8 24.7 + - - +
88E TRP* 3.0 12.1 + - - -
90E HIS* 1.3 79.0 - - - +
92E PHE* 1.3 64.6 + - + +
95E GLU* 3.5 4.7 - - + +
96E LEU* 3.0 36.3 + - + +
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Residues in contact with PHE 92 (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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10E LEU* 3.8 31.4 - - + -
12E CYS* 5.9 4.0 - - + -
88E TRP* 2.9 31.1 + + + +
89E HIS* 4.0 2.0 - - - +
91E THR* 1.3 85.6 - - + +
93E TYR* 1.3 61.7 + + + +
96E LEU* 3.6 6.1 - - + -
97E ARG 2.8 26.5 + - - -
98E VAL* 2.9 17.5 + - + +
100E PRO* 3.3 37.0 - - + -
105E THR* 4.3 16.2 - - + -
107E LEU* 6.2 0.2 - - + -
125E MET* 4.2 21.1 - - + -
129E PHE* 3.7 36.3 - + + -
131E VAL* 5.0 1.8 - - + -
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Residues in contact with TYR 93 (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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89E HIS* 3.0 66.9 + + + +
92E PHE* 1.3 81.5 - - + +
94E ASN* 1.3 70.8 + - - +
97E ARG* 3.1 27.9 - - - +
98E VAL 4.4 11.7 - - - +
99E ALA* 5.7 1.1 - - - -
100E PRO* 4.4 24.0 - - + +
101E GLU* 4.9 7.3 + - - -
129E PHE* 5.0 5.6 - + - -
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Residues in contact with ASN 94 (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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89E HIS* 5.1 4.2 - - - -
90E HIS* 2.9 47.8 + - + +
93E TYR* 1.3 84.2 - - - +
95E GLU* 1.3 62.4 + - + +
97E ARG* 3.1 31.0 + - - +
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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