Contacts of the helix formed by residues 36 - 53 (chain E) in PDB entry 1O94
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 36 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LYS* 2.9 16.9 + - + +
10E THR* 3.6 20.5 + - + +
34E ASP 3.5 2.2 + - - -
35E LEU* 1.3 72.3 - - - +
37E GLU* 1.3 73.1 + - - +
38E TRP* 3.6 14.3 - - - +
39E ASP* 2.9 33.1 + - - +
40E ASP* 3.5 5.2 - - - +
121E GLN 2.9 23.0 + - - -
122E SER* 3.5 5.3 - - - +
123E SER* 2.9 27.2 + - - -
1237E AMP 3.0 23.2 + - - -
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU 3.4 3.9 + - - -
36E ASN* 1.3 77.2 + - - +
38E TRP* 1.3 78.2 + - + +
39E ASP 3.3 0.5 + - - -
40E ASP* 3.3 22.0 + - - +
41E PHE* 3.4 21.5 - - + -
123E SER* 4.7 9.1 + - - -
184E LEU* 3.9 27.7 - - + +
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Residues in contact with TRP 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ASN* 3.2 18.7 - - - +
37E GLU* 1.3 92.5 - - + +
39E ASP* 1.3 63.4 + - - +
40E ASP 3.3 0.2 - - - -
41E PHE* 3.2 8.1 + - - +
42E SER* 3.2 20.1 + - - -
119E GLY* 3.8 14.9 - - - -
120E VAL* 3.6 12.2 - - + +
121E GLN* 3.3 48.0 - - + -
123E SER* 3.9 28.9 - - - -
182E ILE 3.3 24.7 - - - +
183E GLN* 2.9 26.2 - - - +
184E LEU* 3.4 38.2 - - + +
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Residues in contact with ASP 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 5.0 0.2 - - - +
6E ALA 3.4 10.7 - - - +
7E VAL* 3.6 17.7 - - + +
8E LYS 2.6 29.5 + - - +
35E LEU* 3.7 17.0 - - + -
36E ASN* 2.9 25.3 + - - +
38E TRP* 1.3 74.5 - - - +
40E ASP* 1.3 66.8 + - - +
42E SER* 3.3 6.5 + - - -
43E LEU* 3.0 27.8 + - - +
76E CYS* 6.4 0.2 - - - -
119E GLY 3.9 4.3 + - - -
1237E AMP 2.6 26.0 + - - -
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Residues in contact with ASP 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 3.8 17.6 - - - +
36E ASN 3.5 9.7 - - - +
37E GLU* 3.3 21.3 + - - +
39E ASP* 1.3 76.8 - - - +
41E PHE* 1.3 60.2 + - + +
43E LEU* 4.1 2.7 - - - +
44E GLU* 3.2 22.0 + - - +
79E LYS* 3.0 35.9 + - - +
189E PRO* 3.6 28.4 - - + +
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Residues in contact with PHE 41 (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 GLU* 3.4 28.0 - - + -
38E TRP 3.2 7.2 + - - +
39E ASP 3.1 0.6 - - - -
40E ASP* 1.3 79.9 - - + +
42E SER* 1.3 64.9 + - - +
45E GLU* 3.1 7.4 + - - +
182E ILE* 4.2 6.7 - - + -
183E GLN 4.3 3.4 - - - +
184E LEU* 3.6 30.3 - - + -
185E GLY* 3.3 25.8 - - - -
186E ILE* 4.0 11.1 - - + +
187E ASN* 3.0 65.1 + - - -
189E PRO* 3.6 16.4 - - + -
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Residues in contact with SER 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 3.2 17.4 - - - +
6E ALA 4.8 0.2 + - - -
38E TRP 3.2 8.1 + - - -
39E ASP* 3.3 18.2 + - - -
41E PHE* 1.3 73.3 - - - +
43E LEU* 1.3 67.0 + - - +
45E GLU* 3.3 2.2 + - - +
46E ALA* 3.2 17.2 + - - +
117E PHE* 3.5 24.7 - - - -
118E ALA 4.4 9.6 - - - -
182E ILE* 3.7 33.6 - - - +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 4.3 12.3 - - + -
35E LEU* 5.6 0.7 - - + -
39E ASP 3.0 17.1 + - - +
40E ASP 4.1 2.2 - - - +
42E SER* 1.3 77.1 + - - +
44E GLU* 1.3 66.3 + - - +
46E ALA* 3.2 2.8 + - - +
47E MET* 3.0 32.1 + - + +
59E VAL* 3.8 27.1 - - + -
61E VAL* 4.2 8.7 - - + -
76E CYS* 3.7 45.8 - - + +
79E LYS* 3.8 25.1 - - + +
81E ALA* 4.1 18.4 - - + +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ASP 3.2 17.4 + - - +
42E SER 3.4 0.2 - - - -
43E LEU* 1.3 75.6 - - - +
45E GLU* 1.3 57.9 + - - +
47E MET* 3.1 6.9 + - - +
48E LYS* 2.8 37.6 + - + +
79E LYS 5.1 0.3 - - - +
187E ASN* 3.4 34.1 - - + +
188E LYS 3.7 15.2 - - - +
189E PRO* 3.5 9.3 - - + +
190E ARG* 2.9 59.9 + - - +
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE 3.1 12.7 + - - +
42E SER* 3.6 10.1 - - - +
43E LEU 3.1 0.2 - - - -
44E GLU* 1.3 75.6 - - - +
46E ALA* 1.3 62.6 + - - +
48E LYS* 2.8 42.3 + - - +
49E ILE* 3.1 31.1 + - + +
117E PHE* 4.1 9.2 - - + -
149E LEU* 3.8 41.1 + - + +
182E ILE* 5.1 4.7 - - + -
186E ILE* 3.7 27.2 - - + +
187E ASN* 2.9 16.8 + - - +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ILE* 3.8 32.5 - - + +
5E VAL* 4.0 6.7 - - + -
42E SER 3.2 9.8 + - - +
43E LEU 3.2 8.6 + - - +
45E GLU* 1.3 76.4 - - - +
47E MET* 1.3 58.5 + - - +
49E ILE* 3.2 4.5 + - - +
50E LYS* 2.9 28.6 + - - +
59E VAL* 3.9 25.9 - - + +
117E PHE* 3.8 7.7 - - + -
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Residues in contact with MET 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.0 19.6 + - + +
44E GLU* 3.1 9.2 + - - +
46E ALA* 1.3 72.0 - - - +
48E LYS* 1.3 60.9 + - - +
50E LYS* 3.8 21.1 - - + -
51E GLU* 2.9 57.3 + - - +
59E VAL* 4.2 20.6 - - - -
79E LYS 3.9 14.6 - - - +
80E GLY* 3.4 39.5 - - - +
81E ALA 3.9 2.2 - - - -
190E ARG* 3.5 22.0 - - - +
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Residues in contact with LYS 48 (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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44E GLU* 2.8 31.8 + - + +
45E GLU* 2.8 43.2 + - - +
46E ALA 3.3 0.2 - - - -
47E MET* 1.3 73.1 - - - +
49E ILE* 1.3 61.4 + - + +
51E GLU* 3.8 5.6 - - - +
52E SER* 2.9 33.4 + - - -
186E ILE* 3.9 9.3 + - - +
187E ASN* 3.9 19.1 - - + +
190E ARG* 4.7 0.6 - - - +
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Residues in contact with ILE 49 (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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1E MET* 5.7 0.2 - - - -
3E ILE* 3.6 23.1 - - + -
45E GLU* 3.1 20.6 + - + +
46E ALA 3.6 4.9 - - - +
48E LYS* 1.3 76.3 - - + +
50E LYS* 1.3 64.4 + - - +
52E SER* 3.2 15.7 + - - -
53E SER* 3.4 12.5 + - - -
57E VAL* 4.9 2.0 - - + -
117E PHE* 3.8 27.4 - - + -
149E LEU* 3.9 16.4 - - + -
151E TYR* 4.2 28.3 - - + +
153E PRO* 3.8 30.8 - - + +
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Residues in contact with LYS 50 (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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46E ALA 2.9 20.6 + - - +
47E MET* 3.6 30.3 - - + +
49E ILE* 1.3 74.7 - - - +
51E GLU* 1.3 65.5 + - + +
53E SER* 3.4 19.8 + - - +
55E THR 4.4 2.4 - - - +
56E ASP* 5.4 4.0 + - - -
57E VAL* 2.8 45.6 + - + +
59E VAL* 4.1 8.7 - - + -
80E GLY 5.1 1.3 - - - -
82E ASP* 2.5 45.7 + - - +
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Residues in contact with GLU 51 (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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47E MET* 2.9 35.0 + - + +
48E LYS* 4.2 4.3 + - - +
50E LYS* 1.3 79.7 - - + +
52E SER* 1.3 59.4 + - - +
53E SER 3.2 3.6 + - - +
190E ARG* 2.7 44.7 + - - -
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Residues in contact with SER 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LYS 2.9 18.4 + - - -
49E ILE* 3.2 7.5 + - - -
51E GLU* 1.3 77.3 - - - +
53E SER* 1.3 59.1 + - - +
54E ASP 3.8 1.7 + - - -
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Residues in contact with SER 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE 3.6 13.9 - - - -
50E LYS 3.5 10.5 - - - +
51E GLU 3.2 3.3 - - - +
52E SER* 1.3 78.4 - - - +
54E ASP* 1.3 57.6 + - - +
55E THR* 2.6 53.1 + - - +
57E VAL* 4.1 2.4 - - - +
153E PRO* 3.8 23.8 - - - +
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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
------------------------------------------------------------
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