Contacts of the helix formed by residues 66 - 73 (chain E) in PDB entry 1R4N
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 SER 66 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLN* 2.5 25.3 + - - +
265B LEU* 4.1 10.3 - - - -
266B GLU* 3.9 13.7 + - - +
64E GLN 3.2 4.1 + - - -
65E VAL* 1.3 78.2 - - - +
67E GLY* 1.3 64.2 + - - +
68E GLU* 3.1 22.0 - - - +
69E ASP* 2.8 37.5 + - - +
70E ALA* 3.1 5.9 + - - +
81E ILE* 4.3 2.0 - - - +
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Residues in contact with GLY 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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262B GLN* 2.3 38.0 + - - +
66E SER* 1.3 65.7 - - - +
68E GLU* 1.3 56.1 + - - -
69E ASP 2.9 5.2 + - - -
70E ALA* 3.1 3.3 + - - +
71E GLY* 3.0 16.3 + - - -
81E ILE* 3.7 13.5 - - - +
13F TRP* 3.4 21.1 + - - -
14F GLU 3.7 7.9 - - - -
15F GLY 4.0 3.4 - - - -
16F ARG* 4.0 0.5 - - - -
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Residues in contact with GLU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLN* 3.7 2.0 - - - +
266B GLU* 3.3 29.9 - - - +
66E SER* 3.1 18.6 + - - +
67E GLY* 1.3 74.7 - - - +
69E ASP* 1.3 64.3 + - - +
71E GLY* 3.5 5.7 + - - -
72E ASN* 3.6 7.4 + - - -
445E VAL* 6.1 0.7 - - - +
15F GLY 3.0 26.1 + - - +
16F ARG 4.3 2.1 - - - +
18F ASN* 3.8 20.3 + - + +
19F HIS* 3.3 40.3 + - + +
22F LYS* 4.3 8.3 + - - -
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Residues in contact with ASP 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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39E THR* 4.8 8.5 - - - +
64E GLN 3.9 4.9 - - - +
65E VAL* 3.9 9.8 - - + -
66E SER* 2.8 39.7 + - - +
68E GLU* 1.3 79.9 - - - +
70E ALA* 1.3 56.1 + - - +
71E GLY 2.7 13.7 + - - -
72E ASN* 2.8 28.5 + - - +
73E ASN* 3.2 9.8 + - + +
76E LEU* 4.3 8.1 - - + -
85E ARG* 3.5 33.6 + - - -
489E GLU* 5.4 1.6 - - - +
19F HIS* 5.6 2.6 + - - -
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 4.3 3.9 - - + +
66E SER 3.1 1.6 + - - +
67E GLY 3.1 5.0 + - - +
69E ASP* 1.3 78.4 - - - +
71E GLY* 1.3 60.0 + - - +
72E ASN 3.5 0.4 + - - -
73E ASN 3.9 7.0 - - - +
76E LEU* 3.5 26.6 - - - +
77E GLN 3.8 24.5 - - - +
81E ILE* 4.0 15.3 - - + -
13F TRP* 3.6 27.8 - - + -
16F ARG* 5.3 0.2 + - - -
69F LEU* 5.4 2.4 - - - +
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Residues in contact with GLY 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 GLY 3.0 9.4 + - - -
68E GLU 3.5 2.4 + - - -
69E ASP 2.7 3.8 + - - -
70E ALA* 1.3 80.4 - - - +
72E ASN* 1.3 56.9 + - - +
73E ASN 3.6 0.2 - - - -
16F ARG* 3.4 42.9 + - - +
17F TRP* 4.9 6.1 - - - -
19F HIS* 6.0 0.2 - - - -
69F LEU* 4.1 23.0 - - - +
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Residues in contact with ASN 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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40E ALA* 3.5 17.0 - - - +
68E GLU 3.6 7.7 + - - -
69E ASP* 2.8 25.9 + - - +
71E GLY* 1.3 78.2 - - - +
73E ASN* 1.3 64.7 + - - +
489E GLU* 3.2 23.7 + - - +
491E HIS* 2.8 32.6 + - + +
19F HIS* 3.0 43.0 + - + -
69F LEU* 4.2 10.1 - - - +
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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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38E ALA 3.9 4.2 + - - -
39E THR* 3.3 33.9 + - - +
40E ALA* 3.6 2.1 - - - +
43E THR* 3.2 24.2 + - - +
69E ASP* 3.2 15.9 + - - +
70E ALA 3.9 3.8 - - - +
71E GLY 3.6 1.4 - - - -
72E ASN* 1.3 81.6 - - - +
74E PHE* 1.3 59.7 + - - +
75E PHE* 2.9 29.8 + - - +
76E LEU* 3.5 46.1 - - + +
491E HIS* 4.7 1.1 - - - -
69F LEU* 4.1 7.3 - - - +
114F ARG* 5.8 0.2 - - - +
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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