Contacts of the helix formed by residues 34 - 46 (chain E) in PDB entry 3J8C
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 GLU 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E SER* 5.5 1.0 - - - -
31E ILE* 3.7 22.7 + - + +
32E TYR 3.4 7.0 - - - +
33E ASN* 1.3 78.2 - - - +
35E LYS* 1.3 64.5 + - - +
36E GLU* 3.5 5.7 + - + +
37E LEU* 4.2 12.3 + - + +
38E LEU* 4.4 9.2 + - - +
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Residues in contact with LYS 35 (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 ASN 3.3 4.2 + - - +
34E GLU* 1.3 72.6 - - - +
36E GLU* 1.3 61.0 + - - +
37E LEU 3.3 0.2 - - - -
38E LEU* 3.1 5.5 + - - +
39E GLN* 2.8 37.1 + - + +
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Residues in contact with GLU 36 (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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6E LEU* 4.5 22.7 - - + +
23E LEU* 5.5 0.9 - - - +
34E GLU* 3.5 4.0 - - + +
35E LYS* 1.3 78.8 - - - +
37E LEU* 1.3 63.0 + - - +
39E GLN* 4.8 3.6 - - - -
40E GLY* 3.4 19.2 + - - -
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Residues in contact with LEU 37 (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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23E LEU* 3.2 24.1 - - - +
24E GLU* 5.2 0.2 - - - -
26E LEU* 4.1 8.3 - - + -
27E SER* 2.8 43.9 - - - +
34E GLU* 4.2 8.5 + - + +
35E LYS 3.3 1.0 - - - -
36E GLU* 1.3 79.3 - - - +
38E LEU* 1.3 56.3 + - - +
41E LYS* 3.1 27.2 + - - +
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Residues in contact with LEU 38 (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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27E SER* 5.1 5.4 - - - -
32E TYR 5.8 2.2 - - - +
34E GLU 4.4 8.0 + - - +
35E LYS* 3.1 7.2 + - - +
37E LEU* 1.3 80.1 - - + +
39E GLN* 1.3 60.1 + - - +
40E GLY 3.4 0.4 - - - -
41E LYS* 3.9 3.2 - - - +
42E LEU* 2.9 32.3 + - - +
61E LEU 3.3 27.6 - - - +
62E TYR* 4.9 4.3 - - - -
63E SER 5.1 2.3 + - - -
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Residues in contact with GLN 39 (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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35E LYS* 2.8 26.4 + - + +
36E GLU* 4.5 3.1 - - - +
38E LEU* 1.3 72.7 - - - +
40E GLY* 1.3 58.9 + - - +
42E LEU* 3.4 5.2 - - - +
43E ASP* 2.9 30.0 + - - +
63E SER* 5.9 2.0 - - - -
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Residues in contact with GLY 40 (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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23E LEU* 5.2 2.5 - - - -
36E GLU 3.4 13.4 + - - -
39E GLN* 1.3 77.8 - - - +
41E LYS* 1.3 59.9 + - - +
43E ASP* 3.5 5.8 + - - +
44E LEU* 2.8 32.3 + - - +
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Residues in contact with LYS 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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19E VAL 5.6 0.4 - - - -
20E PHE* 4.7 13.8 - - + +
23E LEU* 3.8 18.8 - - + +
24E GLU* 4.8 7.2 - - + +
37E LEU 3.1 23.0 + - - +
38E LEU* 3.9 3.8 - - - +
39E GLN 3.3 0.4 - - - -
40E GLY* 1.3 72.8 - - - +
42E LEU* 1.3 65.3 + - - +
44E LEU* 3.8 4.6 - - - +
45E LEU* 2.8 27.6 + - - +
57E VAL* 5.7 0.9 - - - -
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Residues in contact with LEU 42 (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 LEU 2.9 20.1 + - - +
39E GLN* 3.4 6.1 - - - +
41E LYS* 1.3 77.6 - - - +
43E ASP* 1.3 65.5 + - - +
45E LEU* 3.6 2.5 - - - +
46E SER* 3.0 24.6 + - - -
57E VAL* 4.4 17.4 - - + +
63E SER* 3.4 37.2 - - - +
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Residues in contact with ASP 43 (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 GLN 2.9 16.6 + - - +
40E GLY* 4.0 5.4 - - - +
42E LEU* 1.3 78.3 - - - +
44E LEU* 1.3 62.4 + - - +
46E SER* 3.5 14.1 + - - -
47E ASP* 3.6 9.9 + - - +
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Residues in contact with LEU 44 (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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19E VAL* 5.2 13.9 - - + +
20E PHE* 5.4 7.4 - - + -
40E GLY 2.8 20.6 + - - +
41E LYS* 3.8 4.9 - - - +
42E LEU 3.1 0.2 - - - -
43E ASP* 1.3 74.6 - - - +
45E LEU* 1.3 66.4 - - - +
47E ASP* 3.0 23.5 + - - +
48E THR* 4.6 2.9 - - - -
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Residues in contact with LEU 45 (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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20E PHE* 5.7 6.8 - - + +
41E LYS 2.8 17.9 + - - +
42E LEU* 3.6 5.2 - - - +
44E LEU* 1.3 71.5 - - - +
46E SER* 1.3 56.4 + - - +
47E ASP 2.9 10.4 + - - -
48E THR* 3.0 27.6 + - - +
50E MET 4.9 6.5 - - - +
53E PHE* 4.8 11.9 - - + +
54E ALA* 4.8 24.4 - - + +
57E VAL* 5.4 3.1 - - + -
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Residues in contact with SER 46 (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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42E LEU 3.0 16.2 + - - -
43E ASP* 3.8 9.6 - - - -
44E LEU 3.2 0.4 - - - -
45E LEU* 1.3 75.6 - - - +
47E ASP* 1.3 58.0 + - - +
48E THR 3.2 5.3 + - - +
54E ALA* 6.1 2.9 - - - -
69E ALA* 5.8 7.6 - - - -
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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