Contacts of the helix formed by residues 34 - 43 (chain E) in PDB entry 4I6U
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 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ALA* 4.0 0.4 - - - -
33E LEU* 1.3 77.3 - - - +
35E ARG* 1.3 73.7 + - - +
36E THR* 3.4 20.0 + - - +
37E PHE* 3.1 25.6 + - + +
38E ILE* 3.1 13.9 + - - +
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Residues in contact with ARG 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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24E GLN* 4.1 12.6 + - + +
25E GLU* 3.2 51.4 - - + +
28E ALA* 3.8 13.1 - - + +
33E LEU 3.7 2.4 + - - -
34E ASP* 1.3 76.5 + - - +
36E THR* 1.3 79.1 + - + +
38E ILE* 3.3 4.9 + - - +
39E SER* 2.9 42.6 + - - -
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Residues in contact with THR 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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34E ASP* 3.4 20.3 + - - +
35E ARG* 1.3 100.8 - - + +
37E PHE* 1.3 59.2 + - - +
39E SER* 3.6 7.0 - - - -
40E GLY* 2.8 25.5 + - - -
43E ARG* 5.0 2.3 + - - -
46E ARG* 4.4 9.4 + - - -
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Residues in contact with PHE 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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33E LEU* 4.1 28.7 - - + -
34E ASP* 3.1 21.8 + - + +
36E THR* 1.3 78.8 + - - +
38E ILE* 1.3 66.8 + - - +
40E GLY* 3.0 2.3 + - - -
41E ILE* 3.0 51.9 + - + +
46E ARG* 3.5 43.0 - - + +
47E ASN 3.8 22.2 - - - -
48E LEU* 4.5 3.6 - - - -
49E THR 5.3 0.2 - - - -
52E SER* 4.0 29.2 - - - -
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Residues in contact with ILE 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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13E ILE* 5.8 0.9 - - + -
24E GLN* 4.1 26.9 - - + +
27E LEU* 4.1 27.6 - - + -
28E ALA* 4.0 24.0 - - + +
31E SER* 5.0 0.4 - - - -
33E LEU* 4.2 16.2 - - + -
34E ASP 3.1 14.9 + - - +
35E ARG 3.3 6.0 + - - +
37E PHE* 1.3 78.9 - - + +
39E SER* 1.3 62.7 + - - +
41E ILE* 3.4 8.6 + - + +
42E GLU* 3.1 31.2 + - + +
56E ILE* 4.0 33.7 - - + -
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Residues in contact with SER 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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24E GLN* 3.5 31.4 + - - +
35E ARG* 2.9 26.3 + - - -
36E THR* 3.6 6.3 - - - -
38E ILE* 1.3 76.8 - - - +
40E GLY* 1.3 63.6 + - - +
42E GLU* 3.3 2.4 + - - +
43E ARG* 3.1 43.5 + - - +
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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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36E THR 2.8 16.0 + - - -
37E PHE 3.0 4.2 + - - -
39E SER* 1.3 77.9 + - - +
41E ILE* 1.3 59.6 + - - +
43E ARG* 3.4 9.1 + - - +
44E ASN 3.2 2.4 + - - -
45E SER* 2.8 41.3 + - - -
46E ARG* 3.7 18.4 - - - -
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Residues in contact with ILE 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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6E LEU* 5.5 2.3 - - + +
10E SER* 3.2 28.0 - - - -
13E ILE* 4.4 17.9 - - + -
37E PHE* 3.0 59.9 + - + +
38E ILE* 3.6 9.9 - - + +
40E GLY* 1.3 75.6 - - - +
42E GLU* 1.3 63.3 + - + +
44E ASN* 2.9 16.1 + - - +
46E ARG* 4.0 19.8 - - + +
48E LEU* 3.7 26.5 - - + -
56E ILE* 4.1 11.4 - - + -
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Residues in contact with GLU 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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10E SER* 4.4 15.5 + - - +
13E ILE* 4.2 8.6 - - + +
14E LYS* 3.6 47.6 + - + +
17E ARG* 2.7 49.5 + - - -
24E GLN* 2.9 17.0 + - - +
38E ILE* 3.1 25.1 + - + +
39E SER 3.9 3.6 - - - +
41E ILE* 1.3 84.9 - - + +
43E ARG* 1.3 59.9 + - - +
44E ASN* 3.2 4.6 + - - -
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Residues in contact with ARG 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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36E THR 5.0 1.6 + - - -
39E SER* 3.1 32.6 + - - +
40E GLY* 3.8 11.5 - - - +
41E ILE 3.3 0.2 - - - -
42E GLU* 1.3 75.0 - - - +
44E ASN* 1.3 71.4 + - - +
45E SER* 2.3 51.7 + - - +
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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