Contacts of the helix formed by residues 46 - 54 (chain F) in PDB entry 3E4U
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 HIS 46 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E THR* 4.2 16.2 - - + +
22F LEU* 3.9 9.7 + - + -
25F LEU* 4.1 5.2 - - + +
26F ARG* 3.8 21.9 + - + -
30F ILE 3.0 28.5 - - - -
31F LEU* 2.7 26.4 + - + -
32F THR* 3.6 9.5 - - + -
33F ASP* 3.4 7.2 - - - +
34F VAL* 4.7 0.2 - - - -
45F ALA* 1.3 74.1 - - - +
47F LYS* 1.3 65.2 + - - +
48F THR* 3.1 16.2 + - + +
49F VAL* 3.2 10.6 + - + +
50F LEU* 3.1 20.9 + - - +
91F TYR* 2.7 41.5 + + - +
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Residues in contact with LYS 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 3.7 24.9 - - + -
33F ASP* 2.9 52.9 + - - +
34F VAL* 3.6 15.2 - - + +
45F ALA 4.1 0.2 - - - -
46F HIS* 1.3 70.9 - - - +
48F THR* 1.3 52.3 + - - +
50F LEU* 3.2 10.1 + - - +
51F MET* 2.8 42.8 + - - +
61F PHE* 3.6 28.9 - - + -
68F ASN* 3.9 21.9 + - - +
69F LEU 2.6 34.2 + - - -
70F SER* 4.0 1.2 - - - +
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Residues in contact with THR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 3.8 20.8 - - - +
25E LEU* 3.9 6.1 - - + +
30E ILE 4.9 0.4 - - - +
31E LEU* 4.3 16.6 - - + +
46E HIS* 3.7 36.6 - - + +
48E THR* 4.4 10.8 + - - +
49E VAL* 6.1 0.2 - - - +
22F LEU* 5.7 0.2 - - - +
33F ASP* 5.6 3.6 - - - +
46F HIS* 3.9 9.2 - - + +
47F LYS* 1.3 75.2 - - + +
49F VAL* 1.3 75.3 + - - +
51F MET* 3.4 11.1 + - - +
52F ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 5.1 6.3 - - + -
22E LEU* 4.8 6.1 - - + -
19F LEU* 5.2 2.2 - - + -
22F LEU* 4.3 29.2 - - + -
46F HIS* 3.2 13.4 + - + +
48F THR* 1.3 86.7 + - - +
50F LEU* 1.3 65.7 + - - +
52F ALA* 2.9 16.5 + - - +
53F CYS* 3.1 29.0 + - - -
90F MET* 4.7 5.6 - - + +
91F TYR* 3.7 49.1 - - + +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F VAL* 3.6 31.2 - - + -
36F ILE* 3.7 22.0 - - + -
45F ALA* 3.8 8.7 - - + -
46F HIS 3.1 12.3 + - - +
47F LYS* 3.4 8.5 - - - +
49F VAL* 1.3 78.0 - - - +
51F MET* 1.3 61.2 + - - +
53F CYS* 3.3 2.6 + - - +
54F SER* 3.1 29.6 + - - -
57F PHE* 3.9 33.0 - - + -
61F PHE* 4.6 5.8 - - + -
83F PHE* 5.1 2.7 - - + -
87F LEU* 4.0 15.3 - - + -
90F MET* 3.4 27.6 - - + -
91F TYR* 5.7 0.4 - - + -
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Residues in contact with MET 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASN* 5.1 0.7 + - - +
25E LEU* 4.0 22.2 - - + -
30E ILE* 3.2 35.4 - - + +
31E LEU* 3.6 26.2 - - + -
47F LYS 2.8 23.3 + - - +
48F THR* 3.6 7.6 - - - +
50F LEU* 1.3 77.7 - - - +
52F ALA* 1.3 59.9 + - - +
53F CYS 3.5 0.3 + - - -
54F SER 3.8 10.8 + - - +
55F GLY* 5.3 0.3 - - - -
57F PHE 3.7 18.8 - - - +
58F TYR* 4.1 30.2 - - + +
61F PHE* 3.7 16.4 - - + -
62F THR* 4.1 13.5 - - + -
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E HIS* 5.6 0.2 + - - -
17E ASP* 5.9 0.2 - - - +
18E VAL* 3.9 23.5 - - + +
21E ASN* 2.4 51.8 + - + -
22E LEU* 4.3 10.3 - - + +
25E LEU* 5.2 2.0 - - + -
48F THR 2.9 16.8 + - - +
49F VAL* 2.9 10.7 + - - +
51F MET* 1.3 77.1 - - - +
53F CYS* 1.3 60.3 + - - +
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Residues in contact with CYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E HIS* 3.5 26.0 - - - +
18E VAL* 3.9 8.1 - - - -
49F VAL* 3.1 20.5 + - - +
50F LEU 3.3 0.2 + - - -
52F ALA* 1.3 81.8 - - - +
54F SER* 1.3 57.7 + - - +
55F GLY 4.2 0.8 + - - -
89F PHE* 6.1 0.2 - - + -
90F MET* 3.5 52.5 - - + -
113F GLN 5.3 0.3 - - - +
114F MET* 3.1 23.4 - - + +
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU 3.1 11.5 + - - -
51F MET 3.8 6.7 - - - +
52F ALA 3.7 1.6 - - - -
53F CYS* 1.3 78.3 - - - +
55F GLY* 1.3 63.9 + - - +
56F LEU* 2.9 5.5 + - - +
57F PHE* 2.9 31.8 + - - +
58F TYR 3.1 8.5 + - - -
90F MET* 3.8 11.9 - - - -
112F LEU* 2.3 36.8 + - - +
114F MET* 3.9 6.1 - - - -
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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