Contacts of the helix formed by residues 22 - 34 (chain F) in PDB entry 4DEM
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 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F VAL* 1.3 63.0 + - - +
24F TYR* 3.3 7.9 - - - +
25F ALA* 3.4 14.7 + - - +
26F GLN* 3.0 28.4 + - - +
360F ARG* 4.4 20.4 - - - +
361F LYS* 6.3 0.6 - - - +
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Residues in contact with VAL 23 (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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22F ASP* 1.3 77.2 - - - +
24F TYR* 1.3 85.0 + - + +
26F GLN* 3.6 7.6 + - + +
27F GLU* 3.1 42.0 + - - +
80F VAL* 3.6 29.6 - - + -
83F ARG* 6.5 0.4 - - + -
84F GLU* 4.0 13.0 - - + +
357F GLY* 4.7 11.7 - - - -
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Residues in contact with TYR 24 (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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22F ASP 4.4 3.6 - - - +
23F VAL* 1.3 92.6 - - + +
25F ALA* 1.3 59.0 + - - +
27F GLU* 3.1 3.5 + - - +
28F LYS* 3.0 30.2 + - - +
73F ASN* 4.0 8.1 - - + -
76F LEU* 3.7 29.6 - - + +
77F THR* 2.9 47.3 + - - +
80F VAL* 4.1 16.1 - - + +
354F VAL 5.1 2.4 + - - -
357F GLY* 3.6 28.7 - - - -
358F LEU* 3.6 22.0 + - + +
361F LYS* 4.0 33.2 - - + -
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Residues in contact with ALA 25 (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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22F ASP* 3.4 18.1 + - - +
24F TYR* 1.3 76.7 - - - +
26F GLN* 1.3 63.7 + - - +
28F LYS* 3.4 20.0 + - - +
29F GLN* 4.4 3.5 + - - +
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Residues in contact with GLN 26 (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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22F ASP 3.0 17.5 + - - +
23F VAL* 3.7 11.2 - - + +
24F TYR 3.3 0.2 - - - -
25F ALA* 1.3 77.3 - - - +
27F GLU* 1.3 67.5 + - + +
28F LYS 3.6 0.2 + - - -
29F GLN* 4.7 3.5 + - - +
30F ASP* 5.1 6.8 + - - +
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Residues in contact with GLU 27 (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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23F VAL* 3.1 28.8 + - - +
24F TYR 3.1 3.0 + - - +
26F GLN* 1.3 83.3 - - - +
28F LYS* 1.3 58.2 + - - +
29F GLN 3.5 0.9 - - - -
30F ASP* 3.4 14.5 + - + +
31F PHE* 3.0 27.0 + - - +
76F LEU* 3.8 16.8 - - + -
79F VAL* 3.9 20.4 - - + +
80F VAL* 3.8 16.8 - - + -
83F ARG* 3.1 46.4 + - - +
100F TRP* 5.2 3.9 + - - +
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Residues in contact with LYS 28 (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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24F TYR 3.0 16.1 + - - +
25F ALA* 3.4 14.0 + - - +
27F GLU* 1.3 74.7 - - - +
29F GLN* 1.3 61.8 + - - +
31F PHE* 3.2 2.3 + - + +
32F VAL* 3.0 39.9 + - + +
71F LYS 4.3 18.6 - - - +
72F TYR* 4.6 7.4 - - + -
76F LEU* 3.9 17.7 - - + -
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Residues in contact with GLN 29 (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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25F ALA 4.4 4.5 + - - +
26F GLN 4.7 2.9 + - - +
27F GLU 3.5 0.2 - - - -
28F LYS* 1.3 75.7 - - - +
30F ASP* 1.3 66.1 + - - +
32F VAL* 3.4 4.8 + - - +
33F GLN* 3.0 36.9 + - - +
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Residues in contact with ASP 30 (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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26F GLN 5.1 6.3 + - - +
27F GLU* 3.4 17.1 + - - +
28F LYS 3.3 0.4 - - - -
29F GLN* 1.3 77.7 - - - +
31F PHE* 1.4 57.8 + - - +
33F GLN* 3.3 17.7 + - - +
34F HIS* 2.7 43.7 + - - +
83F ARG* 5.0 7.3 + - - -
100F TRP* 4.3 22.3 - - - +
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Residues in contact with PHE 31 (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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27F GLU* 3.0 17.7 + - + +
28F LYS 3.5 4.3 - - - +
29F GLN 3.2 0.4 - - - -
30F ASP* 1.4 77.4 - - - +
32F VAL* 1.3 63.0 + - + +
34F HIS* 3.2 14.6 + - - +
72F TYR* 3.8 31.9 - + + -
75F GLY* 4.0 8.5 - - - -
76F LEU* 3.6 20.9 - - + -
79F VAL* 3.8 22.0 - - + -
100F TRP* 3.6 19.7 - + + -
103F GLY* 3.7 23.6 - - - -
104F TRP* 2.9 73.7 + + - -
107F GLU* 4.1 5.6 - - + -
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Residues in contact with VAL 32 (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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28F LYS* 3.0 25.9 + - + +
29F GLN* 4.1 5.2 - - - +
31F PHE* 1.3 75.0 - - + +
33F GLN* 1.3 66.3 + - - +
35F PHE* 3.0 20.3 + - + +
36F SER* 4.5 0.7 + - - -
68F ILE* 5.1 10.8 - - + -
72F TYR* 3.6 44.9 - - + +
104F TRP* 4.3 5.8 - - - -
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Residues in contact with GLN 33 (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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29F GLN* 3.0 27.9 + - - +
30F ASP* 3.5 21.0 - - - +
31F PHE 3.3 0.2 - - - -
32F VAL* 1.3 77.4 - - - +
34F HIS* 1.3 66.9 + - + +
35F PHE 3.3 0.5 + - - -
36F SER* 3.6 19.4 + - - -
37F GLN* 4.6 0.9 + - - +
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Residues in contact with HIS 34 (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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30F ASP* 2.7 32.0 + - - +
31F PHE* 3.2 7.1 + - - +
32F VAL 3.1 1.2 - - - -
33F GLN* 1.3 82.6 + - + +
35F PHE* 1.3 63.9 + - - +
36F SER 3.2 0.4 - - - -
37F GLN* 3.1 22.1 + - + +
38F ILE* 3.1 17.1 + - + +
100F TRP* 3.1 75.7 - + + -
104F TRP* 4.3 7.0 - - + +
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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