Contacts of the helix formed by residues 24 - 37 (chain F) in PDB entry 3IFS
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 LEU 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F GLU 3.5 16.2 - - - +
21F ILE 3.0 12.9 + - - +
23F TYR* 1.3 86.1 - - + +
25F ARG* 1.3 65.1 + - - +
26F ASP 3.3 2.9 - - - -
27F ALA* 3.2 14.6 + - + +
28F VAL* 2.9 25.8 + - + +
246F LEU* 4.2 0.2 - - - -
256F VAL* 3.8 38.1 - - + +
259F ASN* 5.5 5.8 - - + -
260F ALA* 6.0 3.4 - - + +
411F LEU* 4.7 14.6 - - + -
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Residues in contact with ARG 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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21F ILE 3.9 2.0 + - - -
22F THR* 3.1 20.1 + - + +
23F TYR 3.4 0.8 - - - -
24F LEU* 1.3 77.3 - - - +
26F ASP* 1.3 83.1 + - - +
28F VAL* 3.4 3.0 + - - +
29F LYS* 3.0 46.2 + - - +
244F SER 5.6 0.5 - - - +
245F GLU* 2.8 42.8 + - - +
246F LEU* 4.1 24.6 + - + +
247F GLU* 5.8 2.2 - - - +
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Residues in contact with ASP 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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23F TYR 4.8 3.3 + - - +
24F LEU 3.3 0.6 - - - -
25F ARG* 1.3 104.5 + - - +
27F ALA* 1.3 66.4 + - - +
29F LYS* 3.3 7.5 + - - +
30F VAL* 3.1 23.8 + - - +
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Residues in contact with ALA 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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24F LEU* 3.2 19.3 + - + +
26F ASP* 1.3 78.4 - - - +
28F VAL* 1.3 62.3 + - - +
30F VAL* 3.2 10.1 - - - +
31F THR* 3.0 29.8 + - - +
411F LEU* 4.3 15.7 - - + -
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU* 2.9 21.2 + - + +
25F ARG 3.7 5.8 - - - +
27F ALA* 1.3 74.5 - - - +
29F LYS* 1.3 59.7 + - - +
31F THR* 3.2 0.7 + - - -
32F HIS* 2.8 29.1 + - - +
244F SER 4.3 8.7 - - - +
246F LEU* 4.0 18.4 - - + -
252F TYR* 3.5 35.2 - - + -
256F VAL* 3.5 30.5 - - + -
407F MSE 3.7 19.9 - - + +
411F LEU* 4.7 3.6 - - + -
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Residues in contact with LYS 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 ARG* 3.0 35.0 + - - +
26F ASP* 3.5 8.5 - - - +
28F VAL* 1.3 76.9 - - - +
30F VAL* 1.3 63.0 + - - +
32F HIS* 3.3 4.6 + - - +
33F HIS* 3.1 47.1 + - + +
244F SER* 2.6 51.2 + - - -
245F GLU* 3.1 26.1 + - - +
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Residues in contact with VAL 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 ASP 3.1 13.1 + - - +
27F ALA* 3.2 20.6 - - - +
29F LYS* 1.3 77.6 - - - +
31F THR* 1.3 64.7 + - - +
33F HIS* 3.4 16.2 + - + +
34F ALA* 3.1 19.7 + - + +
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Residues in contact with THR 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 ALA* 3.0 19.1 + - - +
28F VAL 3.8 0.2 - - - -
30F VAL* 1.3 76.7 - - - +
32F HIS* 1.3 66.2 + - - +
34F ALA* 3.0 8.1 + - + +
35F ILE* 2.9 24.4 + - + +
407F MSE 3.5 29.4 - - + +
410F TYR* 3.3 42.8 - - + +
411F LEU* 4.1 8.8 - - - +
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Residues in contact with HIS 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 VAL 2.8 17.9 + - - +
29F LYS* 3.4 7.9 - - - +
31F THR* 1.3 76.0 - - - +
33F HIS* 1.3 77.6 + + - +
35F ILE* 3.1 4.4 + - - +
36F HIS* 3.0 58.6 + + + +
242F GLY 3.2 25.1 + - - -
244F SER* 3.6 28.3 - - - -
252F TYR* 2.7 37.6 + - + +
407F MSE 3.9 4.0 - - - +
451F SO4 4.6 5.5 + - - -
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Residues in contact with HIS 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 LYS* 3.1 39.6 + - + +
30F VAL* 3.5 17.2 - - + +
32F HIS* 1.3 94.1 - + - +
34F ALA* 1.3 53.9 + - - +
36F HIS* 5.0 1.3 - - - -
37F GLU* 2.8 67.2 + - - +
39F THR* 4.8 0.2 - - - -
244F SER* 5.4 1.2 - - - -
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Residues in contact with ALA 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 VAL* 3.1 12.6 + - + +
31F THR* 3.0 15.2 + - + +
33F HIS* 1.3 76.1 - - - +
35F ILE* 1.3 61.4 + - - +
38F LYS* 3.1 17.8 + - - -
39F THR* 3.2 26.9 + - - +
40F GLY* 4.0 14.9 + - - +
46F LEU* 4.6 2.1 - - - +
410F TYR* 4.9 12.1 + - + -
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Residues in contact with ILE 35 (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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31F THR 2.9 18.1 + - - +
32F HIS 3.1 5.4 + - - +
34F ALA* 1.3 79.6 - - - +
36F HIS* 1.3 68.4 + - + +
38F LYS* 3.4 11.3 + - - +
46F LEU* 3.5 24.8 - - + +
49F VAL* 4.2 21.4 - - + +
252F TYR* 4.6 3.4 - - + +
403F LYS* 4.1 28.5 - - + +
406F ALA* 3.8 27.4 - - + -
407F MSE 4.1 26.2 - - + +
410F TYR* 3.6 23.1 - - + -
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Residues in contact with HIS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.0 53.8 + + + +
33F HIS* 4.4 1.8 - - - +
35F ILE* 1.3 84.5 - - + +
37F GLU* 1.3 62.1 + - + +
38F LYS* 3.4 13.9 + - - +
49F VAL* 4.0 21.4 - - + +
50F ASP* 5.4 2.0 + - - -
238F ARG* 6.3 2.9 - - + -
242F GLY* 4.5 9.0 - - - -
252F TYR* 4.2 0.2 - - - -
399F TYR* 5.4 0.4 - - - -
403F LYS* 2.8 33.3 + - - -
451F SO4 3.0 42.7 + - - +
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Residues in contact with GLU 37 (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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33F HIS* 2.8 53.1 + - - +
36F HIS* 1.3 77.0 - - + +
38F LYS* 1.3 72.7 + - - +
39F THR* 3.4 22.6 + - + +
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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