Contacts of the helix formed by residues 24 - 38 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLU 3.6 15.7 - - - +
21A ILE 3.0 11.1 + - - +
23A TYR* 1.3 82.9 - - + +
25A ARG* 1.3 59.4 + - - +
26A ASP 3.4 2.2 - - - -
27A ALA* 3.2 26.9 + - + +
28A VAL* 2.8 30.0 + - + +
246A LEU* 3.8 3.1 - - - -
256A VAL* 4.0 28.7 - - + -
411A LEU* 4.4 15.7 - - + -
410D TYR 5.6 2.5 - - - +
411D LEU 5.9 2.7 - - - +
413D GLY* 4.1 26.5 - - - +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.2 19.7 + - - +
23A TYR 3.4 1.0 - - - -
24A LEU* 1.3 76.9 - - - +
26A ASP* 1.3 82.7 + - - +
28A VAL* 3.3 1.9 + - - +
29A LYS* 3.0 48.1 + - + +
244A SER 5.0 1.8 - - - +
245A GLU* 2.6 44.6 + - - +
246A LEU* 3.7 24.0 - - + +
247A GLU* 6.3 0.2 - - - -
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR 4.9 3.6 + - - +
24A LEU 3.4 0.6 - - - -
25A ARG* 1.3 101.7 + - - +
27A ALA* 1.3 63.1 + - - +
29A LYS* 3.4 6.9 + - - +
30A VAL* 3.2 23.8 + - - +
30D VAL* 4.5 22.6 - - + +
34D ALA* 5.1 8.3 - - - +
39D THR* 4.9 8.7 + - - -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR 5.5 0.8 + - - +
24A LEU* 3.2 30.1 + - + +
26A ASP* 1.3 75.5 - - - +
28A VAL* 1.3 62.3 + - - +
30A VAL* 3.2 9.9 - - + +
31A THR* 2.7 33.9 + - - +
411A LEU* 4.4 9.0 - - + -
27D ALA* 5.4 9.4 - - + -
30D VAL* 4.4 10.9 - - + +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.8 22.1 + - + +
25A ARG 3.7 4.9 - - - +
27A ALA* 1.3 75.2 - - - +
29A LYS* 1.3 59.4 + - - +
31A THR 3.3 0.5 + - - -
32A HIS* 2.8 28.2 + - - +
244A SER 4.3 8.5 - - - +
246A LEU* 3.9 17.7 - - + -
252A TYR* 3.4 37.0 - - + -
256A VAL* 3.6 29.8 - - + -
407A MSE 3.6 21.1 - - + +
411A LEU* 4.5 4.3 - - + -
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.0 45.1 + - + +
26A ASP* 3.7 7.9 - - - +
27A ALA 3.3 0.2 - - - -
28A VAL* 1.3 76.7 - - - +
30A VAL* 1.3 62.7 + - - +
32A HIS* 3.3 5.5 + - - +
33A HIS* 3.2 49.2 + - + +
244A SER* 3.6 35.6 + - - +
245A GLU* 4.7 4.6 + - - -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP 3.2 10.7 + - - +
27A ALA* 3.2 19.5 - - - +
29A LYS* 1.3 80.4 - - - +
31A THR* 1.3 59.8 + - - +
33A HIS* 3.4 9.0 + - + +
34A ALA* 3.1 24.8 + - - +
26D ASP* 4.0 36.1 - - + +
27D ALA* 5.0 1.8 - - - +
30D VAL* 3.7 27.8 - - + -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 2.7 23.6 + - - +
30A VAL* 1.3 79.8 - - - +
32A HIS* 1.3 63.8 + - - +
34A ALA* 3.1 8.7 + - + +
35A ILE* 3.0 22.2 + - + +
407A MSE 3.5 26.5 - - + -
410A TYR* 3.5 41.9 - - + +
411A LEU* 4.4 7.6 - - - +
26D ASP* 6.5 0.2 - - - -
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL 2.8 17.7 + - - +
29A LYS 3.4 5.6 - - - +
31A THR* 1.3 76.2 - - - +
33A HIS* 1.3 77.2 + + - +
35A ILE* 3.2 4.4 + - - +
36A HIS* 3.0 57.2 + + - -
242A GLY 3.1 34.8 + - - -
243A THR 3.7 3.4 - - - -
244A SER* 3.3 29.2 + - - -
252A TYR* 2.7 34.6 + - + +
407A MSE 3.7 7.3 - - - +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.2 44.5 + - + +
30A VAL* 3.9 9.6 - - + +
31A THR 3.2 0.2 - - - -
32A HIS* 1.3 93.3 - + - +
34A ALA* 1.3 55.4 + - - +
36A HIS* 3.2 5.3 + - + +
37A GLU* 2.7 61.5 + - + +
244A SER* 4.2 7.7 + - - -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL 3.1 14.4 + - - +
31A THR* 3.1 14.6 + - + +
33A HIS* 1.3 76.8 - - - +
35A ILE* 1.3 57.3 + - + +
37A GLU* 5.3 0.2 - - - -
38A LYS* 2.9 23.0 + - - -
39A THR* 3.1 30.2 + - - +
40A GLY* 4.0 14.1 + - - +
46A LEU* 4.7 0.9 - - - +
410A TYR* 5.3 7.2 + - + -
26D ASP* 4.5 11.7 - - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR 3.0 19.2 + - - +
32A HIS* 3.2 6.5 + - - +
34A ALA* 1.3 78.4 - - - +
36A HIS* 1.3 72.7 + - + +
38A LYS* 3.5 10.7 + - - +
46A LEU* 3.5 25.9 - - + +
49A VAL* 4.0 24.1 - - + +
252A TYR* 4.4 12.3 - - + +
403A LYS* 4.3 10.1 - - + -
406A ALA* 3.9 24.2 - - + -
407A MSE 4.2 25.8 - - + +
410A TYR* 3.7 24.0 - - + -
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.0 53.8 + + + +
33A HIS* 4.2 6.1 - - + +
35A ILE* 1.3 84.5 - - + +
37A GLU* 1.3 57.4 + - + +
38A LYS* 3.1 20.3 - - - +
49A VAL* 3.7 26.6 - - + +
50A ASP* 5.1 5.2 + - - -
238A ARG* 5.8 6.7 + - + -
242A GLY* 4.8 9.0 - - - -
399A TYR* 5.2 1.1 - - - -
403A LYS* 2.8 31.1 + - - -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 2.7 47.8 + - + +
34A ALA 4.6 0.4 - - - +
36A HIS* 1.3 72.2 - - + +
38A LYS* 1.3 71.9 + - - +
39A THR* 3.9 24.1 + - + +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 2.9 10.1 + - - -
35A ILE 3.5 7.6 + - - +
36A HIS* 3.1 22.4 - - - +
37A GLU* 1.3 81.9 - - - +
39A THR* 1.3 60.7 + - - +
43A ASN* 3.3 34.4 + - + +
46A LEU* 3.6 42.9 + - + +
47A GLY* 5.5 1.2 - - - -
49A VAL* 5.5 6.0 - - - +
50A ASP* 5.0 12.9 + - - -
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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