Contacts of the helix formed by residues 25 - 44 (chain A) in PDB entry 4GFU
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 VAL 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 1.3 68.3 + - + +
27A ALA* 3.2 9.4 - - - +
28A GLY* 3.2 8.7 + - - +
29A GLU* 2.8 35.2 + - + +
282A ARG* 5.6 1.6 - - - +
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Residues in contact with LEU 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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25A VAL* 1.3 84.3 - - + +
27A ALA* 1.3 57.5 + - - +
29A GLU* 3.3 9.2 + - - +
30A PHE* 2.9 31.0 + - - +
278A GLU* 5.3 1.1 - - - -
281A TYR* 3.8 6.7 - - + -
282A ARG* 3.9 44.3 - - + +
285A TYR* 3.4 59.9 - - + -
286A HIS* 4.5 12.3 - - + +
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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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25A VAL 3.2 4.9 - - - +
26A LEU* 1.3 80.1 - - - +
28A GLY* 1.3 56.9 + - - +
30A PHE* 4.2 1.6 - - - +
31A SER* 3.1 27.4 + - - -
278A GLU* 3.4 25.2 - - - +
282A ARG* 3.3 23.5 - - - +
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Residues in contact with GLY 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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25A VAL* 3.2 11.9 + - - +
27A ALA* 1.3 77.8 - - - +
29A GLU* 1.3 57.9 + - - +
31A SER* 3.3 6.2 + - - -
32A ASP* 2.9 37.5 + - - +
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Residues in contact with GLU 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 VAL* 2.8 22.0 + - + +
26A LEU* 3.3 9.5 + - - +
28A GLY* 1.3 76.2 - - - +
30A PHE* 1.3 62.7 + - - +
32A ASP* 3.1 12.0 + - - +
33A ILE* 3.0 25.7 + - - +
261A PHE* 3.6 21.5 - - + +
281A TYR* 2.7 30.8 + - + +
285A TYR* 2.8 27.0 + - - -
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Residues in contact with PHE 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 LEU 2.9 16.6 + - - +
27A ALA 4.2 2.9 - - - +
29A GLU* 1.3 76.9 - - - +
31A SER* 1.3 62.9 + - - +
33A ILE* 3.1 15.4 + - + +
34A GLN* 3.0 47.3 + - + +
264A VAL* 5.3 0.4 - - + -
268A ARG* 3.7 18.4 - - - -
275A VAL* 3.8 18.2 - - + -
276A GLN 3.5 20.6 - - - -
277A THR* 3.6 14.1 - - - -
278A GLU* 3.4 32.5 - - + -
281A TYR* 3.6 34.9 - + + -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA 3.1 20.0 + - - -
28A GLY* 3.5 7.9 - - - -
29A GLU 3.2 0.2 - - - -
30A PHE* 1.3 77.1 - - - +
32A ASP* 1.3 65.8 + - - +
34A GLN* 3.3 14.3 + - - +
35A ALA* 3.0 22.7 + - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 2.9 18.9 + - - +
29A GLU* 3.1 11.5 + - - +
31A SER* 1.3 79.4 - - - +
33A ILE* 1.3 62.6 + - - +
35A ALA* 3.3 8.3 + - - +
36A CYS* 3.1 28.9 + - - -
261A PHE* 3.9 17.8 - - + -
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Residues in contact with ILE 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 GLU 3.0 13.9 + - - +
30A PHE* 3.1 14.8 + - + +
32A ASP* 1.3 78.4 - - - +
34A GLN* 1.3 61.7 + - - +
36A CYS* 3.3 5.0 + - - +
37A SER* 3.2 20.8 + - - -
261A PHE* 3.4 24.0 - - + +
264A VAL* 3.9 17.7 - - + -
265A LEU* 4.3 18.6 - - + +
268A ARG* 3.4 34.3 - - + +
281A TYR* 3.3 44.0 - - + +
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Residues in contact with GLN 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 PHE* 3.0 52.7 + - + +
31A SER* 3.3 13.7 + - - +
33A ILE* 1.3 74.1 - - - +
35A ALA* 1.3 65.0 + - - +
37A SER* 3.3 2.8 + - - -
38A ALA* 3.0 23.4 + - - +
268A ARG* 4.1 18.7 - - - +
276A GLN 4.2 7.7 + - - -
1252F ASP* 4.5 23.2 + - - +
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Residues in contact with ALA 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 SER 3.0 14.4 + - - +
32A ASP* 3.3 12.3 + - - +
34A GLN* 1.3 75.6 - - - +
36A CYS* 1.3 60.0 + - - +
38A ALA* 3.3 8.6 + - - +
39A ALA* 3.0 27.6 + - - +
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Residues in contact with CYS 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 ASP* 3.1 19.4 + - - -
33A ILE 3.7 7.0 - - - +
34A GLN 3.2 0.2 - - - -
35A ALA* 1.3 79.9 - - - +
37A SER* 1.3 61.4 + - - +
39A ALA* 3.1 6.7 + - - +
40A TRP* 3.0 42.8 + - + +
261A PHE* 5.1 5.4 - - - -
265A LEU* 3.7 30.3 - - + -
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Residues in contact with SER 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 ILE 3.2 7.1 + - - -
34A GLN 3.3 5.8 + - - -
36A CYS* 1.3 75.4 - - - +
38A ALA* 1.3 64.6 + - - +
40A TRP* 3.4 25.1 + - - +
41A LYS* 3.3 22.0 + - - +
68A TYR* 5.2 6.9 + - - -
268A ARG* 3.0 45.1 + - - +
273A ALA 5.6 0.7 + - - -
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Residues in contact with ALA 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 GLN 3.0 14.1 + - - +
35A ALA* 3.5 11.7 - - - +
36A CYS 3.2 0.2 - - - -
37A SER* 1.3 76.7 - - - +
39A ALA* 1.3 62.0 + - - +
41A LYS* 3.4 9.0 + - - +
42A ALA* 3.1 22.1 + - - +
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Residues in contact with ALA 39 (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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35A ALA 3.0 13.7 + - - +
36A CYS* 3.1 11.8 + - - +
38A ALA* 1.3 75.6 - - - +
40A TRP* 1.3 64.1 + - + +
42A ALA* 3.1 8.2 + - - +
43A ASP* 2.8 31.5 + - - +
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Residues in contact with TRP 40 (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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36A CYS* 3.0 25.7 + - + +
37A SER* 3.6 30.3 - - - +
39A ALA* 1.3 81.6 - - + +
41A LYS* 1.3 56.7 - - - +
43A ASP* 3.4 5.6 + - + +
44A GLY* 3.1 30.3 + - - +
46A CYS* 3.9 25.5 + - + +
68A TYR* 5.0 3.8 - - - +
265A LEU* 3.4 52.0 - - + -
268A ARG* 3.8 5.4 - - + -
269A LYS* 3.5 56.4 - - + +
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Residues in contact with LYS 41 (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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37A SER 3.3 9.9 + - - +
38A ALA* 3.6 12.1 - - - +
39A ALA 3.2 0.6 - - - -
40A TRP* 1.3 78.2 - - - +
42A ALA* 1.3 65.1 + - - +
43A ASP 3.5 0.2 + - - -
44A GLY* 3.5 10.4 + - - -
46A CYS* 4.8 10.5 - - - +
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Residues in contact with ALA 42 (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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38A ALA 3.1 14.1 + - - +
39A ALA* 3.1 9.2 + - - +
41A LYS* 1.3 77.4 - - - +
43A ASP* 1.3 62.8 + - - +
44A GLY* 3.6 0.3 + - - -
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Residues in contact with ASP 43 (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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39A ALA 2.8 16.9 + - - +
40A TRP* 3.9 6.5 - - - +
41A LYS 3.3 0.2 - - - -
42A ALA* 1.3 79.2 - - - +
44A GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 44 (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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40A TRP 3.1 10.2 + - - +
41A LYS 3.5 6.7 + - - -
42A ALA 3.4 3.2 - - - -
43A ASP* 1.3 84.4 - - - +
46A CYS 3.0 39.2 + - - -
47A SER* 4.6 8.1 - - - -
70A GLN* 5.8 0.9 - - - -
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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