Contacts of the helix formed by residues 26 - 42 (chain A) in PDB entry 4UAL
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 SER 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY* 5.5 0.4 - - - -
18A PRO* 3.5 14.7 - - - +
25A LEU* 1.3 76.0 - - - +
27A VAL* 1.3 64.4 + - - +
28A GLU* 3.4 5.2 + - - +
29A THR* 3.0 25.9 + - - -
30A LEU* 3.0 22.2 + - - +
409A PHE 3.4 15.3 - - - -
410A SER 3.7 12.1 - - - -
411A ASP* 2.8 28.1 + - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 6.2 0.2 - - - +
25A LEU 4.1 0.4 + - - -
26A SER* 1.3 74.5 - - - +
28A GLU* 1.4 57.2 + - - +
30A LEU* 3.1 19.6 + - + +
31A LEU* 2.9 41.9 + - + +
409A PHE* 3.4 44.9 + - + -
415A LEU* 4.7 10.5 - - + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 3.2 4.9 - - - +
27A VAL* 1.4 75.7 - - - +
29A THR* 1.3 63.1 - - - +
31A LEU* 3.2 13.9 + - + +
32A ASP* 3.2 22.1 + - - +
70A GLN* 4.8 7.6 + - - +
402A THR* 3.6 31.0 - - + +
403A PHE* 3.4 9.5 - - - -
404A THR* 2.7 49.1 + - - -
407A SER* 5.3 2.2 - - - -
409A PHE* 3.1 21.6 + - + +
410A SER* 3.2 20.4 - - - -
411A ASP* 4.6 0.8 + - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.1 32.0 - - + +
26A SER* 3.0 28.3 + - - -
28A GLU* 1.3 75.7 - - - +
30A LEU* 1.3 62.2 + - - +
32A ASP* 3.1 15.2 + - - +
33A VAL* 3.1 12.5 + - + +
125A ARG* 5.3 0.5 + - - -
399A ILE* 4.2 11.7 - - + -
400A GLY* 3.5 34.4 + - - -
402A THR 5.4 1.3 + - - -
411A ASP* 4.0 8.1 + - - -
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Residues in contact with LEU 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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14A LEU* 5.7 9.2 - - + -
25A LEU* 4.6 24.7 - - + +
26A SER 3.0 18.3 + - - +
27A VAL* 3.1 23.7 + - + +
29A THR* 1.3 78.2 - - - +
31A LEU* 1.3 58.8 + - + +
33A VAL* 3.2 17.5 + - + +
34A LEU* 3.1 26.5 + - - +
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Residues in contact with LEU 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 VAL* 2.9 32.1 + - + +
28A GLU* 3.6 13.2 - - + +
29A THR 3.2 0.2 - - - -
30A LEU* 1.3 76.2 - - + +
32A ASP* 1.3 65.1 + - - +
34A LEU* 3.3 9.5 + - + +
35A VAL* 3.0 29.8 + - - +
62A PHE* 3.9 34.3 - - + -
66A VAL* 4.2 17.7 - - + -
70A GLN* 4.1 23.8 - - - +
409A PHE* 6.3 1.1 - - + -
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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
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28A GLU 3.2 11.8 + - - +
29A THR* 3.1 10.1 + - - +
31A LEU* 1.3 75.8 - - - +
33A VAL* 1.3 57.6 + - - +
35A VAL* 3.9 6.0 - - - +
36A CYS* 3.0 29.2 + - - +
70A GLN* 4.9 7.6 + - - +
144A GLN* 3.5 13.7 + - - +
399A ILE* 4.2 9.3 - - + +
400A GLY* 2.7 31.4 + - - +
401A PHE 3.3 10.6 + - - -
402A THR* 2.8 33.7 + - - +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 5.6 4.3 - - + -
29A THR* 3.1 22.3 + - + +
30A LEU* 3.4 21.5 - - + +
31A LEU 3.2 0.4 - - - -
32A ASP* 1.3 73.4 - - - +
34A LEU* 1.3 67.2 + - - +
36A CYS* 3.3 2.4 + - - +
37A LEU* 2.9 26.4 + - + +
399A ILE* 3.6 33.0 - - + -
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Residues in contact with LEU 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 LEU 3.1 15.4 + - - +
31A LEU* 3.8 10.8 - - + +
33A VAL* 1.3 76.2 - - - +
35A VAL* 1.3 62.6 + - + +
37A LEU* 3.2 7.1 + - + -
38A TYR* 2.8 31.1 + - + +
55A PHE* 4.6 20.9 - - + -
58A TRP* 6.0 2.2 - - + -
59A ALA* 5.0 3.8 - - + -
62A PHE* 3.7 34.1 - - + -
63A THR* 3.6 30.1 - - + +
66A VAL* 5.3 2.2 - - + -
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Residues in contact with VAL 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 LEU 3.0 21.6 + - - +
32A ASP* 4.0 6.1 - - - +
34A LEU* 1.3 77.0 - - + +
36A CYS* 1.3 55.9 + - - +
38A TYR* 3.9 5.4 - - - +
39A THR* 2.7 47.1 + - - +
63A THR* 4.4 8.3 - - + -
66A VAL* 4.3 18.8 - - + -
67A LYS* 4.3 30.1 - - + -
70A GLN* 4.8 6.3 - - - +
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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 3.0 18.6 + - - +
33A VAL 3.5 4.9 - - - +
35A VAL* 1.3 79.0 - - - +
37A LEU* 1.3 59.7 + - - +
39A THR* 3.3 6.1 + - - -
40A GLU* 3.0 44.3 + - - +
391A PHE* 5.8 0.9 - - - -
395A HIS* 4.2 27.6 - - - -
396A LEU* 4.0 27.4 - - - -
399A ILE* 4.1 14.4 - - + -
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Residues in contact with LEU 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 VAL* 2.9 20.3 + - + +
34A LEU* 3.8 7.6 - - + +
36A CYS* 1.3 79.2 - - - +
38A TYR* 1.3 63.6 + - - +
40A GLU* 3.3 4.1 + - + +
41A CYS* 2.9 36.9 + - - -
55A PHE* 3.8 29.2 - - + -
391A PHE* 5.1 14.4 - - + -
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Residues in contact with TYR 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 LEU* 2.8 23.3 + - + +
35A VAL 3.9 1.8 - - - +
37A LEU* 1.3 74.1 - - - +
39A THR* 1.3 63.4 + - - +
41A CYS* 3.4 1.0 + - - -
42A SER* 2.8 34.0 + - - -
55A PHE* 4.5 10.3 - + + -
56A LEU* 3.5 46.1 + - + +
59A ALA* 3.9 11.0 - - + -
60A LYS* 3.4 43.1 - - - +
63A THR* 3.7 31.0 - - + +
64A GLN* 4.9 2.9 + - + -
67A LYS* 3.7 26.2 - - - -
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Residues in contact with THR 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 VAL* 2.7 33.8 + - - +
36A CYS* 3.8 4.7 - - - -
38A TYR* 1.3 81.7 - - - +
40A GLU* 1.3 63.1 + - + +
42A SER* 3.2 21.3 + - - -
43A HIS* 3.4 15.0 - - + +
67A LYS* 5.3 5.4 + - - +
395A HIS* 5.3 13.7 - - + +
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Residues in contact with GLU 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 28.4 + - - +
37A LEU* 3.8 4.0 - - + +
39A THR* 1.3 76.0 - - + +
41A CYS* 1.3 63.8 + - - +
43A HIS* 3.0 37.8 + - - -
46A LEU* 3.2 15.6 - - + +
391A PHE* 3.2 37.1 - - + -
392A SER* 2.8 31.1 + - - -
393A GLY* 2.7 30.2 + - - -
394A LEU 3.9 1.9 + - - -
395A HIS* 5.0 5.5 + - - +
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Residues in contact with CYS 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 LEU* 2.9 35.6 + - - +
38A TYR 3.8 4.9 - - - +
40A GLU* 1.3 75.4 - - - +
42A SER* 1.3 60.4 + - - +
43A HIS 3.2 0.7 + - - +
46A LEU* 3.6 9.6 - - - +
47A ARG* 3.2 28.8 + - - +
52A VAL* 3.6 27.7 - - + +
55A PHE* 4.1 18.6 - - + -
56A LEU* 3.8 13.4 - - + +
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Residues in contact with SER 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 TYR* 2.8 25.3 + - - -
39A THR* 3.3 13.8 - - - -
40A GLU 3.1 1.4 - - - -
41A CYS* 1.3 75.2 - - - +
43A HIS* 1.3 53.4 + - - +
47A ARG* 2.6 42.6 + - - +
56A LEU* 3.9 13.1 - - - +
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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