Contacts of the helix formed by residues 24 - 39 (chain A) in PDB entry 1EFU
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 LYS 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 3.7 12.2 + - - +
17A ILE* 3.6 8.3 - - - +
18A GLY* 3.2 47.9 + - - +
19A HIS 4.4 8.7 - - - +
20A VAL* 5.4 6.7 + - - +
22A HIS 5.4 0.4 - - - -
23A GLY* 1.3 76.0 - - - +
25A THR* 1.3 62.6 + - - +
27A LEU* 3.7 2.6 - - - +
28A THR* 2.8 28.6 + - - -
80A ASP* 2.9 44.4 + - - +
81A CYS 3.7 16.6 + - - -
82A PRO* 4.0 6.3 - - - +
104A VAL* 4.3 22.0 - - + -
271B PHE* 4.8 1.3 - - - -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY* 3.3 0.6 - - - -
24A LYS* 1.3 76.6 - - - +
26A THR* 1.3 65.7 + - - +
28A THR* 3.0 4.5 + - - -
29A ALA* 2.8 21.3 + - - +
80A ASP* 5.5 0.7 + - - -
271B PHE* 3.5 24.5 - - - -
274B GLU* 3.8 38.4 + - + +
275B VAL* 3.8 9.0 - - + +
278B MET* 3.5 23.6 - - - -
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY* 3.5 17.9 + - - -
24A LYS 3.4 0.2 - - - -
25A THR* 1.3 78.0 - - - +
27A LEU* 1.3 62.7 + - - +
29A ALA* 3.1 4.8 + - - +
30A ALA* 2.9 22.3 + - - +
135A ASN* 5.1 1.3 - - - +
174A ALA* 3.4 25.1 - - + +
175A LEU* 3.7 28.9 - - + +
178A LEU* 4.0 11.3 - - + +
278B MET* 3.3 25.1 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 4.6 6.1 - - + -
23A GLY 2.9 18.1 + - - +
24A LYS* 3.7 4.0 - - - +
26A THR* 1.3 74.3 - - - +
28A THR* 1.3 57.4 + - - +
30A ALA* 3.1 4.2 + - - +
31A ILE* 2.9 36.8 + - + +
102A ILE* 4.1 6.7 - - + -
104A VAL* 3.6 28.7 - - + -
133A PHE* 3.5 51.1 - - + -
135A ASN* 5.2 0.4 - - - +
174A ALA* 3.5 11.8 - - + +
188A ILE* 3.9 14.1 - - + -
191A LEU* 4.0 15.5 - - + -
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Residues in contact with THR 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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16A THR* 4.1 1.7 + - - +
24A LYS 2.8 13.4 + - - -
25A THR 3.0 8.1 + - - -
27A LEU* 1.3 75.5 - - - +
29A ALA* 1.3 63.7 + - - +
31A ILE* 3.2 9.9 + - - +
32A THR* 3.1 24.9 + - + +
67A VAL* 4.2 13.0 - - + -
69A TYR* 4.9 2.0 - - + -
78A HIS* 3.2 43.3 + - + +
271B PHE* 3.4 19.4 - - + -
275B VAL* 4.0 15.3 - - + -
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Residues in contact with ALA 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 THR 2.8 11.2 + - - +
26A THR 3.3 9.4 - - - +
28A THR* 1.3 74.9 - - - +
30A ALA* 1.3 57.6 + - - +
32A THR* 2.9 19.8 + - - -
33A THR* 3.0 18.7 + - - -
178A LEU* 3.8 13.7 - - + -
275B VAL* 3.6 21.0 - - + +
278B MET* 3.7 29.2 - - + -
279B SER* 4.0 4.0 - - - +
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Residues in contact with ALA 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 THR 2.9 12.0 + - - +
27A LEU 3.3 9.9 - - - +
29A ALA* 1.3 75.1 - - - +
31A ILE* 1.3 60.3 + - - +
33A THR* 4.4 0.9 - - - -
34A VAL* 2.9 36.1 + - - +
174A ALA* 3.9 21.5 - - + +
177A ALA* 4.4 3.8 - - + -
178A LEU* 3.7 12.3 - - + +
188A ILE* 3.6 25.4 - - + -
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Residues in contact with ILE 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 LEU* 2.9 29.1 + - + +
28A THR* 3.2 7.8 + - - +
30A ALA* 1.3 75.1 - - - +
32A THR* 1.3 64.4 + - - +
35A LEU* 3.1 39.5 + - + +
69A TYR* 3.4 51.1 - - + +
78A HIS* 4.4 10.3 - - + -
102A ILE* 4.4 9.6 - - + -
188A ILE* 3.7 16.2 - - + +
191A LEU* 3.8 29.8 - - + -
192A ALA* 5.4 5.2 - - + +
195A LEU* 5.1 2.2 - - + -
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Residues in contact with THR 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 THR* 3.1 14.0 + - + +
29A ALA* 2.9 12.8 + - - -
31A ILE* 1.3 75.8 - - - +
33A THR* 1.3 72.5 + - - +
35A LEU* 4.1 1.0 - - - +
36A ALA* 3.2 25.8 + - - +
41A GLY 4.8 1.9 - - - +
67A VAL* 3.4 33.7 - - + -
68A GLU 4.4 4.0 - - - +
69A TYR* 4.2 23.1 - - + -
275B VAL* 4.6 3.6 - - + +
279B SER* 3.7 13.7 + - - -
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Residues in contact with THR 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 ALA 3.0 16.7 + - - -
30A ALA 3.8 2.9 - - - +
32A THR* 1.3 83.3 + - - +
34A VAL* 1.3 64.4 + - + +
36A ALA* 3.7 3.7 - - - +
37A LYS* 2.9 28.1 + - + +
178A LEU* 3.8 16.0 - - + +
185A GLU* 5.5 1.6 - - - +
279B SER* 3.9 19.2 + - - -
281B GLN 5.0 1.5 + - - +
282B SER* 2.9 42.2 + - - +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 2.9 22.9 + - - +
33A THR* 1.3 77.2 - - + +
35A LEU* 1.3 53.1 + - - +
37A LYS* 3.6 6.4 - - + +
38A THR* 2.7 44.0 + - - +
177A ALA* 4.5 7.4 - - + +
185A GLU* 3.9 44.2 - - + +
188A ILE* 3.7 20.9 - - + -
189A LEU* 3.5 35.2 - - + -
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Residues in contact with LEU 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 ILE* 3.1 29.3 + - + +
32A THR* 4.1 2.9 - - - +
34A VAL* 1.3 76.3 - - + +
36A ALA* 1.3 54.8 + - - +
38A THR* 4.4 0.2 - - - -
39A TYR* 2.6 63.2 + - + +
41A GLY 4.1 4.3 - - - +
42A ALA 3.4 2.7 + - - -
69A TYR* 3.5 35.4 - - + -
70A ASP 3.6 22.2 - - - +
71A THR* 3.8 11.0 - - + -
188A ILE* 5.2 2.2 - - + -
189A LEU* 3.8 12.1 - - + -
192A ALA* 3.7 23.6 - - + -
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Residues in contact with ALA 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 THR 3.2 18.6 + - - +
33A THR* 3.7 4.5 - - - +
35A LEU* 1.3 74.0 - - - +
37A LYS* 1.3 62.5 + - - +
40A GLY* 2.6 31.7 + - - +
41A GLY* 3.2 23.9 + - - +
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Residues in contact with LYS 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 THR 2.9 17.8 + - - +
34A VAL* 3.6 7.9 - - + +
36A ALA* 1.3 77.7 - - - +
38A THR* 1.3 62.3 + - - +
40A GLY 4.7 0.3 + - - -
180A GLY* 4.0 6.3 + - - -
185A GLU* 2.9 37.2 + - - +
282B SER* 2.8 39.0 + - - +
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Residues in contact with THR 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 VAL* 2.7 25.2 + - - +
35A LEU 3.9 1.8 - - - -
37A LYS* 1.3 83.1 - - - +
39A TYR* 1.3 87.1 + - + +
40A GLY 3.4 0.6 + - - -
189A LEU* 3.7 30.9 - - + +
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Residues in contact with TYR 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 LEU* 2.6 53.4 + - + +
38A THR* 1.3 88.9 - - + +
40A GLY* 1.3 54.7 + - - -
41A GLY 3.0 5.6 + - - -
42A ALA 3.6 9.7 + - - +
70A ASP 4.0 9.4 - - - +
71A THR* 4.3 4.9 - - + +
72A PRO* 3.4 46.3 - - + +
189A LEU* 3.8 22.6 + - + +
192A ALA* 5.5 1.4 - - - +
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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
------------------------------------------------------------
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