Contacts of the helix formed by residues 28 - 44 (chain A) in PDB entry 1UWB
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 GLU 28 (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 3.1 4.0 + - - -
27A THR* 1.3 83.6 + - - +
29A GLU* 1.3 63.9 + - + +
31A ILE* 3.3 27.5 - - - +
32A LYS* 3.6 8.8 + - - +
134A SER 4.1 1.1 - - - +
135A ILE* 3.9 30.8 - - + +
136A ASN* 4.6 15.5 + - - +
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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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27A THR* 2.6 22.7 + - - +
28A GLU* 1.3 77.2 - - + +
30A LYS* 1.3 81.9 + - + +
31A ILE 3.0 7.8 + - - -
32A LYS* 3.5 16.4 + - - +
33A ALA* 4.2 2.1 + - - +
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Residues in contact with LYS 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* 3.8 14.3 - - + +
27A THR* 2.9 15.8 + - + +
29A GLU* 1.3 95.7 - - + +
31A ILE* 1.3 57.7 + - - +
32A LYS 3.5 0.2 - - - -
33A ALA* 3.5 15.5 - - - +
34A LEU* 3.3 28.4 + - - +
62A ALA* 3.1 29.0 - - - +
63A ILE* 3.2 33.2 - - + +
64A LYS* 4.1 15.6 - - - +
71A TRP* 3.1 35.1 - - - +
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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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25A PRO* 5.2 1.3 - - + -
26A LEU* 3.5 39.5 - - + +
27A THR 3.2 4.1 + - - +
28A GLU* 3.3 16.8 - - - +
29A GLU 3.0 0.8 - - - -
30A LYS* 1.3 75.5 - - - +
32A LYS* 1.3 68.4 + - + +
33A ALA 3.1 0.9 - - - -
34A LEU* 3.2 7.9 + - + +
35A VAL* 2.9 33.6 + - + +
132A ILE* 4.1 10.5 - - + -
133A PRO* 3.0 45.3 - - + +
134A SER* 2.9 35.7 - - - +
135A ILE 4.2 7.0 - - - +
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Residues in contact with LYS 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 3.6 5.0 + - - +
29A GLU* 3.5 11.0 + - - +
31A ILE* 1.3 81.0 - - + +
33A ALA* 1.3 57.7 + - - +
35A VAL* 3.5 8.5 + - + +
36A GLU* 2.8 31.4 + - - +
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Residues in contact with ALA 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 4.2 1.2 + - - +
30A LYS* 3.5 32.9 - - - +
32A LYS* 1.3 75.6 - - - +
34A LEU* 1.3 58.0 + - - +
36A GLU* 2.9 6.6 + - - -
37A ILE* 2.6 54.5 + - + +
62A ALA* 5.3 1.6 - - + -
71A TRP* 4.4 7.4 - - + -
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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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26A LEU* 4.1 15.9 - - + -
30A LYS 3.3 12.5 + - - +
31A ILE* 3.2 10.9 + - + +
33A ALA* 1.3 76.9 - - - +
35A VAL* 1.3 57.3 + - - +
37A ILE* 3.7 4.7 - - - +
38A CYS* 2.8 36.5 + - - -
60A VAL* 3.3 51.4 - - + +
61A PHE 3.4 6.7 - - - +
62A ALA* 3.3 25.6 - - + -
73A LYS* 4.2 11.9 - - + -
132A ILE* 3.5 25.8 - - + -
133A PRO* 6.2 0.7 - - + -
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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 ILE* 2.9 25.0 + - + +
32A LYS* 3.6 8.1 - - - +
34A LEU* 1.3 74.5 - - - +
36A GLU* 1.3 59.8 + - - +
38A CYS* 2.9 5.2 + - - +
39A THR* 2.8 40.0 + - - +
132A ILE* 3.6 24.2 - - + -
133A PRO 5.3 0.2 - - - +
134A SER* 6.1 1.3 - - - -
142A ILE* 3.8 22.9 - - + -
144A TYR* 4.3 4.0 + - - +
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Residues in contact with GLU 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 LYS 2.8 23.5 + - - +
33A ALA* 3.6 4.9 - - - +
35A VAL* 1.3 73.5 - - - +
37A ILE* 1.3 62.0 + - + +
39A THR* 3.7 7.8 + - - -
40A GLU* 3.6 19.1 + - - +
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Residues in contact with ILE 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 ALA* 2.6 42.3 + - + +
34A LEU* 3.7 7.4 - - - +
36A GLU* 1.3 76.0 - - + +
38A CYS* 1.3 58.3 + - - +
40A GLU* 3.6 5.9 + - - +
41A MET* 2.9 47.5 + - + +
62A ALA* 5.3 2.7 - - + -
71A TRP* 3.8 28.3 - - + +
72A ARG 4.6 10.1 - - - +
73A LYS* 4.4 16.6 - - + +
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Residues in contact with CYS 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 28.8 + - - +
35A VAL 3.7 2.0 - - - +
37A ILE* 1.3 77.6 - - - +
39A THR* 1.3 56.5 + - - +
40A GLU 3.2 0.7 - - - -
41A MET* 3.5 9.9 - - - +
42A GLU* 2.6 37.0 + - - +
47A ILE* 3.7 17.8 - - + +
73A LYS* 4.4 20.0 - - - -
130A PHE* 4.4 9.2 - - - -
132A ILE* 3.6 22.9 - - + -
144A TYR* 4.4 15.2 - - + -
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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* 2.8 30.1 + - - +
36A GLU* 3.8 9.7 - - - -
38A CYS* 1.3 75.1 - - - +
40A GLU* 1.3 54.6 + - - +
42A GLU* 3.2 22.1 + - - +
43A LYS* 2.7 49.2 + - - +
144A TYR* 4.3 7.6 + - - -
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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 GLU 3.6 9.7 + - - +
37A ILE* 3.8 8.1 - - - +
39A THR* 1.3 80.7 - - - +
41A MET* 1.3 51.1 + - - +
43A LYS* 2.5 42.4 + - - +
44A GLU* 2.4 64.7 + - + +
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Residues in contact with MET 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 ILE* 2.9 40.3 + - + +
38A CYS* 3.5 3.1 - - - +
40A GLU* 1.3 77.9 - - - +
42A GLU* 1.3 58.1 + - - +
44A GLU* 3.2 12.2 + - + +
45A GLY 3.2 2.8 + - - -
46A LYS* 2.8 34.5 + - + +
47A ILE* 3.3 30.6 + - + -
73A LYS* 4.2 27.8 - - + -
116A PHE* 3.4 40.4 - - + -
146A TYR* 4.8 2.0 - - + +
151A GLN* 5.9 0.2 - - - +
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Residues in contact with GLU 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 CYS 2.6 20.3 + - - +
39A THR* 3.2 23.6 - - - +
41A MET* 1.3 72.7 - - - +
43A LYS* 1.3 58.9 + - - +
44A GLU 3.1 0.4 - - - -
45A GLY* 2.9 20.4 + - - -
47A ILE* 3.5 33.2 - - + +
48A SER* 5.0 0.2 - - - -
49A LYS* 3.5 33.3 - - - +
144A TYR* 3.9 13.9 - - + -
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Residues in contact with LYS 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 THR* 2.7 25.2 + - - +
40A GLU* 2.5 49.6 + - - +
42A GLU* 1.3 70.6 - - - +
44A GLU* 1.3 59.0 + - - +
45A GLY 3.0 7.1 + - - -
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Residues in contact with GLU 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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1A PRO* 4.6 6.9 - - - +
2A ILE* 4.5 9.4 - - - +
40A GLU* 2.4 68.7 + - + +
41A MET* 3.4 13.2 - - + +
42A GLU 3.1 0.4 - - - -
43A LYS* 1.3 74.0 - - - +
45A GLY* 1.3 55.8 + - - +
46A LYS* 3.0 41.4 + - + +
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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
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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