Contacts of the strand formed by residues 43 - 54 (chain E) in PDB entry 5IXM
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 GLY 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E HIS 3.6 3.3 - - - +
38E TYR* 4.6 7.9 - - - -
39E MET* 2.8 41.9 + - - +
42E ARG* 1.3 77.8 - - - +
44E LEU* 1.3 60.5 + - - -
66E LEU* 4.0 7.6 - - - +
68E ASN* 4.5 4.3 - - - -
70E ARG* 4.7 8.3 - - - +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PRO* 4.2 10.8 - - + -
37E HIS 3.8 19.1 - - - +
38E TYR* 4.0 16.2 - - + +
43E GLY* 1.3 70.8 - - - -
45E GLN* 1.3 70.6 + - - +
46E TRP* 3.7 33.5 - - + +
66E LEU* 3.5 4.2 - - - +
67E PRO* 2.9 28.1 - - + +
68E ASN 5.9 0.6 - - - +
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Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E PRO* 3.5 4.3 - - - +
37E HIS* 2.9 45.1 + - + +
39E MET* 3.5 19.7 - - + -
43E GLY 3.8 0.2 + - - -
44E LEU* 1.3 76.5 - - - +
46E TRP* 1.3 69.9 + - - +
47E GLN* 2.8 34.7 + - - +
64E ASP* 4.2 4.2 - - - +
65E TRP 3.5 14.6 - - - +
66E LEU* 3.6 14.7 - - + +
84E ARG 5.3 0.2 + - - -
113E TYR* 3.4 24.2 + - - -
117E LEU* 3.5 27.4 - - - +
118E THR 4.9 1.6 + - - +
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Residues in contact with TRP 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ILE* 4.1 22.7 - - + -
35E THR 3.6 2.2 - - - -
36E PRO* 3.9 32.3 - - + -
44E LEU* 3.7 37.5 + - + +
45E GLN* 1.3 79.6 - - - +
47E GLN* 1.3 62.5 + - - +
48E ASN* 3.9 11.9 - - - +
63E LEU 3.6 2.8 - - - +
64E ASP* 3.3 3.3 - - - -
65E TRP* 2.8 69.4 + + + +
67E PRO* 4.7 2.3 - - + +
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Residues in contact with GLN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 4.7 6.8 - - - +
33E THR* 3.5 5.7 - - - +
34E ILE* 3.5 0.2 - - - -
35E THR* 2.9 56.9 + - - +
37E HIS* 3.6 20.9 + - + -
45E GLN* 2.8 28.6 + - - +
46E TRP* 1.3 74.3 - - - +
48E ASN* 1.3 62.1 + - - +
49E GLU* 4.2 0.4 + - - -
64E ASP* 3.5 28.8 + - - +
118E THR 3.6 17.4 + - - -
119E SER* 5.4 0.8 - - - +
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Residues in contact with ASN 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E THR 3.5 3.6 - - - +
34E ILE* 3.6 35.2 - - + +
46E TRP* 3.9 14.3 - - - +
47E GLN* 1.3 75.4 - - - +
49E GLU* 1.3 60.9 + - - +
62E ALA* 3.2 7.5 - - - +
63E LEU* 2.9 60.6 + - + +
64E ASP* 3.9 1.5 + - - +
65E TRP* 5.3 2.9 - - - +
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Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ALA* 3.2 5.1 - - - +
33E THR* 2.9 52.8 + - + +
47E GLN 5.6 0.4 - - - +
48E ASN* 1.3 76.3 - - - +
50E PHE* 1.3 62.3 + - - +
51E ARG* 4.2 17.5 + - + +
60E THR* 3.5 19.1 - - + +
61E MET 3.5 4.9 - - - +
62E ALA* 4.8 2.7 - - + -
120E GLN* 3.5 14.4 + - - +
121E TYR* 2.3 30.9 + - - +
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Residues in contact with PHE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ILE* 4.3 13.0 - - + -
30E PHE* 3.4 40.6 - + + -
31E ASP 3.0 24.2 - - - -
32E ALA* 4.5 8.5 - - + -
49E GLU* 1.3 73.0 - - - +
51E ARG* 1.3 64.3 + - - +
52E TYR* 4.1 21.6 + + + -
60E THR* 3.5 1.8 - - - -
61E MET* 2.9 59.7 + - + +
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Residues in contact with ARG 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TYR* 4.9 6.3 + - - -
29E ASN 4.6 0.2 - - - -
30E PHE* 3.5 3.3 - - - -
31E ASP* 2.9 69.2 + - + +
49E GLU* 4.2 17.5 + - + +
50E PHE* 1.3 77.2 - - - +
52E TYR* 1.3 62.7 + - - +
59E GLY 3.5 5.8 - - - +
60E THR* 3.6 26.2 - - + +
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Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ASN 3.4 5.8 - - - -
30E PHE* 3.9 24.9 - + + -
50E PHE* 4.2 19.5 - + + -
51E ARG* 1.3 77.2 - - - +
53E LEU* 1.3 62.1 + - - +
54E LEU* 4.1 22.7 - - + -
57E GLY 4.2 3.1 - - - -
58E SER* 3.5 3.8 - - - -
59E GLY* 2.9 57.4 + - - +
60E THR 3.8 2.5 - - - -
61E MET* 4.2 13.5 - - + -
89E TRP* 2.7 37.1 + + - -
91E HIS* 3.0 35.9 + + - +
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E PRO 6.1 0.4 - - - +
29E ASN* 3.1 45.4 + - + +
52E TYR* 1.3 76.3 - - - +
54E LEU* 1.3 73.0 + - - +
57E GLY 4.0 1.3 - - - -
58E SER* 3.8 22.9 - - - +
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ASN* 3.6 9.0 - - - +
30E PHE* 3.5 33.7 - - + -
52E TYR* 4.1 22.2 - - + -
53E LEU* 1.3 90.7 - - - +
55E ALA* 1.3 62.2 + - - +
56E PRO* 3.3 19.1 - - + -
57E GLY* 2.9 31.0 + - - +
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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