Contacts of the strand formed by residues 43 - 52 (chain E) in PDB entry 4M7A
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 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.6 13.0 - - + -
34E LEU* 4.1 10.1 - - + -
36E GLY 3.7 4.3 - - - +
37E PHE* 4.0 15.7 - - + +
41E VAL* 4.0 9.6 - - + +
42E ASN* 1.3 83.3 - - - +
44E ILE* 1.3 61.2 + - - +
45E LEU* 3.4 30.1 - - + -
71E MET 3.4 0.9 - - - +
72E LEU* 3.3 4.5 - - - +
73E LEU* 2.6 53.1 + - + +
78E ILE* 4.3 6.3 - - + -
81E LEU* 4.5 18.6 - - + -
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Residues in contact with ILE 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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11D VAL* 4.4 8.3 - - + +
12D THR* 3.9 16.4 - - + -
15D PHE* 3.7 37.2 - - + -
34E LEU* 3.8 0.5 - - - -
35E VAL* 2.9 37.8 + - + -
36E GLY* 2.9 29.5 + - - +
43E VAL* 1.3 71.8 - - - +
45E LEU* 1.3 66.9 + - - +
70E ARG* 3.8 28.3 - - + +
71E MET 3.2 7.6 - - - +
72E LEU* 3.5 25.6 - - + -
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Residues in contact with LEU 45 (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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20E VAL* 4.1 10.3 - - + -
22E ILE* 3.5 27.6 - - + -
30E PHE* 4.0 15.9 - - + +
32E GLY* 4.7 7.0 - - - +
33E THR 3.4 5.8 - - - +
34E LEU* 4.0 10.3 - - + -
35E VAL* 4.4 1.6 - - - -
43E VAL* 3.4 18.3 + - + -
44E ILE* 1.3 82.7 - - - +
46E GLU* 1.3 62.0 + - - +
47E ASP 4.3 0.2 + - - -
48E ALA* 4.1 16.6 - - + -
70E ARG* 3.5 5.9 - - - +
71E MET* 2.8 60.8 + - + +
73E LEU* 3.9 9.2 - - + -
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Residues in contact with GLU 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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19E LYS* 5.6 0.5 - - - -
32E GLY* 3.5 0.5 - - - -
33E THR* 2.8 41.7 + - - +
35E VAL* 3.6 22.9 - - + +
45E LEU* 1.3 74.6 - - - +
47E ASP* 1.3 92.0 + - - +
48E ALA 3.5 1.3 + - - -
69E GLY* 3.3 23.3 - - - +
70E ARG* 4.7 10.1 - - + -
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Residues in contact with ASP 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 LYS* 6.0 0.7 - - - -
31E GLU 3.9 4.9 - - - +
32E GLY* 3.9 2.6 - - - -
45E LEU 4.3 0.4 + - - -
46E GLU* 1.3 92.5 - - + +
48E ALA* 1.3 61.7 + - - +
49E VAL* 3.8 2.8 + - - +
66E GLN* 4.3 10.0 + - - +
67E HIS* 3.2 16.9 - - - +
68E HIS* 3.6 8.6 + - - +
69E GLY 3.1 27.1 + - - +
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Residues in contact with ALA 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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30E PHE* 4.6 2.5 - - + -
31E GLU 3.3 12.6 - - - +
32E GLY* 4.2 0.9 - - - -
45E LEU* 4.1 28.0 - - + -
47E ASP* 1.3 74.6 - - - +
49E VAL* 1.3 65.1 + - - +
66E GLN* 4.4 1.3 - - - -
67E HIS* 3.0 42.2 + - + +
71E MET* 4.3 22.4 - - + -
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Residues in contact with VAL 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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29E GLU 3.7 0.5 - - - +
30E PHE* 3.1 8.3 - - - +
31E GLU* 2.8 45.6 + - + +
47E ASP 4.7 2.0 - - - +
48E ALA* 1.3 74.3 - - - +
50E GLU* 1.3 60.8 + - - +
51E TRP* 3.5 32.5 + - + +
63E LYS* 3.9 31.9 - - + -
65E MET 3.6 3.1 - - - +
66E GLN* 3.8 17.9 - - - +
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Residues in contact with GLU 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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27D LYS* 3.0 31.6 + - - -
80D TYR* 2.7 27.8 + - - -
28E ARG* 3.4 16.2 + - + -
29E GLU 3.6 2.5 - - - -
30E PHE* 3.5 27.9 - - + -
49E VAL* 1.3 74.6 - - - +
51E TRP* 1.3 63.1 + - - +
63E LYS* 3.7 4.9 - - - +
64E VAL* 2.8 38.3 + - + -
65E MET* 3.0 24.6 + - - +
67E HIS* 3.0 15.5 + - - +
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Residues in contact with TRP 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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21E LEU* 5.9 2.2 - - + -
28E ARG* 3.2 10.6 - - - +
29E GLU* 2.8 49.0 + - + +
31E GLU* 5.1 7.3 - - + +
49E VAL* 3.5 36.1 - - + +
50E GLU* 1.3 77.0 - - - +
52E LEU* 1.3 59.9 + - - +
53E ILE* 3.9 18.4 - - + -
61E ASN* 3.9 17.7 - - + -
62E GLU 3.3 16.8 - - - -
63E LYS* 3.2 48.2 - - + -
64E VAL* 3.8 4.7 - - - -
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Residues in contact with LEU 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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57D GLU* 4.5 12.6 - - + +
27E ASN* 3.4 16.8 - - + +
28E ARG* 3.6 46.4 - - + +
51E TRP* 1.3 73.5 - - - +
53E ILE* 1.3 61.2 + - - +
61E ASN* 3.5 4.2 - - - +
62E GLU* 2.9 60.4 + - + +
64E VAL* 3.6 14.3 - - + +
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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