Contacts of the strand formed by residues 28 - 37 (chain E) in PDB entry 4M75
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 ARG 28 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LYS* 2.8 29.4 - - - +
29D ALA 5.0 4.8 + - - -
31D GLY* 4.5 10.7 - - - -
57D GLU* 3.5 21.8 + - - -
79D MSE 3.8 21.8 - - - +
22E ILE 4.1 0.7 - - - +
23E VAL* 5.4 1.5 - - - +
24E LEU* 3.3 31.3 + - + +
26E SER* 2.8 21.8 + - - +
27E ASN* 1.3 76.5 - - - +
29E GLU* 1.3 66.1 + - - +
30E PHE* 3.7 32.7 - - + -
50E GLU* 3.3 6.8 + - - +
51E TRP 2.8 23.6 - - - +
52E LEU* 3.9 21.3 - - + +
53E ILE* 4.4 1.6 - - - +
64E VAL* 5.2 1.0 - - - +
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Residues in contact with GLU 29 (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* 3.5 28.8 - - + +
22E ILE 3.7 6.1 - - - +
23E VAL* 4.4 11.2 - - + +
28E ARG* 1.3 76.9 - - - +
30E PHE* 1.3 62.8 + - - +
51E TRP* 2.7 51.3 + - + +
53E ILE* 2.8 43.2 - - + +
61E ASN* 5.2 0.9 + - - -
87F ARG* 2.6 36.0 + - - +
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Residues in contact with PHE 30 (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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79D MSE 3.4 25.1 - - + -
80D TYR* 3.0 35.0 - + - -
20E VAL 3.9 0.3 - - - +
21E LEU* 3.6 1.8 - - - -
22E ILE* 2.7 41.3 + - + +
24E LEU* 4.1 11.9 - - + -
28E ARG* 3.7 18.8 - - + -
29E GLU* 1.3 75.1 - - - +
31E GLU* 1.3 61.5 + - - +
45E LEU* 4.3 7.4 - - + +
48E ALA* 5.1 1.3 - - + -
49E VAL 3.4 12.3 - - - -
50E GLU* 3.2 28.9 - - + -
67E HIS* 4.4 2.2 - + - -
71E MSE 4.4 12.3 - - + -
73E LEU* 3.6 35.2 - - + -
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Residues in contact with GLU 31 (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* 3.2 31.1 - - + +
20E VAL 3.3 15.5 - - - +
21E LEU* 3.5 21.4 - - + +
29E GLU 4.3 0.4 - - - -
30E PHE* 1.3 75.6 - - - +
32E GLY* 1.3 62.8 + - - +
45E LEU* 4.5 2.9 - - - +
48E ALA* 3.1 3.1 - - - -
49E VAL* 2.6 51.8 + - + +
51E TRP* 4.5 15.8 + - - +
84E GLY 3.9 10.5 - - - +
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Residues in contact with GLY 32 (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* 4.3 8.7 - - - -
20E VAL* 2.6 43.0 + - - +
31E GLU* 1.3 78.9 - - - +
33E THR* 1.3 58.7 + - - -
45E LEU* 4.3 6.9 - - - +
46E GLU 3.5 11.9 - - - -
47E ASP 4.2 4.9 - - - -
48E ALA* 4.2 2.7 - - - -
49E VAL* 5.6 0.4 - - - -
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Residues in contact with THR 33 (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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17E ASN* 4.3 21.0 + - - +
18E GLN 4.1 3.5 - - - -
19E LYS* 4.0 16.7 + - - +
32E GLY* 1.3 73.2 - - - -
34E LEU* 1.3 68.9 + - - +
35E VAL* 2.9 9.8 + - + +
45E LEU* 3.3 2.9 - - - -
46E GLU* 2.7 60.2 + - + +
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Residues in contact with LEU 34 (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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12E ILE* 3.8 40.4 - - + +
15E THR* 4.5 5.2 - - - +
16E ILE* 3.4 20.6 - - + +
17E ASN* 3.0 24.6 + - - -
18E GLN 3.4 15.3 + - - +
20E VAL* 4.1 18.4 - - + +
22E ILE* 4.7 1.1 - - + -
32E GLY 3.7 2.0 + - - -
33E THR* 1.3 71.5 - - - +
35E VAL* 1.3 62.6 + - - +
36E GLY* 3.8 15.5 - - - +
37E PHE* 4.9 0.4 - - + +
43E VAL* 2.9 43.1 - - + -
44E ILE 3.6 2.0 - - - -
45E LEU* 4.0 5.4 - - + -
81E LEU* 4.9 4.7 - - + -
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Residues in contact with VAL 35 (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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16E ILE* 3.6 12.3 - - - +
17E ASN* 5.9 1.6 - - - +
33E THR* 2.9 16.4 + - + +
34E LEU* 1.3 73.3 - - - +
36E GLY* 1.3 54.2 + - - +
44E ILE* 2.8 37.8 + - + -
45E LEU 4.0 1.1 - - - -
46E GLU* 3.8 27.8 - - + +
70E ARG* 3.6 43.5 - - - +
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Residues in contact with GLY 36 (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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16E ILE* 4.5 11.4 - - - -
34E LEU* 3.3 13.9 - - - -
35E VAL* 1.3 82.1 - - - +
37E PHE* 1.3 62.9 + - - +
43E VAL* 3.8 1.6 - - - +
44E ILE* 2.8 37.2 + - - +
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Residues in contact with PHE 37 (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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9E LEU* 3.9 34.1 - - + -
12E ILE* 3.6 48.9 - - + -
13E ASP* 3.9 22.4 - - - -
16E ILE* 5.2 6.5 - - + +
34E LEU* 4.9 2.0 - - + -
36E GLY* 1.3 77.0 - - - +
38E ASP* 1.3 70.2 + - - +
41E VAL* 4.0 23.8 - - + +
42E ASN 3.2 14.6 - - - +
43E VAL* 4.3 6.7 - - + -
44E ILE* 5.1 2.4 - - - +
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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