Contacts of the strand formed by residues 45 - 54 (chain E) in PDB entry 4EMG
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 MSE 45 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 4.4 2.5 - - - -
14E VAL* 5.2 2.0 - - + -
22E VAL* 5.2 1.1 - - - -
24E VAL* 3.8 30.7 - - + -
36E LEU* 3.9 28.5 - - + -
38E ALA 3.2 6.3 - - - +
39E TYR* 3.9 8.7 - - + -
43E LEU* 3.5 7.9 - - + +
44E ASN* 1.3 81.9 - - - +
46E VAL* 1.3 62.6 + - - +
47E LEU* 4.0 9.6 - - + -
78E LEU 3.6 0.3 - - - +
79E PHE* 3.4 5.5 - - - -
80E VAL* 2.7 50.6 + - + -
85E VAL* 3.4 33.7 - - + -
88E ILE* 3.9 25.1 - - + -
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Residues in contact with VAL 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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9B GLU 4.9 1.1 - - - +
10B PRO* 3.4 34.8 - - + +
13B LEU* 3.8 25.8 - - + +
35E ARG 3.7 0.2 - - - +
36E LEU* 3.9 0.2 - - - -
37E HIS* 2.9 34.8 + - + +
38E ALA* 2.9 20.7 + - + +
45E MSE 1.3 74.2 - - - +
47E LEU* 1.3 68.8 + - - +
77E MSE 3.8 29.6 - - + -
78E LEU 3.1 7.2 - - - +
79E PHE* 4.4 2.5 - - + -
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Residues in contact with LEU 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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22E VAL* 4.2 11.2 - - + -
24E VAL* 4.3 12.1 - - + -
32E LEU* 3.9 39.7 - - + -
33E ASN 4.6 1.1 - - - -
34E GLY* 4.0 21.5 - - - +
35E ARG 3.4 1.8 - - - -
36E LEU* 4.0 26.7 - - + -
45E MSE 4.0 12.3 - - + -
46E VAL* 1.3 82.1 - - - +
48E GLY* 1.3 59.1 + - - +
50E ALA* 3.8 16.1 - - + +
77E MSE 3.5 2.4 - - - -
78E LEU* 2.7 44.5 + - + +
80E VAL* 4.1 5.4 - - + -
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Residues in contact with GLY 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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34E GLY* 3.5 0.5 - - - -
35E ARG* 2.8 37.3 + - - +
37E HIS* 3.6 26.7 + - - -
47E LEU* 1.3 71.4 - - - +
49E ASP* 1.3 74.6 + - - +
50E ALA 3.3 2.0 + - - -
76E GLU 3.4 7.2 - - - -
77E MSE 4.0 2.7 - - - -
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Residues in contact with ASP 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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33E ASN 4.0 3.8 - - - +
34E GLY* 4.0 3.1 - - - -
35E ARG* 5.6 4.5 - - + +
48E GLY* 1.3 74.9 - - - +
50E ALA* 1.3 61.5 + - - +
51E GLU* 4.0 0.5 + - - +
74E HIS* 3.5 24.4 + - - -
75E TYR 3.3 7.0 - - - -
76E GLU* 2.8 20.0 + - - +
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Residues in contact with ALA 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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32E LEU* 5.7 0.4 - - + -
33E ASN 3.1 11.7 - - - +
47E LEU* 3.8 30.1 - - + +
48E GLY 4.0 0.7 - - - -
49E ASP* 1.3 74.2 - - - +
51E GLU* 1.3 61.7 + - - +
74E HIS* 3.3 7.6 - - - -
75E TYR* 2.7 42.7 + - + +
78E LEU* 4.1 27.6 - - + -
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Residues in contact with GLU 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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31E GLU 3.8 0.2 - - - +
32E LEU* 3.2 8.3 - - - +
33E ASN* 2.8 47.6 + - + +
49E ASP 4.0 0.8 + - - +
50E ALA* 1.3 75.3 - - - +
52E GLU* 1.3 62.9 + - - +
53E ILE* 3.8 22.5 - - + +
72E ARG* 2.7 39.1 + - + +
73E LYS 3.4 10.3 - - - +
74E HIS* 4.5 8.1 - - + +
75E TYR* 5.3 0.2 - - - -
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Residues in contact with GLU 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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23B TYR* 4.7 2.9 + - - -
25B LYS* 5.2 0.7 - - - +
87B LEU* 3.8 13.2 - - - +
30E ARG* 2.6 45.8 + - + -
31E GLU 3.4 4.3 - - - -
32E LEU* 3.6 17.9 - - + -
50E ALA 4.2 0.4 - - - -
51E GLU* 1.3 73.5 - - - +
53E ILE* 1.3 66.3 + - - +
54E VAL* 4.0 5.9 - - + +
71E ILE 3.8 0.9 - - - +
72E ARG* 3.3 6.2 - - - +
73E LYS* 2.8 40.7 + - + +
75E TYR* 2.7 39.0 + - + -
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Residues in contact with ILE 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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29E ASP 3.7 3.3 - - - +
30E ARG* 3.7 0.2 - - - -
31E GLU* 2.9 50.0 + - + +
33E ASN* 4.0 16.6 - - - +
51E GLU* 3.8 27.8 - - + +
52E GLU* 1.3 79.1 - - - +
54E VAL* 1.3 62.5 + - - +
55E THR* 3.9 16.1 + - + +
70E THR* 3.9 21.5 - - + +
71E ILE 3.8 2.5 - - - -
72E ARG* 3.5 35.7 - - + +
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Residues in contact with VAL 54 (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 ASP* 3.4 14.6 - - + +
30E ARG* 3.4 36.3 - - + +
52E GLU* 4.0 9.2 - - - +
53E ILE* 1.3 74.5 - - - +
55E THR* 1.3 71.6 + - - +
70E THR* 3.1 4.0 - - - -
71E ILE* 2.8 62.1 + - + +
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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