Contacts of the strand formed by residues 30 - 39 (chain F) 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 ARG 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E LYS* 3.2 39.4 - - - +
28E GLY 5.8 1.2 - - - +
86E ILE* 4.9 11.8 - - - +
87E LEU* 4.5 8.1 - - - -
25F LYS* 3.5 5.4 - - - +
26F LEU* 2.9 55.3 + - + +
27F ARG 4.5 4.8 + - - +
28F GLY 3.2 10.9 + - - +
29F ASP* 1.3 80.5 - - - +
31F GLU* 1.3 70.2 + - - +
32F LEU* 4.9 0.9 - - + -
52F GLU* 2.7 49.9 + - + +
53F ILE 3.6 1.6 - - - +
54F VAL* 3.4 24.9 - - + +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS* 4.2 11.3 - - - +
23F TYR* 2.7 42.8 + - + +
24F VAL 3.3 5.4 - - - +
25F LYS* 4.0 10.5 - - + +
26F LEU 4.7 0.2 - - - +
29F ASP 5.7 0.2 - - - -
30F ARG* 1.3 80.4 - - - +
32F LEU* 1.3 75.1 + - - +
33F ASN* 5.4 0.7 - - - +
52F GLU* 3.4 0.9 - - - +
53F ILE* 2.9 49.5 + - + +
55F THR* 4.0 21.4 - - + +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E LEU* 4.4 3.8 - - + -
22F VAL 4.5 0.7 - - - -
23F TYR* 3.5 3.5 - - - -
24F VAL* 2.8 38.8 + - + +
26F LEU* 4.0 22.9 - - + -
30F ARG* 4.9 1.6 - - + -
31F GLU* 1.3 84.1 - - - +
33F ASN* 1.3 72.5 + - - +
47F LEU* 3.9 17.5 - - + -
50F ALA* 5.7 0.4 - - + -
51F GLU 3.2 7.0 - - - +
52F GLU* 3.7 28.7 - - + -
78F LEU* 3.9 17.7 - - + -
80F VAL* 3.4 42.2 - - + -
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Residues in contact with ASN 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 4.9 9.1 - - + +
22F VAL 3.3 7.5 - - - +
23F TYR* 3.8 26.2 - - - +
31F GLU* 5.4 0.4 - - - +
32F LEU* 1.3 81.7 + - - +
34F GLY* 1.3 59.2 + - - +
47F LEU* 4.7 2.7 - - - -
49F ASP 3.9 0.9 - - - +
50F ALA* 3.0 5.5 - - - +
51F GLU* 2.8 59.4 + - + +
53F ILE* 4.1 16.4 - - - +
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Residues in contact with GLY 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.2 11.8 - - - +
22F VAL* 2.8 34.2 + - - +
33F ASN* 1.3 77.2 - - - +
35F ARG* 1.3 63.2 + - - -
36F LEU 3.6 0.7 + - - -
47F LEU* 4.0 14.8 - - - +
48F GLY 3.4 10.5 - - - -
49F ASP 4.0 4.5 - - - -
50F ALA* 4.1 1.6 - - - -
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Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ASP* 3.0 49.9 + - - +
20F GLU* 3.4 5.9 - - - +
21F ILE* 4.0 30.7 - - + +
34F GLY* 1.3 72.5 - - - -
36F LEU* 1.3 58.9 + - - +
37F HIS* 3.1 33.1 + - + +
47F LEU* 3.3 3.3 - - - -
48F GLY 2.7 40.5 + - - +
49F ASP* 5.6 5.3 - - + +
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL* 3.4 40.4 - - + +
17F SER* 3.6 25.6 - - - +
18F LEU* 3.7 14.4 - - + +
19F ASP* 2.7 30.7 + - - -
20F GLU 3.0 10.7 + - - +
22F VAL* 4.2 14.1 - - + -
34F GLY 3.6 2.2 + - - -
35F ARG* 1.3 68.9 - - - +
37F HIS* 1.3 60.6 + - - +
38F ALA 3.5 24.9 - - - +
39F TYR* 4.4 2.2 - - + -
45F MSE 3.9 24.5 - - + -
46F VAL 3.9 5.8 - - - +
47F LEU* 4.0 8.3 - - + -
88F ILE* 6.0 1.3 - - + -
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Residues in contact with HIS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLU* 4.5 5.5 - - - +
18F LEU* 4.0 9.7 - - - +
19F ASP* 4.2 20.4 + - - +
35F ARG* 3.1 25.1 + - + -
36F LEU* 1.3 73.2 - - - +
38F ALA* 1.3 63.8 + - + +
46F VAL* 3.0 21.3 + - + +
47F LEU 4.4 0.2 - - - -
48F GLY* 3.6 35.5 + - - -
77F MSE 3.7 22.1 - - + -
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLU* 3.3 31.2 - - + +
10E PRO* 3.7 18.8 - - + -
18F LEU* 4.1 5.8 - - - +
36F LEU* 3.5 8.1 - - - +
37F HIS* 1.3 83.5 - - + +
39F TYR* 1.3 64.6 + - - +
45F MSE 3.2 3.8 - - - -
46F VAL* 2.9 31.9 + - + -
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Residues in contact with TYR 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLU* 5.0 3.0 - - - +
10E PRO* 3.3 11.3 - - - +
11F LEU* 4.7 13.4 + - + +
14F VAL* 3.7 27.1 - - + -
15F ARG* 3.1 43.2 - - + +
18F LEU* 3.5 35.0 - - + -
36F LEU* 4.4 3.1 - - + -
38F ALA* 1.3 77.2 - - - +
40F ASP* 1.3 79.2 + - - +
41F GLU* 6.1 0.2 - - - -
43F LEU* 5.0 5.8 - - + -
44F ASN 3.0 14.1 - - - +
45F MSE 3.9 12.1 - - + -
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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