Contacts of the strand formed by residues 45 - 54 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H PRO* 4.5 3.1 - - - -
14N VAL* 5.2 2.2 - - + -
22N VAL* 5.0 1.6 - - - -
24N VAL* 3.8 30.5 - - + -
36N LEU* 3.8 28.0 - - + -
38N ALA 3.2 5.4 - - - +
39N TYR* 3.9 8.7 - - + -
43N LEU* 3.5 8.2 + - + +
44N ASN* 1.3 81.0 - - - +
46N VAL* 1.3 61.9 + - - +
47N LEU* 4.0 10.8 - - + -
78N LEU 3.6 0.2 - - - +
79N PHE* 3.4 5.5 - - - -
80N VAL* 2.7 51.2 + - + +
85N VAL* 3.4 33.0 - - + -
88N ILE* 4.0 25.1 - - + -
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLU 5.1 0.7 - - - +
10H PRO* 3.4 33.6 - - + +
13H LEU* 3.8 26.2 - - + -
36N LEU* 3.9 0.3 - - - -
37N HIS* 3.0 32.3 + - + -
38N ALA* 2.9 21.0 + - + +
45N MSE 1.3 76.6 - - - +
47N LEU* 1.3 71.4 + - - +
77N MSE 3.9 29.6 - - + -
78N LEU 3.1 7.4 - - - +
79N PHE* 4.3 3.4 - - + -
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Residues in contact with LEU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N VAL* 4.1 11.0 - - + -
24N VAL* 4.2 12.6 - - + -
32N LEU* 3.9 39.5 - - + -
34N GLY* 4.0 22.0 - - - +
35N ARG 3.4 0.9 - - - -
36N LEU* 4.0 26.5 - - + -
45N MSE 4.0 11.4 - - + -
46N VAL* 1.3 83.9 - - - +
48N GLY* 1.3 59.4 + - - +
50N ALA* 3.9 16.1 - - + +
77N MSE 3.5 1.9 - - - -
78N LEU* 2.7 45.5 + - + +
80N VAL* 4.1 6.5 - - + -
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Residues in contact with GLY 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N GLY* 3.5 0.5 - - - -
35N ARG* 2.8 35.3 + - - +
37N HIS* 3.6 25.3 + - - -
47N LEU* 1.3 72.5 - - - +
49N ASP* 1.3 74.3 + - - +
50N ALA 3.3 2.5 + - - -
76N GLU 3.4 7.4 - - - -
77N MSE 3.9 2.7 - - - -
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Residues in contact with ASP 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N ASN 3.9 4.7 - - - +
34N GLY* 4.0 3.1 - - - -
35N ARG* 4.8 5.6 + - + +
48N GLY* 1.3 74.7 - - - +
50N ALA* 1.3 59.7 + - - +
51N GLU 3.9 0.5 + - - -
74N HIS* 3.6 24.9 + - - -
75N TYR 3.3 7.4 - - - -
76N GLU* 2.7 19.5 + - - +
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Residues in contact with ALA 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N LEU* 5.7 0.4 - - + -
33N ASN 3.1 11.4 - - - +
47N LEU* 3.9 35.0 - - + +
48N GLY 3.9 0.7 - - - +
49N ASP* 1.3 74.6 - - - +
51N GLU* 1.3 60.5 + - - +
52N GLU 4.2 0.2 - - - -
73N LYS 3.9 0.2 - - - +
74N HIS* 3.3 7.7 - - - -
75N TYR* 2.7 43.1 + - + +
78N LEU* 4.1 21.3 - - + -
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Residues in contact with GLU 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N GLU 3.8 0.2 - - - +
32N LEU* 3.2 9.1 - - - +
33N ASN* 2.8 49.9 + - + +
49N ASP 3.9 1.2 + - - +
50N ALA* 1.3 74.3 - - - +
52N GLU* 1.3 61.9 + - - +
53N ILE* 3.7 21.3 + - + +
72N ARG* 2.7 40.0 + - + +
73N LYS 3.4 10.3 - - - +
74N HIS* 4.6 6.7 - - + +
75N TYR* 5.4 0.4 - - - -
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Residues in contact with GLU 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 4.7 3.4 + - - -
87H LEU* 3.9 11.4 - - - +
30N ARG* 2.6 47.1 + - + -
31N GLU 3.4 4.0 - - - -
32N LEU* 3.7 18.8 - - + -
50N ALA 4.2 0.4 + - - -
51N GLU* 1.3 73.6 - - - +
53N ILE* 1.3 66.7 + - - +
54N VAL* 4.1 6.2 - - + +
71N ILE 3.8 0.7 - - - +
72N ARG* 3.3 6.8 - - - +
73N LYS* 2.8 42.1 + - + +
75N TYR* 2.7 38.1 + - + -
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Residues in contact with ILE 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N ASP 3.6 3.3 - - - +
31N GLU* 2.9 47.3 + - + +
33N ASN* 4.1 15.7 - - - +
51N GLU* 3.7 27.4 - - + +
52N GLU* 1.3 80.1 - - - +
54N VAL* 1.3 62.4 + - - +
55N THR* 3.8 15.8 + - + +
70N THR* 3.9 21.8 - - + +
71N ILE 3.8 1.8 - - - -
72N ARG* 3.4 36.1 - - + +
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Residues in contact with VAL 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N ASP* 3.4 12.6 - - + +
30N ARG* 3.4 35.9 - - + +
52N GLU* 4.1 9.4 - - - +
53N ILE* 1.3 73.6 - - - +
55N THR* 1.3 69.8 + - - +
70N THR* 3.1 3.8 + - - -
71N 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