Contacts of the strand formed by residues 47 - 56 (chain E) in PDB entry 1I8F
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 LEU 47 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D THR* 4.0 4.5 - - - -
16E LEU* 5.7 1.3 - - + -
24E VAL* 6.1 0.2 - - + -
26E VAL* 4.0 27.8 - - + -
38E LEU* 3.6 26.9 - - + -
40E SER 3.6 2.0 - - - -
41E PHE* 3.7 18.4 - - + -
45E VAL* 3.7 11.7 - - + +
46E ASN* 1.3 75.4 - - - +
48E LEU* 1.3 65.5 + - - +
49E LEU* 4.0 5.4 - - + -
66E MET 3.5 0.2 - - - +
67E VAL* 3.1 9.5 - - - +
68E VAL* 2.7 60.7 + - + -
73E VAL* 4.5 2.0 - - + -
76E ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 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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10D ALA* 4.3 14.8 - - - +
11D THR* 4.2 13.7 + - - +
14D ALA* 5.9 0.4 - - + -
15D THR* 3.2 26.0 - - - +
38E LEU* 3.9 0.7 - - - +
39E ARG* 3.0 45.9 + - + -
40E SER* 2.9 30.5 + - - +
47E LEU* 1.3 73.5 - - - +
49E LEU* 1.3 66.4 + - - +
50E GLU* 5.5 2.2 - - + -
65E THR* 3.6 23.3 - - + -
66E MET 3.5 6.5 - - - +
67E VAL* 4.7 0.7 - - + -
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Residues in contact with LEU 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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24E VAL* 4.1 15.9 - - + -
26E VAL* 4.5 12.6 - - + -
34E ILE* 3.7 30.1 - - + -
36E GLY* 4.1 13.7 - - - +
37E ILE 3.4 4.7 - - - +
38E LEU* 3.8 32.5 - - + +
47E LEU* 4.6 5.8 - - + -
48E LEU* 1.3 79.5 - - - +
50E GLU* 1.3 61.2 + - - +
52E ALA* 4.0 12.3 - - + -
64E GLY 4.4 0.9 - - - -
65E THR* 3.3 7.8 - - - +
66E MET* 2.8 41.2 + - + +
68E VAL* 4.1 20.0 - - + -
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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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36E GLY 3.8 0.2 - - - -
37E ILE* 2.8 37.0 + - + +
39E ARG* 1.9 64.7 + - + +
48E LEU* 5.5 3.1 - - + -
49E LEU* 1.3 75.5 - - - +
51E ASP* 1.3 70.2 + - + +
52E ALA 3.0 2.1 + - - -
64E GLY 4.0 1.6 - - - -
65E THR* 4.2 17.4 + - + +
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Residues in contact with ASP 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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23E GLN* 5.3 6.1 - - - +
35E ARG 4.2 0.3 - - - +
36E GLY* 4.1 6.4 - - - -
37E ILE* 4.4 15.8 - - + +
50E GLU* 1.3 76.2 - - + +
52E ALA* 1.3 63.5 + - - +
53E GLU* 4.1 8.1 + - - +
62E LYS* 4.5 22.0 + - - +
64E GLY* 3.2 16.9 + - - -
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Residues in contact with ALA 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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34E ILE* 4.7 0.2 - - + -
35E ARG 3.2 12.1 - - - +
36E GLY* 3.9 1.6 - - - -
49E LEU* 4.0 16.4 - - + -
50E GLU 3.0 1.0 - - - -
51E ASP* 1.3 79.2 - - - +
53E GLU* 1.3 57.8 + - - +
62E LYS* 3.7 3.5 - - - +
63E ARG* 2.7 30.2 + - - -
64E GLY 2.8 21.2 + - - +
66E MET* 3.9 33.0 - - + -
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Residues in contact with GLU 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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23E GLN* 4.2 8.5 - - - +
34E ILE* 3.3 8.7 - - - +
35E ARG* 2.5 84.1 + - + +
51E ASP* 4.8 5.6 - - - +
52E ALA* 1.3 77.0 - - - +
54E GLU* 1.3 61.4 + - - +
55E ILE* 4.0 2.9 - - + +
60E VAL* 3.5 23.2 - - + +
61E TYR 3.2 15.0 - - - +
62E LYS* 3.1 28.2 + - + -
63E ARG* 4.2 3.4 - - - +
66E MET* 5.0 0.7 - - - -
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Residues in contact with GLU 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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25D LEU* 4.0 0.2 - - - +
27D LYS* 2.4 38.1 + - - +
75D PHE* 3.4 28.2 - - + -
32E HIS* 4.5 6.1 + - - -
33E GLU 3.7 6.1 - - - +
34E ILE* 4.3 8.2 - - + +
53E GLU* 1.3 76.2 - - - +
55E ILE* 1.3 61.2 + - - +
56E ILE* 3.6 16.1 + - + +
59E ASN 3.5 1.0 - - - +
60E VAL* 3.5 4.9 - - - +
61E TYR* 2.9 36.8 + - + +
63E ARG* 2.6 44.2 + - + +
66E MET* 4.5 1.1 - - + -
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Residues in contact with ILE 55 (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 SER 5.6 1.0 - - - +
33E GLU* 3.0 60.8 + - + +
34E ILE* 4.1 2.0 - - - -
35E ARG* 3.8 48.5 - - + +
53E GLU* 4.0 12.8 - - + +
54E GLU* 1.3 76.0 - - - +
56E ILE* 1.3 66.7 + - - +
57E ASP 5.3 0.2 - - - +
58E GLY* 4.4 18.2 - - - +
59E ASN 3.3 10.8 - - - +
60E VAL* 4.7 7.2 - - + -
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Residues in contact with ILE 56 (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* 3.5 27.6 - - - +
1004D GOL 3.8 24.7 - - - +
32E HIS* 6.1 2.0 - - + +
54E GLU* 3.6 10.7 + - + +
55E ILE* 1.3 83.3 - - - +
57E ASP* 1.3 78.0 + - - +
58E GLY 3.1 0.2 - - - -
59E ASN* 2.8 37.5 + - - +
61E TYR* 3.8 29.7 + - + -
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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