Contacts of the strand formed by residues 51 - 61 (chain E) in PDB entry 4FAO
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 THR 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E ARG 3.9 0.3 - - - +
47E ASN* 3.8 2.4 - - - +
48E SER* 3.3 34.9 + - - -
49E SER 3.2 5.4 + - - -
50E GLY* 1.3 76.2 - - - +
52E ILE* 1.3 60.2 + - - +
53E GLU* 3.7 3.7 + - - +
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Residues in contact with ILE 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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45E TRP* 3.8 32.8 - - + +
46E ARG 3.7 3.1 - - - -
47E ASN* 3.5 15.9 - - - +
50E GLY 3.5 8.4 + - - +
51E THR* 1.3 70.3 - - - +
53E GLU* 1.3 62.6 + - - +
54E LEU* 4.0 2.5 + - + +
95E PHE* 4.2 19.3 - - + -
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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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16E ALA* 5.6 2.9 - - - +
45E TRP* 3.4 2.9 - - - +
46E ARG* 2.8 72.2 + - + +
51E THR 3.7 3.6 + - - +
52E ILE* 1.3 71.7 - - - +
54E LEU* 1.3 71.6 + - - +
55E VAL* 4.0 2.3 - - - +
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Residues in contact with LEU 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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14E TYR* 4.0 34.3 + - + +
16E ALA* 3.6 17.4 - - - +
43E ALA* 5.3 0.2 - - + -
44E SER 3.3 16.6 - - - +
45E TRP* 4.0 6.3 - - + -
52E ILE* 4.0 4.2 + - + +
53E GLU* 1.3 80.9 - - - +
55E VAL* 1.3 72.8 + - - +
56E LYS 3.8 8.5 - - - +
57E LYS* 3.6 42.6 - - + +
95E PHE* 4.6 15.7 - - + -
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Residues in contact with VAL 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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92A VAL* 6.3 0.7 - - + -
93A PRO* 3.8 37.0 - - + +
14E TYR* 4.5 0.9 - - - -
15E ASN* 4.0 1.6 - - - +
16E ALA* 3.3 24.7 + - + +
17E ASN* 4.5 1.3 + - + -
44E SER* 2.9 23.0 + - - +
45E TRP* 4.2 1.3 - - - -
46E ARG* 4.0 42.2 - - + +
53E GLU* 4.0 9.9 - - - +
54E LEU* 1.3 79.2 - - - +
56E LYS* 1.3 79.4 + - + +
81E VAL* 5.5 2.0 - - + -
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Residues in contact with LYS 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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85A LEU* 4.4 9.4 - - + -
93A PRO 3.4 19.8 + - - +
94A THR* 3.8 16.2 - - - +
95A LEU* 4.0 10.5 - - + +
13E TYR* 6.0 0.4 - - - -
14E TYR* 3.2 13.2 - - - +
15E ASN* 2.8 33.4 + - + +
17E ASN* 4.1 4.2 - - - +
21E GLU* 2.9 33.8 + - - -
42E TYR* 3.8 21.7 - - + +
43E ALA* 3.3 2.6 - - - -
44E SER* 2.9 40.6 + - - +
54E LEU* 3.8 1.8 - - - +
55E VAL* 1.3 87.9 + - + +
57E LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 57 (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* 3.2 27.5 - - + +
13E TYR* 3.4 8.7 - - - -
14E TYR* 2.7 43.4 + - + +
42E TYR* 3.4 14.5 + - - +
43E ALA* 3.8 11.9 - - + -
54E LEU* 3.6 30.5 - - + +
56E LYS* 1.3 78.5 - - - +
58E GLY* 1.3 58.7 + - - +
92E ASN* 3.4 21.0 + - - +
93E GLU* 3.2 30.1 + - - -
95E PHE* 4.1 18.9 - - - -
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Residues in contact with GLY 58 (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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11E CYS* 4.0 7.0 - - - -
12E ILE 3.1 15.3 + - - -
13E TYR* 4.4 3.6 - - - -
29E GLU* 3.9 7.6 - - - -
41E CYS* 3.4 4.3 - - - -
42E TYR* 2.8 46.3 + - - +
57E LYS* 1.3 74.4 - - - +
59E CYS* 1.3 60.8 + - - -
92E ASN* 3.7 1.0 + - - -
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Residues in contact with CYS 59 (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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95A LEU* 4.2 4.4 - - - +
97A TYR* 3.4 31.3 - - + +
11E CYS* 3.8 5.8 - - - -
29E GLU* 2.9 41.4 + - - +
31E CYS* 2.0 54.5 - - - -
40E HIS 3.6 4.5 - - - -
42E TYR* 3.4 12.7 - - - -
58E GLY* 1.3 76.1 - - - -
60E TRP* 1.3 59.0 + - - +
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Residues in contact with TRP 60 (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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28A ALA 3.6 16.8 - - - -
29A PRO* 3.9 15.3 - - + -
83A SER* 3.3 37.7 - - - -
84A VAL* 3.6 2.2 - - - -
85A LEU* 3.8 7.2 - - + -
95A LEU* 3.9 23.8 - - + -
97A TYR* 3.5 7.7 + - - -
39E LEU* 3.9 3.1 - - - +
40E HIS* 2.9 46.1 + - + +
41E CYS 4.3 0.7 - - - -
42E TYR* 4.0 28.0 - + + -
59E CYS* 1.3 75.0 - - - +
61E LEU* 1.3 69.2 + - - +
63E ASP* 3.2 27.6 + - + +
66E CYS* 4.0 21.9 - - - -
83E PHE* 3.7 38.1 - + - -
85E CYS* 4.4 0.7 - - + -
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Residues in contact with LEU 61 (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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81A PRO* 3.7 37.9 - - + +
82A ILE* 4.4 4.8 - - - +
83A SER* 3.2 27.3 + - - +
97A TYR* 3.6 42.4 - - + +
98A HIS* 4.3 10.5 - - + +
32E GLU 4.2 5.4 - - - +
33E GLY* 4.7 4.7 - - - -
34E GLU 5.4 2.5 - - - +
37E LYS* 6.5 0.7 - - + -
38E ARG 4.9 0.9 - - - +
39E LEU* 3.8 18.4 - - + -
40E HIS* 3.7 1.3 - - - -
60E TRP* 1.3 79.2 + - - +
62E ASP* 1.3 72.1 + - + +
63E ASP* 2.5 16.8 + - - +
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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