Contacts of the strand formed by residues 39 - 48 (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 LEU 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A TYR* 4.0 9.6 - - - +
9E ARG* 3.0 49.3 + - + +
31E CYS* 3.7 25.8 - - + +
32E GLU 4.1 0.4 - - - +
33E GLY* 3.9 21.8 - - - +
34E GLU 5.2 0.4 - - - +
37E LYS 4.6 4.7 - - - +
38E ARG* 1.3 81.8 - - - +
40E HIS* 1.3 73.7 + - - +
60E TRP 4.1 2.0 - - - +
61E LEU* 3.8 24.7 - - + -
87E GLU* 3.6 12.3 + - - +
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Residues in contact with HIS 40 (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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9E ARG* 3.6 3.1 - - - +
11E CYS* 3.4 9.8 - - - -
31E CYS* 4.4 2.3 - - - -
38E ARG* 3.9 8.3 - - - +
39E LEU* 1.3 82.6 + - - +
41E CYS* 1.3 64.9 + - - +
59E CYS* 3.6 1.6 - - - +
60E TRP* 2.9 42.8 + + + +
61E LEU 3.7 2.2 - - - -
62E ASP* 3.4 30.6 - - - -
63E ASP 3.4 22.8 + - - -
66E CYS* 3.0 38.0 + - + +
67E TYR* 3.8 18.2 - + - -
86E CYS 3.3 14.1 + - - +
87E GLU* 4.1 11.1 - - - +
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Residues in contact with CYS 41 (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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9E ARG* 4.4 4.9 - - - -
10E GLU 3.7 10.1 - - - -
11E CYS* 2.0 46.4 - - - -
40E HIS* 1.3 75.0 - - - +
42E TYR* 1.3 61.2 + - - +
58E GLY 3.4 1.8 - - - -
60E TRP* 4.3 2.7 - - - -
85E CYS* 3.0 6.2 - - - +
86E CYS* 2.9 33.9 + - - -
88E GLY 4.2 5.6 - - - -
90E PHE 4.4 1.6 - - - -
91E CYS* 3.6 23.6 - - - -
92E ASN* 3.6 19.3 - - - -
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Residues in contact with TYR 42 (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* 4.8 9.4 - - + -
95A LEU* 3.0 32.2 - - + +
13E TYR* 5.6 3.1 - - - -
41E CYS* 1.3 76.1 - - - +
43E ALA* 1.3 66.6 + - - +
44E SER* 4.2 4.0 - - - -
56E LYS* 3.8 35.4 - - + +
57E LYS* 3.4 6.5 + - - -
58E GLY* 2.8 66.0 + - - -
59E CYS 3.4 15.9 - - - -
60E TRP* 4.0 14.8 - + + -
83E PHE* 3.8 31.9 - + + -
84E CYS 3.2 11.0 - - - +
85E CYS* 4.5 0.2 - - + -
92E ASN* 2.7 24.2 + - - -
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Residues in contact with ALA 43 (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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42E TYR* 1.3 76.9 - - - +
44E SER* 1.3 62.7 + - - +
45E TRP* 3.6 17.2 - - + -
54E LEU* 5.3 0.2 - - + -
56E LYS 3.3 8.5 - - - -
57E LYS* 3.8 19.7 - - + -
72E CYS* 4.3 4.2 - - - -
83E PHE* 3.6 2.4 - - - -
84E CYS* 3.0 39.3 + - - +
92E ASN* 4.4 4.0 - - + +
95E PHE* 4.5 12.1 - - + -
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Residues in contact with SER 44 (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* 3.7 29.0 - - - +
42E TYR* 4.2 1.7 - - - -
43E ALA* 1.3 76.8 - - - +
45E TRP* 1.3 65.2 + - - +
54E LEU* 3.3 5.0 - - - +
55E VAL* 2.9 25.7 + - - +
56E LYS* 2.9 29.8 + - - +
81E VAL* 4.1 6.1 - - - -
82E TYR 3.0 13.9 - - - -
83E PHE* 4.4 2.9 - - - -
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Residues in contact with TRP 45 (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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43E ALA* 3.6 21.5 - - + -
44E SER* 1.3 87.2 - - - +
46E ARG* 1.3 72.2 + - - +
47E ASN* 4.7 5.7 + - + +
52E ILE* 3.8 16.8 - - + +
53E GLU 3.4 14.4 - - - +
54E LEU* 4.0 8.1 - - + -
55E VAL* 3.9 6.3 - - - +
74E ALA* 3.9 20.9 - - + -
81E VAL* 3.8 3.5 - - - +
82E TYR* 2.9 68.1 + + + +
83E PHE 4.4 0.4 - - - -
84E CYS* 3.9 13.2 - - + -
95E PHE* 3.0 51.1 - + + -
96E THR 3.9 18.4 - - - -
97E HIS* 5.0 2.5 - - + +
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Residues in contact with ARG 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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91A GLY 3.7 11.9 + - - -
92A VAL* 4.8 5.7 - - - +
93A PRO* 3.4 31.8 - - - +
45E TRP* 1.3 83.3 - - - +
47E ASN* 1.3 62.4 + - - +
48E SER* 4.1 1.3 - - - +
51E THR 4.6 0.2 - - - -
52E ILE* 3.7 1.7 - - - -
53E GLU* 2.8 60.1 + - + +
55E VAL* 4.0 22.8 - - + +
80E GLN 4.0 17.7 - - - +
81E VAL* 4.8 11.1 - - + +
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Residues in contact with ASN 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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45E TRP* 4.7 4.0 + - + -
46E ARG* 1.3 74.5 - - - +
48E SER* 1.3 58.7 + - - +
49E SER* 3.2 7.4 + - - +
50E GLY* 3.5 23.3 - - - +
51E THR 3.8 6.4 - - - +
52E ILE* 3.5 27.4 - - - +
80E GLN 4.7 2.2 + - - -
82E TYR* 3.4 49.8 + - + -
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Residues in contact with SER 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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46E ARG* 4.1 1.4 - - - +
47E ASN* 1.3 68.6 - - - +
49E SER* 1.3 74.8 + - - +
50E GLY 3.5 0.2 - - - -
51E THR* 3.3 25.5 + - - -
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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