Contacts of the strand formed by residues 53 - 60 (chain E) in PDB entry 1UGI
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 GLU 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E GLU* 5.5 1.2 - - - +
47E TYR* 3.3 7.8 - - - -
48E ASP* 2.8 34.3 + - + +
51E THR* 3.0 37.0 + - - +
52E ASP* 1.3 79.2 - - - +
54E ASN* 1.3 61.1 - - - +
55E VAL* 5.1 4.3 - - + +
72E ILE* 3.6 27.5 - - + +
73E GLN 3.3 10.5 - - - +
74E ASP* 4.2 15.6 - - + +
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Residues in contact with ASN 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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19E GLN* 4.9 6.1 + - - -
45E THR* 5.4 6.1 - - - +
46E ALA 3.8 3.2 + - - -
47E TYR* 3.8 32.0 - - - +
53E GLU* 1.3 74.7 - - - +
55E VAL* 1.3 61.0 + - - +
56E MET* 3.9 13.5 + - + +
71E VAL 3.6 1.9 - - - +
72E ILE* 3.4 4.2 - - - +
73E GLN* 2.8 54.9 + - + +
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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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8E ILE* 4.2 18.6 - - + +
11E GLU* 4.2 17.0 - - + -
12E THR* 3.7 26.7 - - + -
44E HIS 3.6 1.9 - - - +
45E THR* 3.4 2.8 - - - -
46E ALA* 2.9 46.6 + - - +
48E ASP* 5.1 3.1 - - + -
53E GLU* 4.9 9.6 - - + +
54E ASN* 1.3 75.7 - - - +
56E MET* 1.3 63.9 + - - +
57E LEU 4.0 0.2 + - - -
70E LEU* 3.8 26.7 - - + -
71E VAL 3.8 1.3 - - - -
72E ILE* 4.4 17.7 - - + -
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Residues in contact with MET 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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43E VAL* 4.0 10.3 - - + -
44E HIS 3.7 3.6 - - - -
45E THR* 3.6 22.0 - - + -
54E ASN* 4.4 11.9 - - + +
55E VAL* 1.3 74.4 - - - +
57E LEU* 1.3 61.1 + - - +
58E LEU* 3.6 9.7 - - + +
70E LEU* 3.4 6.2 - - - -
71E VAL* 2.8 70.3 + - + +
73E GLN* 4.0 26.5 - - + +
79E ASN* 4.7 2.9 - - - +
1105E SO4 3.5 25.6 - - - -
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Residues in contact with LEU 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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4E LEU* 3.5 49.6 - - + +
7E ILE* 4.0 20.6 - - + -
8E ILE* 3.9 13.2 - - + -
43E VAL* 3.5 0.3 - - - -
44E HIS* 2.8 54.4 + - + +
55E VAL 4.0 1.0 - - - -
56E MET* 1.3 72.4 - - - +
58E LEU* 1.3 68.8 + - - +
59E THR* 3.9 9.9 - - + -
67E PRO* 4.5 0.9 - - + -
69E ALA 3.6 11.2 - - - +
70E LEU* 4.0 13.2 - - + -
84E LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 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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24E MET* 5.3 3.4 - - - -
29E VAL* 4.3 8.5 - - + -
32E VAL* 6.2 0.7 - - + -
33E ILE* 4.2 18.4 - - + -
41E ILE* 3.6 24.5 - - + -
42E LEU 3.3 3.8 - - - -
43E VAL* 4.2 15.5 - - + -
56E MET* 3.6 23.3 - - + +
57E LEU* 1.3 77.1 - - - +
59E THR* 1.3 63.2 + - - +
67E PRO* 3.8 0.5 - - - +
68E TRP* 2.8 50.5 + - + +
69E ALA* 2.8 23.8 + - + +
71E VAL* 4.0 14.4 - - + -
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Residues in contact with THR 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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4E LEU* 4.0 11.4 - - + -
41E ILE* 3.2 13.3 - - - +
42E LEU* 2.8 32.2 + - - +
44E HIS* 2.9 34.9 + - + +
57E LEU* 3.9 13.7 - - + -
58E LEU* 1.3 79.3 - - - +
60E SER* 1.3 75.7 + - - +
65E TYR* 3.6 21.1 - - + +
66E LYS 3.2 10.1 - - - -
67E PRO* 4.1 8.7 - - + -
68E TRP 4.3 0.2 - - - +
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Residues in contact with SER 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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39E SER* 4.3 17.3 - - - -
40E ASP 3.8 8.7 - - - -
41E ILE* 4.1 5.0 - - - +
42E LEU* 4.1 3.0 - - - +
59E THR* 1.3 90.7 + - - +
61E ASP* 1.3 65.9 + - - +
64E GLU* 4.1 6.4 + - - +
65E TYR* 3.2 12.5 + - - -
66E LYS* 2.8 38.8 + - - +
68E TRP* 5.1 0.4 - - - +
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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