Contacts of the strand formed by residues 66 - 71 (chain I) in PDB entry 2XEW
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 66 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C PHE* 4.1 23.5 - - - -
6C LYS* 4.7 1.0 - - - +
64C GLU* 4.1 20.4 - - + +
66C THR* 4.4 3.2 + - - -
4I PHE* 3.3 20.4 - - + +
6I LYS* 3.9 34.7 + - + -
45I PHE* 3.5 18.8 - - - -
64I GLU 3.7 2.5 + - - -
65I SER* 1.3 75.2 + - - +
67I LEU* 1.3 74.8 + - - +
68I HIS* 5.0 2.0 - - + -
1077I EDO 4.1 8.5 + - - -
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Residues in contact with LEU 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ILE* 4.4 17.9 - - + -
4I PHE 2.7 15.8 + - - +
5I VAL* 4.3 14.1 - - + -
6I LYS* 2.9 24.9 + - - +
23I ILE* 5.4 0.4 - - + -
26I VAL* 4.5 5.2 - - + -
43I LEU* 4.4 20.2 - - + -
44I ILE 3.4 9.0 - - - +
45I PHE* 3.9 24.9 - - + -
50I LEU* 3.9 19.5 - - + -
56I LEU* 4.8 7.2 - - + -
61I ILE* 4.1 22.4 - - + -
65I SER* 4.6 3.8 - - - -
66I THR* 1.3 85.0 - - - +
68I HIS* 1.3 66.3 + - - +
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Residues in contact with HIS 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 5.1 2.4 - - - +
63C LYS* 3.1 28.9 + - + -
64C GLU* 3.3 25.7 + - + -
65C SER* 3.5 5.1 + - - -
6I LYS* 3.3 18.9 + - + +
7I THR 4.9 2.7 - - - -
8I LEU* 3.5 28.6 - - + +
42I ARG 3.5 0.9 - - - +
43I LEU* 3.3 7.7 - - - +
44I ILE* 2.8 51.2 + - + +
66I THR* 5.0 1.1 - - + -
67I LEU* 1.3 75.4 + - - +
69I LEU* 1.3 61.1 + - - +
70I VAL* 4.0 1.1 - - + -
1077I EDO 2.9 34.3 - - - +
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Residues in contact with LEU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I VAL* 3.5 19.1 - - + -
6I LYS 3.0 11.6 + - - +
7I THR* 3.8 23.9 - - + +
8I LEU* 4.6 1.9 + - - +
13I ILE* 4.2 14.1 - - + -
30I ILE* 4.1 21.8 - - + -
36I ILE* 4.2 17.7 - - + -
40I GLN 5.3 0.2 - - - +
41I GLN* 3.5 40.6 - - + +
42I ARG 3.4 4.5 - - - +
43I LEU* 3.9 7.6 - - + -
67I LEU 4.1 0.2 + - - -
68I HIS* 1.3 72.7 - - - +
70I VAL* 1.3 70.2 + - - +
71I LEU* 6.6 0.2 - - + -
71L LEU* 4.2 16.7 - - + +
73L LEU* 6.2 0.2 - - + -
1075L EDO 4.7 2.1 + - - -
1076L EDO 5.4 0.3 + - - -
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Residues in contact with VAL 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 4.2 17.7 - - + -
40I GLN 3.7 1.7 - - - +
41I GLN* 3.9 1.6 - - - -
42I ARG* 2.8 71.3 + - + +
44I ILE* 4.0 20.0 - - + -
68I HIS* 4.0 2.0 - - + -
69I LEU* 1.3 84.2 - - - +
71I LEU* 1.3 62.2 + - - +
9L THR* 3.5 15.3 - - + +
11L LYS* 5.7 0.9 - - + -
71L LEU* 5.5 0.4 - - - -
1075L EDO 2.9 26.7 - - - +
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ILE* 5.2 4.9 - - + -
40I GLN* 3.6 19.5 - - + +
42I ARG* 5.2 0.2 - - - +
70I VAL* 1.3 74.8 - - - +
72I ARG* 1.3 59.3 + - - +
73I LEU* 4.6 6.3 - - + -
7L THR* 4.1 13.7 - - + -
11L LYS* 2.9 13.0 + - - +
36L ILE* 3.5 35.2 - - + -
69L LEU* 3.8 24.0 - - + +
70L VAL* 5.8 0.2 - - - -
71L LEU* 3.3 41.6 - - + +
1075L EDO 2.6 40.9 + - - +
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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