Contacts of the strand formed by residues 60 - 67 (chain E) in PDB entry 1XE0
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 HIS 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.8 25.1 - - + -
55E ALA* 3.9 12.5 - - + +
56E LYS 3.1 20.9 + - - -
58E GLU* 2.8 30.0 + - - +
59E LEU* 1.3 77.2 - - - +
61E VAL* 1.3 61.8 + - - +
62E VAL* 5.3 2.0 - - + +
79E ALA 3.7 1.0 - - - +
80E SER* 3.3 4.9 - - - -
81E LEU* 2.8 38.0 + - + +
104E LEU* 4.3 1.7 - - + +
106E SER 3.1 6.7 + - - +
107E GLY* 3.6 5.3 - - - -
108E SER* 3.3 17.0 - - - -
109E GLY* 2.9 40.5 + - - -
111E VAL* 3.8 12.3 - - + +
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Residues in contact with VAL 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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51D LEU 5.0 1.3 - - - +
52D GLY* 5.4 2.2 - - - -
53D ALA* 5.0 9.0 - - + +
59E LEU* 3.9 16.4 - - + -
60E HIS* 1.3 79.6 - - - +
62E VAL* 1.3 71.0 + - - +
63E GLU* 5.3 1.3 - - + -
77E ALA* 4.9 13.9 - - + -
79E ALA 3.4 7.2 - - - +
80E SER* 3.7 17.9 - - - +
104E LEU* 3.5 6.4 - - - +
105E LYS* 2.9 49.2 + - + -
106E SER* 2.9 27.5 + - - +
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Residues in contact with VAL 62 (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 LEU* 4.1 17.7 - - + -
49E VAL* 4.1 14.4 - - + -
60E HIS* 5.3 2.0 - - + -
61E VAL* 1.3 80.3 - - - +
63E GLU* 1.3 68.6 + - - +
77E ALA* 3.7 2.4 - - - -
78E LEU* 2.8 40.1 + - + +
79E ALA 2.9 18.1 + - - +
81E LEU* 5.9 1.3 - - + -
102E LEU* 5.1 2.2 - - + -
103E ARG 3.4 9.9 - - - +
104E LEU* 4.3 10.5 - - + -
111E VAL* 3.8 29.6 - - + -
113E VAL* 4.4 12.1 - - + -
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Residues in contact with GLU 63 (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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61E VAL* 5.3 1.6 - - + -
62E VAL* 1.3 78.8 - - - +
64E ALA* 1.3 60.0 + - - +
75E LYS* 3.5 32.7 + - - +
76E ILE 3.2 16.0 - - - +
77E ALA* 4.3 3.4 - - + -
78E LEU* 4.2 4.7 - - - +
102E LEU* 3.5 4.0 - - - +
103E ARG* 2.7 84.0 + - + +
105E LYS* 4.0 32.9 + - + +
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Residues in contact with ALA 64 (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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19D LEU* 4.5 5.1 - - + +
63E GLU* 1.3 76.7 - - - +
65E GLU* 1.3 59.5 + - - +
66E GLY 4.3 0.2 - - - -
74E ILE 3.9 0.5 - - - +
75E LYS* 3.3 3.0 - - - +
76E ILE* 2.8 49.7 + - + +
78E LEU* 3.9 20.4 - - + +
96E ILE* 4.7 5.6 - - + -
100E VAL* 4.2 15.3 - - + -
101E ILE 3.4 6.3 - - - -
102E LEU* 4.3 4.0 - - + -
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64E ALA* 1.3 75.3 - - - +
66E GLY* 1.3 59.3 + - - +
73E THR* 3.6 24.3 - - + +
74E ILE 3.3 12.6 - - - +
75E LYS* 3.9 17.1 + - + +
99E PRO 4.4 0.2 - - - +
100E VAL* 3.5 7.8 - - - +
101E ILE* 2.9 57.4 + - + +
103E ARG* 2.9 42.8 + - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.6 15.5 - - - +
65E GLU* 1.3 77.4 - - - +
67E ILE* 1.3 70.0 + - - -
73E THR* 4.3 3.1 - - - -
74E ILE* 2.9 32.8 + - - +
99E PRO 4.3 12.1 - - - -
100E VAL* 4.9 0.9 - - - -
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Residues in contact with ILE 67 (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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18D PHE* 3.9 13.2 - - + +
19D LEU* 3.2 24.4 + - - +
66E GLY* 1.3 76.6 - - - -
68E ASN* 1.3 76.1 + - - +
71E GLY* 3.4 26.0 - - - +
72E LYS 3.5 1.8 - - - +
73E THR* 3.0 42.0 - - - +
99E PRO* 5.0 2.9 + - + -
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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