Contacts of the strand formed by residues 88 - 96 (chain I) 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 THR 88 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I THR* 4.4 3.1 - - - -
49I VAL 3.4 11.9 - - - +
50I SER* 3.6 6.7 - - - -
81I LEU* 4.4 0.7 - - - -
86I GLN* 3.4 7.0 + - - +
87I PRO* 1.3 77.4 + - - +
89I VAL* 1.3 75.1 + - - +
90I SER 4.4 0.2 + - - -
78J LEU 4.4 4.9 - - - +
79J ALA* 4.3 10.3 - - - -
80J SER* 2.7 38.4 + - - -
86J GLN* 2.9 26.2 + - - +
89J VAL* 3.8 33.0 - - + -
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Residues in contact with VAL 89 (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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88H THR* 3.9 26.9 - - + -
90H SER* 4.7 7.2 - - - +
48I THR* 3.3 3.5 - - - -
49I VAL* 2.9 34.9 + - + +
79I ALA* 4.3 7.0 - - + -
81I LEU* 3.0 29.6 - - + +
86I GLN* 3.6 25.1 - - - +
88I THR* 1.3 76.3 - - - +
90I SER* 1.3 69.5 + - - +
91I LEU* 3.8 17.7 + - + -
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Residues in contact with SER 90 (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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90H SER* 3.2 24.6 + - - -
47I ARG 3.3 13.1 + - - -
48I THR* 4.3 5.2 - - - +
88I THR* 4.2 2.4 - - - +
89I VAL* 1.3 73.5 - - - +
91I LEU* 1.3 57.9 + - - +
92I GLY* 3.4 9.2 + - - -
89J VAL* 4.3 10.3 - - - +
90J SER 3.1 29.3 + - - -
91J LEU* 3.6 17.2 + - - -
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Residues in contact with LEU 91 (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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47H ARG* 2.9 23.2 + - - -
48H THR* 3.5 30.7 - - + -
90H SER* 3.6 11.1 + - - -
46I LEU* 3.6 46.9 - - + +
47I ARG 2.8 12.2 + - - +
48I THR 5.0 0.2 - - - -
49I VAL* 3.7 29.6 - - + -
78I LEU* 4.2 15.5 - - + +
89I VAL* 4.1 17.0 - - + +
90I SER* 1.3 71.9 - - - +
92I GLY* 1.3 58.4 + - - +
93I GLY 3.3 0.9 + - - -
94I PHE* 4.0 14.6 + - + -
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Residues in contact with GLY 92 (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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47H ARG* 3.4 11.8 + - - -
90H SER* 5.3 0.2 - - - -
92H GLY* 5.6 2.9 - - - -
47I ARG* 3.6 27.1 + - - -
90I SER* 3.4 12.6 + - - -
91I LEU* 1.3 78.1 - - - +
93I GLY* 1.3 56.9 + - - +
91J LEU 4.7 1.1 - - - -
92J GLY* 5.5 3.3 - - - +
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Residues in contact with GLY 93 (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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47H ARG* 3.5 17.8 + - - -
45I SER* 3.1 20.5 + - - -
46I LEU 3.1 10.3 + - - -
47I ARG* 3.7 17.0 - - - +
92I GLY* 1.3 77.1 - - - +
94I PHE* 1.3 62.7 + - - +
95I GLU* 3.2 11.3 + - - +
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Residues in contact with PHE 94 (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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19H LEU* 4.4 3.6 - - + -
47H ARG* 3.6 33.0 - - + +
48H THR* 5.0 0.4 - - + -
114H SER* 3.4 22.0 - - - -
115H GLY* 3.5 30.3 - - - -
116H GLN* 3.9 14.8 - - + -
44I LEU 3.4 2.8 - - - +
46I LEU* 2.8 45.1 + - + +
76I ILE* 3.8 16.2 - - + -
78I LEU* 3.5 23.1 - - + -
91I LEU* 4.0 19.2 + - + -
92I GLY 3.8 0.4 - - - -
93I GLY* 1.3 72.4 - - - +
95I GLU* 1.3 70.0 - - - +
96I ILE* 3.8 15.9 + - + +
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Residues in contact with GLU 95 (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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17H ASN* 3.1 16.4 + - - +
19H LEU* 5.3 0.9 - - - +
116H GLN* 3.2 24.2 + - - +
43I GLN* 3.8 27.2 + - + +
44I LEU 3.3 4.5 - - - +
45I SER* 3.7 20.0 + - - +
93I GLY 3.2 8.0 + - - +
94I PHE* 1.3 78.4 - - - +
96I ILE* 1.3 64.4 - - - +
118I LEU* 3.9 23.0 - - - +
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Residues in contact with ILE 96 (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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17H ASN* 3.8 2.2 - - - -
19H LEU* 3.8 33.7 - - + -
43I GLN* 3.2 7.2 + - - +
44I LEU* 2.7 40.0 + - + +
46I LEU* 3.9 29.6 - - + -
64I ALA* 4.4 17.3 - - + -
66I GLY* 6.1 0.2 - - - -
78I LEU* 4.9 0.7 - - + -
94I PHE* 4.1 16.2 - - + +
95I GLU* 1.3 82.1 - - - +
97I THR* 1.3 75.2 + - - +
98I PRO* 3.6 1.2 - - - +
100I VAL* 3.8 30.0 - - + +
102I LEU* 5.2 0.9 - - + -
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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