Contacts of the strand formed by residues 87 - 93 (chain E) in PDB entry 1IBL
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 SER 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A C 4.2 0.7 + - - -
82E VAL 4.1 0.2 - - - +
83E GLU* 3.4 2.8 - - - +
84E PHE* 2.5 43.0 + - - +
86E ALA* 1.3 80.4 - - - +
88E LYS* 1.3 57.5 + - - +
125E SER* 2.5 34.7 + - - -
127E ASN 3.9 4.9 + - - -
130E ASN* 3.5 27.5 - - - +
131E ILE* 3.5 15.0 - - - -
134E ALA* 4.9 1.3 - - - -
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Residues in contact with LYS 88 (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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560A U 5.5 1.8 + - - -
566A G 5.8 5.5 - - - -
81E GLU* 2.6 37.6 + - - +
82E VAL 3.3 8.3 - - - +
83E GLU* 3.6 37.9 - - + +
86E ALA 4.9 2.5 - - - +
87E SER* 1.3 75.9 - - - +
89E ILE* 1.3 64.7 + - - +
90E VAL* 4.9 1.6 - - + -
122E GLU* 3.6 2.8 - - - -
123E LEU* 2.7 75.1 + - + +
124E GLY* 4.7 0.9 - - - +
131E ILE* 3.9 4.1 - - - +
134E ALA* 5.2 0.2 - - - -
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Residues in contact with ILE 89 (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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80E ILE 4.2 0.6 - - - +
81E GLU* 3.5 2.3 - - - -
82E VAL 2.9 30.3 + - - +
88E LYS* 1.3 75.9 - - - +
90E VAL* 1.3 93.7 + - - +
91E LEU* 3.7 18.8 - - + -
106E PRO* 4.3 12.3 - - + -
120E THR* 4.0 11.2 - - + +
121E LYS 3.7 11.9 - - - +
122E GLU* 4.5 7.4 - - + +
131E ILE* 4.5 6.5 - - + -
134E ALA* 4.0 18.1 - - + +
135E THR* 3.9 22.0 - - - +
138E ALA* 3.9 26.9 - - + -
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Residues in contact with VAL 90 (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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7A G 4.6 21.8 - - + +
79E GLU* 6.3 0.9 - - + -
80E ILE 3.8 3.6 - - - +
81E GLU* 3.3 36.1 - - + +
88E LYS* 4.2 3.8 - - + +
89E ILE* 1.3 82.8 - - - +
91E LEU* 1.3 70.8 + - - +
92E LYS* 5.0 4.7 - - + +
119E LEU 5.5 0.2 - - - +
120E THR* 3.3 6.6 - - - -
121E LYS* 3.0 42.0 + - + +
123E LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 91 (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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76E ILE* 5.4 3.4 - - + -
78E HIS 4.8 1.3 - - - +
79E GLU* 3.2 7.8 - - - +
80E ILE* 2.8 55.7 + - + +
89E ILE* 3.7 20.0 - - + -
90E VAL* 1.3 79.8 - - - +
92E LYS* 1.3 60.8 + - - +
93E PRO* 4.7 0.2 - - - -
106E PRO* 5.3 0.4 - - + -
110E LEU* 4.2 11.7 - - + -
118E ILE* 3.9 22.2 - - + -
119E LEU 3.5 1.6 - - - -
120E THR* 3.0 27.8 - - - +
135E THR* 4.8 6.3 - - + -
138E ALA* 4.0 13.0 - - + -
139E LEU* 4.0 28.3 - - + -
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Residues in contact with LYS 92 (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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6A G 3.7 26.3 - - - -
7A G 3.4 44.1 + - + +
298A A 5.4 2.0 + - - -
76E ILE* 4.4 0.9 - - - -
79E GLU* 3.9 14.6 - - + -
90E VAL* 5.3 6.5 - - + -
91E LEU* 1.3 75.9 - - - +
93E PRO* 1.3 77.7 - - + +
118E ILE* 3.3 6.5 - - - +
119E LEU* 2.6 57.1 + - + +
105H ARG* 5.2 6.7 - - - +
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Residues in contact with PRO 93 (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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6A G 4.6 2.4 - - - +
75E THR* 3.4 11.9 - - + +
76E ILE* 3.2 28.0 - - + +
78E HIS* 3.3 35.2 - - - +
79E GLU* 3.4 9.6 - - + -
92E LYS* 1.3 91.9 - - + +
94E ALA* 1.3 59.6 + - - +
118E ILE* 4.9 0.2 - - + -
119E LEU* 4.3 5.7 - - - +
105H ARG* 3.3 47.6 + - + +
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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