Contacts of the strand formed by residues 118 - 124 (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 ILE 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75E THR* 4.8 0.2 - - - +
76E ILE* 4.6 16.8 - - + -
91E LEU* 3.9 28.5 - - + -
92E LYS 3.3 16.4 - - - +
94E ALA* 3.8 5.1 - - - +
99E GLY 3.0 8.6 + - - +
100E VAL* 3.8 17.3 - - + -
101E ILE* 3.1 23.8 + - - +
110E LEU* 3.7 43.5 - - + -
115E VAL* 3.9 15.3 - - + -
117E ASP* 1.3 75.8 - - - +
119E LEU* 1.3 74.7 + - - +
120E THR* 4.8 2.0 - - - +
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Residues in contact with LEU 119 (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 3.5 48.5 - - + +
7A G 4.3 21.3 - - + +
90E VAL* 3.8 0.7 - - - +
91E LEU* 3.5 2.3 - - - -
92E LYS* 2.6 75.8 + - + +
93E PRO 4.3 1.3 - - - +
94E ALA* 4.0 9.0 - - + -
98E THR* 4.2 10.8 - - + -
101E ILE* 3.4 31.6 - - + -
118E ILE* 1.3 75.8 - - - +
120E THR* 1.3 60.0 + - - +
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Residues in contact with THR 120 (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 2.4 31.4 + - - -
8A A 3.2 8.9 - - - +
9A G 4.3 2.9 - - - +
89E ILE* 4.0 8.9 - - + +
90E VAL* 3.3 3.6 - - - -
91E LEU* 3.0 29.5 - - - +
101E ILE 3.0 15.6 + - - -
102E ALA* 3.3 29.3 - - + +
103E GLY 4.0 6.3 - - - +
106E PRO* 4.5 5.0 - - + +
110E LEU* 3.8 10.7 - - - +
118E ILE* 4.6 0.8 - - - +
119E LEU* 1.3 74.0 - - - +
121E LYS* 1.3 66.8 + - - +
122E GLU 4.6 0.2 - - - +
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Residues in contact with LYS 121 (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 3.4 40.2 - - + +
8A A 4.4 11.2 + - - +
9A G 2.7 25.8 + - - +
298A A 6.3 0.7 - - - +
558A G 4.0 4.8 + - - -
559A A 2.9 35.3 + - - -
560A U 5.8 2.7 - - - -
89E ILE* 4.1 1.3 - - - -
90E VAL* 3.0 40.2 + - + +
120E THR* 1.3 82.3 - - - +
122E GLU* 1.3 83.0 + - - +
123E LEU* 3.7 19.7 + - + -
126E ARG* 4.4 0.4 - - - +
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Residues in contact with GLU 122 (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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9A G 2.7 48.0 + - - +
10A A 5.1 2.1 + - - -
559A A 5.1 0.5 + - - -
88E LYS 3.7 4.7 - - - -
89E ILE* 4.5 3.8 - - + +
103E GLY* 3.4 17.5 - - - -
105E VAL* 5.0 2.8 + - - +
106E PRO* 3.6 18.4 - - + +
120E THR* 5.0 1.1 - - + -
121E LYS* 1.3 81.3 + - - +
123E LEU* 1.3 69.2 + - - +
126E ARG* 3.5 35.0 + - - +
131E ILE* 3.2 41.9 - - + +
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Residues in contact with LEU 123 (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 4.8 3.8 - - - +
559A A 5.5 1.1 - - - +
560A U 4.0 48.0 - - + +
88E LYS* 2.7 67.3 + - + +
90E VAL* 4.0 13.5 - - + -
121E LYS* 3.8 29.2 - - + +
122E GLU* 1.3 85.7 - - - +
124E GLY* 1.3 67.7 - - - +
125E SER 3.6 5.2 + - - +
126E ARG* 5.2 0.9 - - - -
131E ILE* 4.4 0.9 - - - +
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Residues in contact with GLY 124 (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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20A U 5.2 5.2 - - - -
560A U 5.6 5.0 + - - +
86E ALA 3.3 10.3 - - - -
88E LYS* 4.7 2.4 - - - +
123E LEU* 1.3 75.0 - - - +
125E SER* 1.3 65.4 + - - -
126E ARG* 3.3 10.4 + - - +
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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