Contacts of the helix formed by residues 105 - 111 (chain E) in PDB entry 1IB1
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 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E TRP* 3.4 16.8 - - + -
101E GLU* 3.6 24.0 - - - +
103E ARG* 4.1 4.9 - - + +
104E LEU* 1.3 78.2 - - - +
106E GLN* 1.3 65.0 + - - +
107E GLU* 3.4 25.0 - - - +
108E SER* 2.4 27.8 + - - -
180E ALA* 4.5 6.3 - - + -
181E ILE* 3.0 15.9 - - - +
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Residues in contact with GLN 106 (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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73D GLU* 5.0 10.5 - - - +
105E THR* 1.3 75.7 - - - +
107E GLU* 1.3 65.2 + - - +
108E SER 3.0 1.7 + - - -
109E LEU* 3.1 31.5 + - - +
180E ALA* 3.6 10.4 + - - +
181E ILE* 3.4 19.3 - - - +
182E VAL* 2.9 55.5 + - - +
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Residues in contact with GLU 107 (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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71D GLY* 3.6 3.5 - - - +
72D ALA* 4.0 1.7 - - - -
73D GLU* 3.0 58.4 + - + +
74D LYS 4.6 0.5 + - - -
99E TRP* 3.9 5.5 - - - -
101E GLU* 5.3 1.0 - - - +
105E THR* 3.4 17.5 - - - +
106E GLN* 1.3 78.3 - - - +
108E SER* 1.3 56.1 + - - +
109E LEU 3.1 5.9 + - - -
110E ALA* 3.3 9.6 + - - +
111E LEU* 3.0 44.5 - - + +
113E ARG* 3.4 16.8 + - - -
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Residues in contact with SER 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E TRP* 3.5 44.9 - - - -
104E LEU* 3.9 4.0 - - - +
105E THR* 2.4 41.5 + - - -
107E GLU* 1.3 74.3 - - - +
109E LEU* 1.3 63.1 + - - +
110E ALA 3.2 0.7 - - - -
111E LEU* 3.4 14.0 + - - +
120E HIS* 3.5 11.8 + - - -
122E HIS* 3.4 13.9 - - - -
181E ILE* 3.8 6.1 - - - +
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Residues in contact with LEU 109 (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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64E PRO 5.3 10.1 - - - +
65E LEU* 4.3 8.8 - - + +
69E GLU* 5.2 4.9 - - - +
73E PHE* 3.5 7.1 - - - -
106E GLN* 3.1 25.5 + - - +
107E GLU 3.1 0.8 - - - -
108E SER* 1.3 79.2 + - - +
110E ALA* 1.3 58.7 + - + +
111E LEU 3.4 0.2 - - - -
120E HIS* 4.4 7.2 - - + -
122E HIS* 3.3 27.2 + - + +
159E MET* 3.7 29.4 - - + -
181E ILE* 3.6 27.6 - - + -
182E VAL 5.2 0.2 - - - +
183E VAL* 4.2 15.0 - - + -
401E COT 6.3 0.7 - - + -
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Residues in contact with ALA 110 (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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69E GLU* 4.8 12.1 - - + +
72E HIS* 4.1 19.2 - - - +
73E PHE* 3.9 9.6 - - - -
107E GLU 3.3 6.5 + - - +
108E SER 3.2 0.2 - - - -
109E LEU* 1.3 78.9 - - + +
111E LEU* 1.3 66.8 + - + +
112E HIS 4.2 0.2 + - - -
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Residues in contact with LEU 111 (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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70D GLU* 6.3 0.4 - - + -
71D GLY* 3.4 35.0 - - - +
73E PHE* 4.0 3.5 - - - -
97E SER* 2.9 17.9 + - - -
98E LEU 3.9 4.7 - - - +
99E TRP* 4.2 11.4 - - + -
107E GLU* 3.0 52.3 - - + +
108E SER* 3.4 16.5 + - - +
109E LEU 3.4 0.4 + - - -
110E ALA* 1.3 84.9 - - + +
112E HIS* 1.3 63.2 + - - +
113E ARG* 3.8 19.1 - - - +
120E HIS* 5.1 0.7 + - - -
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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