Contacts of the helix formed by residues 107 - 115 (chain F) in PDB entry 4R8A
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 GLU 107 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106F LEU* 1.3 76.0 - - - +
108F LEU* 1.3 65.1 + - - +
109F ALA* 4.0 9.9 - - + +
110F GLN* 3.0 31.7 + - + +
111F LEU* 3.0 21.3 + - - +
143F GLN* 5.8 1.1 - - - +
147F PRO 3.7 13.1 - - - +
149F ALA* 3.3 30.5 + - + +
155F TRP* 4.1 0.4 - - - -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 1.3 74.3 + - - +
109F ALA* 1.3 60.3 + - - +
111F LEU* 3.9 5.6 - - + +
112F PHE* 3.3 37.3 + - + -
124F PHE* 3.5 33.2 - - + -
139F LEU* 3.5 20.0 - - + -
142F LEU* 4.1 7.4 - - + +
143F GLN* 4.0 33.3 + - - +
146F PHE* 3.5 29.9 + - + +
147F PRO 5.7 0.2 + - - -
148F GLU 4.7 1.0 + - - -
155F TRP* 3.6 23.9 - - + -
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 3.0 6.9 - - + +
108F LEU* 1.3 80.3 - - - +
110F GLN* 1.3 59.2 + - + +
111F LEU 3.5 0.2 - - - -
112F PHE* 3.5 14.2 - - - +
113F GLY* 3.8 4.0 + - - -
139F LEU* 3.6 20.8 - - + +
143F GLN* 4.0 25.2 + - - +
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Residues in contact with GLN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 4.1 29.3 - - + +
105F THR 3.7 8.9 + - - -
106F LEU* 3.4 14.4 - - + +
107F GLU* 3.0 48.1 - - + +
109F ALA* 1.3 74.8 - - - +
111F LEU* 1.3 64.1 + - - +
112F PHE 3.1 1.6 - - - -
113F GLY* 3.1 12.1 + - - +
114F LEU* 3.4 18.0 + - - +
165F GLU* 5.9 1.0 + - - -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 4.4 18.3 - - + +
107F GLU 3.0 15.1 + - - +
108F LEU* 3.9 9.0 - - + +
110F GLN* 1.3 77.6 - - - +
112F PHE* 1.3 63.0 + - - +
113F GLY 3.1 0.4 - - - -
114F LEU* 3.1 10.0 + - + +
115F LEU* 3.1 47.7 + - + +
120F LEU* 4.3 3.6 - - + -
123F LEU* 4.5 4.9 - - + -
124F PHE* 4.1 19.5 - - + -
152F LEU* 4.6 12.1 - - + -
155F TRP* 3.5 49.1 - - + +
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Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LEU* 3.3 42.0 + - + +
109F ALA 3.5 13.0 - - - +
111F LEU* 1.3 80.8 - - - +
113F GLY* 1.3 51.7 + - - +
115F LEU 3.1 8.8 - - - +
120F LEU* 3.7 43.7 - - + -
124F PHE* 4.3 1.3 - + - -
135F LYS* 2.7 72.0 + - + -
138F LEU* 3.8 16.2 - - + -
139F LEU* 3.6 33.0 - - + -
142F LEU* 4.0 13.2 - - + -
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Residues in contact with GLY 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F ALA 3.8 3.5 + - - -
110F GLN* 3.1 11.4 + - - -
111F LEU 3.1 0.8 - - - -
112F PHE* 1.3 79.8 - - - +
114F LEU* 1.3 62.1 + - - +
115F LEU 4.6 1.0 - - - +
135F LYS* 4.6 5.2 + - - -
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 3.7 43.3 - - + +
74F PHE* 4.2 2.7 - - - +
75F ARG* 3.2 46.2 + - + +
106F LEU* 3.6 30.5 - - + -
110F GLN 3.7 9.0 - - - +
111F LEU* 3.1 9.1 + - + +
113F GLY* 1.3 82.1 - - - +
115F LEU* 1.3 68.6 + - + +
116F LYS* 5.6 0.5 - - - +
152F LEU* 5.5 0.7 - - + -
163F VAL* 3.6 21.5 - - + -
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ARG* 3.6 9.4 - - - +
111F LEU* 3.1 35.5 + - + +
112F PHE 3.1 16.5 - - - +
113F GLY 4.5 0.7 - - - +
114F LEU* 1.3 91.7 - - + +
116F LYS* 1.3 64.5 + - - +
119F GLU* 3.6 14.6 - - + +
120F LEU* 3.6 28.6 - - + +
123F LEU* 4.8 6.7 - - + -
135F LYS* 3.3 10.6 + - - -
152F LEU* 5.6 1.8 - - + -
156F GLN* 4.7 10.3 - - + +
159F PHE* 3.5 40.4 - - + -
163F VAL* 6.0 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