Contacts of the helix formed by residues 109 - 115 (chain E) in PDB entry 1QRP
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 GLY 109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E LEU* 5.6 3.1 - - - +
49E ALA* 4.9 2.1 + - - +
107E GLU 3.9 4.2 + - - +
108E PRO* 1.3 76.2 - - - +
110E SER* 1.3 65.9 + - - +
111E PHE 3.5 3.1 + - - -
112E LEU* 4.2 1.8 + - - -
113E TYR* 4.1 14.4 + - - +
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Residues in contact with SER 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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109E GLY* 1.3 70.7 - - - -
111E PHE* 1.3 66.0 + - - +
113E TYR* 3.1 16.7 + - - +
114E TYR* 3.3 35.5 + - - -
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Residues in contact with PHE 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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13E GLU* 5.1 2.5 - - - -
77E THR* 3.5 47.6 - - + -
78E GLY* 4.0 7.9 - - - +
109E GLY 3.5 1.4 - - - -
110E SER* 1.3 81.4 + - - +
112E LEU* 1.3 87.3 + - + +
114E TYR* 3.4 4.6 + - - +
115E ALA* 3.1 25.7 + - + +
117E PHE* 4.0 19.5 - + - -
327E HH0 3.5 40.4 - - + -
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Residues in contact with LEU 112 (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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39E TRP* 4.4 21.5 - - + -
49E ALA* 3.6 17.2 - - + +
53E HIS* 3.1 20.4 + - - -
75E TYR* 6.3 1.6 - - + -
77E THR 5.4 0.2 - - - +
78E GLY* 4.5 3.8 - - - -
79E SER 3.3 36.1 - - - +
107E GLU* 3.9 24.9 - - + +
108E PRO 4.7 4.4 + - - +
109E GLY 4.2 4.8 + - - +
110E SER 3.5 0.4 - - - -
111E PHE* 1.3 102.5 - - + +
113E TYR* 1.3 60.4 + - - +
114E TYR 3.5 0.2 + - - -
115E ALA* 3.6 10.4 + - + +
117E PHE* 4.1 22.7 - - + +
118E ASP 6.0 0.4 - - - +
120E ILE* 5.5 2.2 - - + -
327E HH0 5.8 0.4 - - + -
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Residues in contact with TYR 113 (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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48E LEU* 3.5 45.4 - - + +
49E ALA* 3.5 14.5 - - - +
51E THR* 4.6 2.5 - - - -
52E ASN* 2.8 61.7 + - + +
53E HIS* 3.5 4.7 - - - -
109E GLY 4.1 9.5 + - - +
110E SER* 3.1 13.1 + - - +
112E LEU* 1.3 78.0 - - - +
114E TYR* 1.3 94.8 - + - +
115E ALA 4.2 0.3 - - - +
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Residues in contact with TYR 114 (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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9E TYR* 5.2 3.8 + - - -
110E SER* 3.3 38.1 + - - +
111E PHE* 4.2 4.0 - - - +
113E TYR* 1.3 103.5 - + - +
115E ALA* 1.3 65.5 + - - +
116E PRO* 3.6 4.9 - - - +
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Residues in contact with ALA 115 (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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13E GLU* 4.8 1.6 - - - +
53E HIS* 2.8 31.7 + - - -
111E PHE* 3.1 24.3 + - + +
112E LEU* 3.7 11.9 - - + +
113E TYR 3.5 0.6 - - - +
114E TYR* 1.3 78.1 - - - +
116E PRO* 1.3 61.4 - - - +
117E PHE* 3.4 37.5 - - + +
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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