Contacts of the helix formed by residues 105 - 119 (chain F) in PDB entry 5UQ9
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 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103F ASN 5.3 2.0 - - - +
104F SER* 1.3 73.1 - - - +
106F TYR* 1.3 69.2 + - + +
107F ARG* 3.2 11.5 - - + +
108F ASP* 3.0 39.8 + - - +
109F THR* 3.2 12.9 + - - -
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Residues in contact with TYR 106 (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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104F SER 3.6 2.6 + - - -
105F GLU* 1.3 74.4 - - + +
107F ARG* 1.3 103.8 + - + +
109F THR* 3.2 4.8 + - - -
110F THR* 2.9 34.3 + - - -
178F GLY 3.7 9.1 - - - +
181F HIS* 3.8 10.7 - - + +
182F PHE* 3.7 51.9 - + + +
185F MET* 3.6 26.0 - - + +
270F SER* 4.4 1.6 + - - -
273F GLU* 4.3 0.3 + - - -
274F TYR* 3.0 27.7 + - - -
349F PHE* 4.3 13.0 - + - -
351F TRP* 4.4 11.7 - + - -
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F GLU* 3.2 10.9 - - + +
106F TYR* 1.3 123.1 + - + +
108F ASP* 1.3 66.1 + - - +
110F THR* 3.4 6.9 + - - -
111F ARG* 3.1 21.8 + - - +
270F SER* 5.8 1.0 - - - -
273F GLU* 2.5 38.4 + - - -
274F TYR* 4.1 7.5 + - - -
349F PHE* 5.2 5.3 - - + -
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Residues in contact with ASP 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLY* 5.2 6.6 - - - -
104F SER* 5.5 0.6 - - - -
105F GLU* 3.0 34.5 + - - +
107F ARG* 1.3 80.2 - - - +
109F THR* 1.3 59.0 + - - +
111F ARG* 3.2 22.4 + - - +
112F ARG* 2.9 64.6 + - - +
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Residues in contact with THR 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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100F ASP* 4.8 1.6 + - - -
104F SER* 4.1 4.7 - - - -
105F GLU 3.2 9.8 + - - -
106F TYR 3.2 8.8 + - - -
108F ASP* 1.3 76.2 - - - +
110F THR* 1.3 57.9 + - - +
112F ARG* 3.5 2.7 + - - +
113F CYS* 2.9 30.7 + - - +
123F PHE* 3.5 27.1 - - + -
125F GLY* 3.5 20.0 - - - +
145F GLY* 6.0 0.2 - - - -
177F GLU 4.6 0.9 - - - -
178F GLY* 3.5 24.5 - - - +
181F HIS* 2.6 28.0 + - + +
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Residues in contact with THR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F TYR* 2.9 18.5 + - - -
107F ARG* 3.7 8.1 - - - -
109F THR* 1.3 74.8 - - - +
111F ARG* 1.3 64.9 + - - +
113F CYS* 3.3 2.6 + - - +
114F ARG* 3.1 59.8 + - - +
177F GLU* 2.6 38.7 + - + +
349F PHE* 5.3 5.4 - - + -
351F TRP* 3.6 14.1 - - + -
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Residues in contact with ARG 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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82F ASP* 3.0 40.9 + - - -
107F ARG 3.1 13.8 + - - +
108F ASP* 3.2 25.3 + - - +
110F THR* 1.3 77.9 - - - +
112F ARG* 1.3 80.4 + - - +
114F ARG* 3.5 8.7 + - - +
115F ASP* 2.5 47.0 + - - +
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Residues in contact with ARG 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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78F GLY* 3.0 29.5 + - - +
81F VAL* 3.3 14.8 - - - +
82F ASP* 2.7 27.5 + - - +
85F ILE* 4.0 20.2 - - + -
100F ASP* 3.2 24.7 + - - -
104F SER* 4.0 12.5 + - - -
108F ASP* 2.9 44.5 + - - +
109F THR* 4.5 1.2 + - - +
111F ARG* 1.3 97.9 - - - +
113F CYS* 1.3 58.5 + - - +
115F ASP* 4.5 4.3 - - - -
116F LEU* 2.9 36.8 + - + +
123F PHE* 3.9 22.6 - - + -
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Residues in contact with CYS 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 THR 2.9 19.0 + - - +
110F THR 3.6 5.2 - - - +
111F ARG 3.2 0.4 - - - -
112F ARG* 1.3 77.5 - - - +
114F ARG* 1.3 61.6 + - - +
116F LEU* 4.4 0.7 - - - +
117F LYS* 3.2 27.5 + - - +
123F PHE* 3.8 21.7 + - + +
145F GLY* 3.6 34.8 - - - -
146F ASN* 3.9 10.7 + - - -
177F GLU* 3.8 22.9 - - + -
178F GLY 4.8 0.7 - - - +
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Residues in contact with ARG 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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110F THR* 3.1 38.3 + - - +
111F ARG* 4.1 7.5 - - - +
113F CYS* 1.3 76.5 - - - +
115F ASP* 1.3 66.2 + - - +
117F LYS* 3.5 8.0 + - - +
118F ALA* 3.4 19.9 + - - +
177F GLU* 2.5 42.1 + - + +
349F PHE* 4.5 17.6 + - - +
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Residues in contact with ASP 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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111F ARG* 2.5 48.1 + - - +
112F ARG* 4.1 4.3 - - - +
114F ARG* 1.3 79.2 - - - +
116F LEU* 1.3 65.3 + - + +
118F ALA* 3.3 15.1 + - - +
119F LYS* 3.5 23.9 + - - +
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Residues in contact with LEU 116 (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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85F ILE* 3.7 26.0 - - + -
89F VAL* 3.6 29.8 - - + -
98F ILE* 4.3 5.4 - - + -
112F ARG* 2.9 19.6 + - + +
115F ASP* 1.3 79.9 - - + +
117F LYS* 1.3 60.5 + - - +
119F LYS* 3.1 17.3 + - + +
121F ILE* 2.8 52.7 + - + +
123F PHE* 3.5 40.2 - - + -
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Residues in contact with LYS 117 (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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113F CYS* 3.2 21.9 + - - +
114F ARG* 3.7 8.3 - - - +
115F ASP 3.2 0.2 - - - -
116F LEU* 1.3 77.5 - - - +
118F ALA* 1.3 60.7 + - - +
120F GLY* 3.3 12.2 + - - +
121F ILE 3.5 8.0 + - - +
122F LEU* 5.9 0.7 - - + -
146F ASN* 3.8 29.1 + - - +
148F GLU* 5.8 3.1 - - - -
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Residues in contact with ALA 118 (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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114F ARG 3.4 8.7 + - - +
115F ASP* 3.3 10.9 + - - +
116F LEU 3.3 0.8 - - - -
117F LYS* 1.3 77.6 - - - +
119F LYS* 1.3 59.4 + - + +
120F GLY 3.4 0.8 + - - -
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Residues in contact with LYS 119 (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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89F VAL* 4.2 30.4 - - + +
94F THR* 4.6 4.9 + - - -
115F ASP* 3.6 19.7 - - - +
116F LEU* 3.1 15.1 + - + +
118F ALA* 1.3 80.9 - - + +
120F GLY* 1.3 61.2 + - - +
121F ILE* 3.4 13.7 + - + +
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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