Contacts of the helix formed by residues 112 - 129 (chain C) in PDB entry 5UHO
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 SER 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C LYS* 3.6 6.0 - - - +
110C MET 4.8 0.2 - - - -
111C TYR* 1.3 75.9 - - - +
113C VAL* 1.3 58.8 + - - +
114C GLU* 2.7 26.8 + - - -
115C GLU* 2.9 43.0 + - - +
116C ALA* 3.0 26.5 + - - +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER* 1.3 74.3 + - - +
114C GLU* 1.4 76.9 + - + +
116C ALA* 3.4 7.0 - - - +
117C GLU* 3.4 22.9 + - - +
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER* 2.7 27.9 + - - -
113C VAL* 1.4 89.0 - - + +
115C GLU* 1.4 67.7 + - - +
116C ALA 3.2 1.1 - - - -
117C GLU* 3.3 22.4 + - - +
118C GLN* 3.0 27.3 + - + +
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LYS* 2.8 32.4 + - - +
111C TYR* 3.3 24.8 - - + -
112C SER* 2.9 35.7 + - - +
114C GLU* 1.4 76.5 - - - +
116C ALA* 1.4 56.6 + - - +
118C GLN* 3.3 9.2 + - - +
119C LEU* 3.0 33.0 + - + +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C TYR* 4.4 1.9 - - + +
112C SER 3.0 20.2 + - - +
113C VAL* 3.4 9.0 - - - +
115C GLU* 1.4 74.4 - - - +
117C GLU* 1.3 51.5 + - - +
119C LEU* 3.2 4.6 + - - +
120C MET* 2.9 44.5 + - + +
164C PHE* 3.5 37.6 - - + -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL 3.4 9.7 + - - +
114C GLU* 3.3 30.2 + - - +
116C ALA* 1.3 77.2 - - - +
118C GLN* 1.4 61.9 + - - +
120C MET* 3.4 15.3 - - - +
121C THR* 2.7 42.0 + - - +
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET* 3.3 43.2 - - + +
114C GLU* 3.0 17.5 + - + +
115C GLU* 3.4 10.8 - - - +
117C GLU* 1.4 81.2 - - - +
119C LEU* 1.4 54.6 + - - +
121C THR* 3.1 7.7 + - - +
122C LEU* 2.8 32.1 + - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR* 4.9 14.8 - - + +
111C TYR* 3.7 48.5 - - + +
115C GLU* 3.0 12.9 + - + +
116C ALA 3.6 7.4 - - - +
118C GLN* 1.4 74.1 - - - +
120C MET* 1.4 52.4 + - - +
122C LEU* 3.2 23.8 + - + +
123C ILE* 2.7 48.3 + - + +
133C PHE* 4.3 17.0 - - + -
135C TYR* 5.0 7.4 - - + -
161C VAL* 6.0 0.4 - - + -
164C PHE* 3.9 18.8 - - + -
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Residues in contact with MET 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ALA* 2.9 20.2 + - + +
117C GLU* 3.4 15.7 - - - +
119C LEU* 1.4 74.2 - - - +
121C THR* 1.4 53.3 + - - +
123C ILE* 3.1 4.7 + - - +
124C SER* 2.7 40.8 + - - +
163C GLN* 5.2 5.2 - - + +
164C PHE* 3.6 57.7 - - + +
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Residues in contact with THR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET* 3.6 18.4 - - + -
79C LYS* 5.9 3.6 - - - -
117C GLU* 2.7 24.0 + - - +
118C GLN* 3.4 12.7 + - - +
120C MET* 1.4 76.0 - - - +
122C LEU* 1.4 56.6 + - - +
124C SER* 3.5 8.8 - - - -
125C ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET* 3.4 25.1 - - + +
78C ARG* 3.6 43.1 - - + +
79C LYS* 4.7 1.1 - - + +
82C PHE* 3.7 19.4 - - + -
93C TYR* 5.4 1.1 - - + -
95C TYR* 5.0 9.0 - - + -
118C GLN 2.8 13.1 + - - +
119C LEU* 3.3 24.9 - - + +
121C THR* 1.4 72.4 - - - +
123C ILE* 1.4 59.3 + - - +
124C SER 3.2 1.1 - - - -
125C ALA* 3.0 8.2 + - - +
126C ALA* 3.0 26.0 + - - +
133C PHE* 3.8 25.1 - - + -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 2.7 33.8 + - + +
120C MET 3.7 3.1 - - - +
122C LEU* 1.4 69.7 - - - +
124C SER* 1.3 56.9 + - - +
126C ALA* 3.1 21.7 + - - +
127C ARG* 3.3 18.2 + - - +
133C PHE* 3.9 43.5 - - + -
161C VAL* 4.9 2.5 - - + -
164C PHE* 3.6 31.6 - - + +
165C GLY 3.6 29.2 - - - +
166C CYS* 3.7 20.9 - - + +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C MET* 2.7 23.9 + - - +
121C THR* 3.5 9.7 - - - -
123C ILE* 1.3 75.2 - - - +
125C ALA* 1.3 57.7 + - - +
127C ARG* 3.4 23.2 + - - +
128C GLU* 3.1 26.5 + - - +
164C PHE 4.9 1.4 + - - -
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LYS* 3.8 35.2 - - + -
82C PHE* 4.3 6.1 - - + -
121C THR 3.0 14.4 + - - +
122C LEU* 3.0 11.5 + - - +
124C SER* 1.3 74.5 - - - +
126C ALA* 1.4 63.9 + - - +
128C GLU* 3.7 11.8 - - - +
129C TYR* 3.1 34.3 + - + -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 4.2 21.9 - - + -
122C LEU 3.0 10.7 + - - +
123C ILE 3.1 10.9 + - - +
125C ALA* 1.4 76.9 - - - +
127C ARG* 1.4 56.8 + - + +
129C TYR* 3.3 3.6 + - - -
130C GLU 3.2 3.8 + - - -
131C ILE* 2.7 47.5 + - + +
133C PHE* 3.9 26.5 - - + -
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Residues in contact with ARG 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ILE* 3.3 24.3 + - + +
124C SER* 3.6 21.3 + - - +
125C ALA 3.3 0.2 - - - -
126C ALA* 1.4 72.5 - - + +
128C GLU* 1.4 57.5 + - - +
130C GLU* 2.8 27.8 + - - +
131C ILE 4.4 6.1 - - - +
164C PHE 3.9 7.1 + - - -
165C GLY* 3.0 45.3 + - - -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LYS* 6.3 0.7 - - - -
86C GLN* 3.8 6.2 - - - +
124C SER 3.1 13.2 + - - +
125C ALA* 3.7 11.4 - - - +
127C ARG* 1.4 77.5 - - - +
129C TYR* 1.3 89.1 + - + +
130C GLU* 3.6 5.9 + - - +
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LYS* 4.5 14.8 - - + -
82C PHE* 3.7 31.0 - - + +
83C ARG* 2.7 55.9 + - + -
86C GLN* 3.2 46.2 - - - +
125C ALA* 3.1 26.8 + - + +
126C ALA 3.9 0.9 - - - +
127C ARG 3.2 1.0 - - - -
128C GLU* 1.3 101.6 + - + +
130C GLU* 1.3 66.3 + - - +
131C ILE* 3.2 9.6 - - - +
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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