Contacts of the helix formed by residues 120 - 133 (chain C) in PDB entry 1TU8
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 ILE 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C LYS* 4.3 13.7 - - + -
115C PRO* 4.0 9.9 - - + +
116C TYR* 3.2 36.1 + - + +
119C SER* 1.3 86.3 - - - +
121C LEU* 1.3 68.1 + - - +
122C PRO* 3.4 3.0 - - - -
123C GLY* 3.4 4.6 + - - -
124C GLU* 3.3 33.0 + - + +
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Residues in contact with LEU 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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97C LEU* 4.2 9.9 - - + -
116C TYR* 2.9 34.7 + - + +
117C ILE* 4.1 15.3 - - + +
120C ILE* 1.3 74.2 - - - +
122C PRO* 1.3 68.1 - - + +
124C GLU* 3.1 4.6 + - - -
125C LEU* 2.9 43.5 + - + +
161C HIS* 3.2 41.7 - - + +
164C LEU* 5.2 1.3 - - + -
165C ASP* 4.8 8.1 - - + +
168C CYS* 3.9 28.3 - - + -
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Residues in contact with PRO 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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117C ILE 3.3 24.0 - - - +
118C LYS* 3.7 14.6 - - - +
119C SER 4.3 1.1 - - - -
120C ILE 3.4 11.0 - - - +
121C LEU* 1.3 89.7 - - + +
123C GLY* 1.3 55.8 - - - +
125C LEU* 3.4 1.5 + - + -
126C ALA* 2.9 26.7 + - - +
172C PHE* 3.5 24.5 - - + -
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Residues in contact with GLY 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 SER 5.5 1.2 + - - -
120C ILE 3.4 5.6 + - - -
121C LEU 3.3 0.6 - - - -
122C PRO* 1.3 79.2 - - - +
124C GLU* 1.3 66.7 + - - +
126C ALA* 3.5 7.9 + - - +
127C LYS* 3.4 28.4 + - - +
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Residues in contact with GLU 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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97C LEU* 3.9 31.7 - - + +
100C LYS* 4.3 24.2 + - + -
120C ILE* 3.3 25.4 + - + +
121C LEU 3.1 6.8 + - - +
123C GLY* 1.3 76.2 - - - +
125C LEU* 1.3 64.3 + - - +
127C LYS* 2.9 49.6 + - - +
128C PHE* 3.3 24.1 - - + -
47D PHE* 5.1 2.8 - - - +
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Residues in contact with LEU 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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97C LEU* 4.4 13.7 - - + -
121C LEU* 2.9 47.5 + - + +
122C PRO* 4.8 0.7 - - + -
124C GLU* 1.3 72.6 - - - +
126C ALA* 1.3 66.5 + - - +
128C PHE* 3.1 7.7 + - + -
129C GLU* 2.9 19.8 + - - +
158C LEU* 4.0 27.6 - - + -
161C HIS* 5.6 4.7 - - + -
168C CYS* 3.6 30.3 - - + +
169C LEU* 4.0 9.9 - - + -
172C PHE* 3.7 22.2 - - + -
175C LEU* 3.4 14.0 - - + +
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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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122C PRO 2.9 17.2 + - - +
123C GLY* 3.7 10.1 - - - +
124C GLU 3.3 0.2 - - - -
125C LEU* 1.3 76.2 - - - +
127C LYS* 1.3 62.2 + - + +
129C GLU* 3.3 3.5 + - - +
130C LYS* 3.1 25.3 + - - +
172C PHE* 3.6 19.0 - - + -
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Residues in contact with LYS 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 GLY 3.4 15.6 + - - +
124C GLU* 2.9 44.6 + - - +
125C LEU 3.1 0.6 - - - -
126C ALA* 1.3 78.9 - - + +
128C PHE* 1.3 57.2 + - - +
130C LYS* 3.5 5.0 + - - +
131C LEU* 3.0 28.9 + - - +
42D LYS* 4.6 9.6 - - - +
46D GLN 3.8 21.1 - - - +
47D PHE* 2.9 44.9 + - + +
48D GLY* 4.3 6.3 - - - +
49D GLN* 5.3 2.0 - - - +
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Residues in contact with PHE 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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90C PHE* 3.5 26.4 - + + -
93C GLY 3.4 24.7 - - - -
94C VAL* 3.6 28.3 - - + -
97C LEU* 3.9 28.7 - - + -
124C GLU* 3.3 28.0 + - + -
125C LEU* 3.1 12.8 + - + +
127C LYS* 1.3 74.0 - - - +
129C GLU* 1.3 60.4 + - - +
131C LEU* 3.9 3.9 - - + +
132C LEU* 2.8 34.8 + - - +
154C LEU* 4.4 8.3 - - + -
158C LEU* 6.1 0.7 - - + -
175C LEU* 3.9 19.7 - - + -
47D PHE* 3.6 26.5 - + - -
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Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C LEU 2.9 13.4 + - - +
126C ALA* 3.6 9.0 - - - +
128C PHE* 1.3 77.8 - - - +
130C LYS* 1.3 64.3 + - - +
132C LEU* 4.0 2.2 - - - +
133C ALA* 3.6 13.3 + - - +
171C LYS 5.7 0.2 - - - +
172C PHE* 3.4 29.1 - - + +
173C PRO* 3.4 13.8 - - + +
174C LEU* 2.9 48.7 + - + +
175C LEU* 3.0 36.8 + - + +
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Residues in contact with LYS 130 (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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126C ALA 3.1 17.0 + - - +
127C LYS* 3.8 5.6 - - - +
129C GLU* 1.3 78.3 - - - +
131C LEU* 1.3 62.3 + - - +
133C ALA* 3.4 18.9 + - - +
134C THR* 4.0 8.6 - - + +
43D SER* 4.5 16.3 + - - -
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Residues in contact with LEU 131 (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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86C TYR* 2.8 26.5 + - + +
89C MET* 4.2 14.6 - - + -
90C PHE* 3.4 31.2 - - + -
127C LYS 3.0 18.8 + - - +
128C PHE* 3.9 4.3 - - - +
130C LYS* 1.3 75.0 - - - +
132C LEU* 1.3 63.6 + - - +
134C THR* 2.8 38.6 + - + +
46D GLN* 4.0 30.7 - - + +
47D PHE* 3.9 27.1 - - + -
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Residues in contact with LEU 132 (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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86C TYR* 4.5 1.5 + - - -
90C PHE* 4.0 13.0 - - + -
128C PHE 2.8 19.1 + - - +
129C GLU 4.0 4.5 - - - +
131C LEU* 1.3 76.5 - - - +
133C ALA* 1.3 61.3 + - - +
134C THR 3.1 1.7 + - - -
135C ARG* 3.5 10.4 + - - +
138C GLY* 3.1 33.9 + - - +
140C ASN 5.3 0.7 - - - +
141C LEU 4.3 7.2 - - - +
142C ILE* 4.0 38.8 - - + +
154C LEU* 4.8 3.4 - - + -
174C LEU* 3.8 33.4 - - + +
175C LEU* 4.1 15.5 - - + -
178C PHE* 4.2 15.3 - - + -
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Residues in contact with ALA 133 (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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129C GLU 3.6 4.9 + - - +
130C LYS* 3.4 13.8 + - - +
131C LEU 3.1 0.2 - - - -
132C LEU* 1.3 77.6 - - - +
134C THR* 1.3 60.4 + - - +
135C ARG 3.3 0.9 - - - -
137C ASN* 3.3 24.0 + - - +
138C GLY* 3.6 12.1 - - - +
174C LEU* 3.8 19.9 - - + +
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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