Contacts of the helix formed by residues 117 - 128 (chain C) in PDB entry 1TAD
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 LYS 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 6.0 0.2 - - - +
212B GLU* 3.6 34.5 + - - +
115C MET 3.8 1.2 + - - -
116C PRO* 1.3 71.1 - - - +
118C GLU* 1.3 58.8 + - - +
120C SER* 3.6 8.3 - - - -
121C ASP* 2.9 61.0 + - - +
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Residues in contact with GLU 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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102C LYS* 6.0 2.8 - - - +
106C MET* 3.8 29.4 - - + +
116C PRO* 3.1 4.6 + - + +
117C LYS* 1.3 81.2 - - - +
119C MET* 1.3 60.6 + - - +
121C ASP* 4.0 6.3 - - - +
122C ILE* 3.3 31.6 + - + +
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Residues in contact with MET 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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74C LEU* 4.1 18.6 - - + -
103C LEU* 3.7 17.0 - - + -
106C MET* 3.7 28.6 - - + +
107C ALA* 3.9 12.3 - - - +
110C ILE* 3.5 47.6 - - + -
114C THR 4.3 1.1 - - - +
115C MET* 3.7 22.4 - - - +
116C PRO* 2.8 24.0 + - + +
118C GLU* 1.3 78.1 - - - +
120C SER* 1.3 64.5 + - - +
122C ILE* 3.2 6.2 + - - +
123C ILE* 3.0 28.6 + - + +
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Residues in contact with SER 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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115C MET* 3.5 21.3 + - - +
116C PRO 2.8 19.4 + - - -
117C LYS* 3.6 8.6 - - - -
119C MET* 1.3 75.9 - - - +
121C ASP* 1.3 58.3 + - - +
123C ILE* 3.3 1.9 + - - +
124C GLN* 2.8 35.8 + - - +
155C LEU* 3.9 10.2 - - - +
159C VAL* 3.6 31.2 - - - +
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Residues in contact with ASP 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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117C LYS* 2.9 53.9 + - - +
118C GLU* 4.0 7.1 - - - +
120C SER* 1.3 78.3 - - - +
122C ILE* 1.3 61.5 + - + +
124C GLN* 3.4 7.6 - - - +
125C ARG* 3.1 43.7 + - - +
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Residues in contact with ILE 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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99C ASP* 3.5 29.6 - - + +
102C LYS* 3.5 33.2 - - + -
103C LEU* 3.8 13.7 - - + +
106C MET* 4.2 17.7 - - - -
118C GLU* 3.3 21.3 + - + +
119C MET 3.2 8.2 + - - +
121C ASP* 1.3 75.8 - - + +
123C ILE* 1.3 66.2 + - - +
125C ARG* 3.1 28.7 + - - +
126C LEU* 2.9 33.3 + - + +
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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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73C THR* 5.1 2.0 - - + -
74C LEU* 4.6 5.2 - - + -
77C ILE* 3.8 28.2 - - + +
103C LEU* 3.8 17.0 - - + -
115C MET* 3.9 23.8 - - + -
119C MET* 3.0 36.7 + - + +
120C SER* 4.8 0.4 - - - -
122C ILE* 1.3 74.1 - - - +
124C GLN* 1.3 54.7 + - - +
126C LEU* 3.2 8.8 + - - +
127C TRP* 2.8 34.8 + - + +
152C LEU* 3.6 26.0 - - + -
155C LEU* 3.5 21.5 - - + -
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Residues in contact with GLN 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 SER* 2.8 18.6 + - - +
121C ASP* 3.4 11.4 - - - +
123C ILE* 1.3 78.0 - - - +
125C ARG* 1.3 62.7 + - + +
127C TRP* 3.5 8.8 + - - +
128C LYS* 3.4 40.0 + - - +
152C LEU 4.5 4.6 + - - -
153C SER 5.9 0.4 + - - -
155C LEU* 3.5 32.8 - - - +
156C GLU* 3.6 34.4 + - - +
159C VAL* 4.8 5.0 - - - +
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Residues in contact with ARG 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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96C ARG* 3.5 35.2 - - - +
99C ASP* 2.8 34.9 + - - +
102C LYS* 4.3 5.5 - - - +
121C ASP* 3.1 32.5 + - - +
122C ILE* 3.1 24.0 + - - +
124C GLN* 1.3 79.9 - - + +
126C LEU* 1.3 64.5 + - - +
128C LYS* 3.3 26.5 + - - +
129C ASP 3.5 7.1 + - - -
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Residues in contact with LEU 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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77C ILE* 4.2 12.8 - - + -
81C VAL* 4.2 11.9 - - + -
91C TYR* 4.0 16.6 - - + -
96C ARG* 3.6 40.2 - - + +
99C ASP* 4.3 4.3 - - + -
100C ALA* 4.1 10.3 - - + +
103C LEU* 3.7 30.7 - - + -
122C ILE* 2.9 29.5 + - + +
123C ILE 3.6 5.6 - - - +
125C ARG* 1.3 76.3 - - - +
127C TRP* 1.3 58.5 + - - +
129C ASP* 2.8 26.0 + - - +
132C ILE* 3.2 17.1 - - + +
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Residues in contact with TRP 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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77C ILE* 4.7 3.5 - - + +
80C ILE* 4.0 9.6 - - + -
123C ILE* 2.8 23.9 + - + +
124C GLN* 3.8 9.4 - - - +
125C ARG 3.4 0.2 - - - -
126C LEU* 1.3 72.9 - - - +
128C LYS* 1.3 66.8 + - + +
129C ASP 3.4 0.9 + - - +
132C ILE* 4.1 7.1 - - + +
133C GLN* 2.7 58.0 + - - +
136C PHE* 3.8 45.3 - + + -
149C GLY* 3.9 20.6 - - - -
152C LEU* 3.5 53.4 - - + +
153C SER* 3.6 19.9 - - - +
155C LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 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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124C GLN* 3.4 23.3 + - + +
125C ARG* 3.3 34.4 + - - +
126C LEU 3.0 1.4 + - - -
127C TRP* 1.3 82.6 - - + +
129C ASP* 1.3 63.3 + - - +
130C SER 3.6 1.7 + - - -
133C GLN* 5.0 2.7 - - - +
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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