Contacts of the helix formed by residues 117 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A MET 3.8 1.2 + - - -
116A PRO* 1.3 71.5 - - - +
118A GLU* 1.3 62.9 + - - +
120A SER* 3.3 10.6 + - - +
121A ASP* 2.8 61.5 + - - +
156A GLU* 5.5 6.5 - - - -
159A VAL* 6.1 4.5 - - + +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 6.1 2.0 - - - -
106A MET* 3.4 30.7 - - + -
116A PRO* 3.2 20.2 - - + +
117A LYS* 1.3 82.8 + - - +
119A MET* 1.3 60.3 + - - +
121A ASP* 3.9 8.3 - - - +
122A ILE* 3.2 30.8 + - + +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 4.0 26.0 - - + -
103A LEU* 3.6 15.7 - - + -
106A MET* 3.7 39.0 - - + -
107A ALA* 4.1 1.3 - - - +
110A ILE* 3.5 38.6 - - + -
114A THR 4.4 0.2 - - - +
115A MET* 3.7 24.5 - - - +
116A PRO* 2.8 24.1 + - + +
118A GLU* 1.3 80.4 - - - +
120A SER* 1.3 65.4 + - - +
122A ILE* 3.2 4.3 + - - +
123A ILE* 3.0 29.4 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 4.0 13.0 + - - -
116A PRO 2.9 17.1 + - - -
117A LYS* 3.3 21.5 + - - +
119A MET* 1.3 72.7 - - - +
121A ASP* 1.3 57.9 + - - +
123A ILE* 3.3 2.3 + - - +
124A GLN* 2.8 37.6 + - - +
155A LEU* 3.8 12.9 - - - +
159A VAL* 3.8 38.2 - - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS* 2.8 57.2 + - - +
118A GLU* 3.9 7.9 + - - +
120A SER* 1.3 77.3 + - - +
122A ILE* 1.3 62.3 + - + +
124A GLN* 3.2 10.8 + - - +
125A ARG* 3.1 42.6 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 3.4 32.9 - - + +
102A LYS* 4.0 38.4 - - + -
103A LEU* 3.8 19.5 - - + +
106A MET* 4.1 10.8 - - - -
118A GLU* 3.2 17.6 + - + +
119A MET 3.2 6.9 + - - +
121A ASP* 1.3 79.5 - - + +
123A ILE* 1.3 63.4 + - - +
125A ARG* 3.1 29.3 + - - +
126A LEU* 3.0 27.6 + - + +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 4.8 3.8 - - + -
74A LEU* 4.7 2.7 - - + -
77A ILE* 3.9 28.0 - - + -
103A LEU* 4.0 14.8 - - + -
115A MET* 3.8 32.5 - - + -
119A MET* 3.0 29.1 + - + +
120A SER* 3.7 4.5 - - - +
122A ILE* 1.3 75.4 - - - +
124A GLN* 1.3 63.3 + - - +
126A LEU* 3.3 7.5 + - - +
127A TRP* 2.9 23.6 + - + +
152A LEU* 3.5 30.5 - - + -
155A LEU* 3.6 12.8 - - + -
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 2.8 30.6 + - - +
121A ASP* 3.2 11.6 + - - +
123A ILE* 1.3 73.6 - - - +
125A ARG* 1.3 63.3 + - + +
127A TRP* 3.2 6.7 + - - +
128A LYS* 3.1 42.0 + - - +
152A LEU 6.0 0.4 - - - -
155A LEU* 3.6 18.5 - - + +
156A GLU* 3.2 56.5 + - - +
159A VAL* 5.0 2.0 - - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 3.7 29.9 - - - +
99A ASP* 3.0 43.8 + - - +
121A ASP* 3.1 29.3 + - - +
122A ILE* 3.1 22.0 + - - +
124A GLN* 1.3 78.6 - - - +
126A LEU* 1.3 62.3 + - - +
128A LYS* 3.2 29.5 + - - +
129A ASP 3.3 8.7 + - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 4.3 17.0 - - + -
81A VAL* 4.1 19.1 - - + -
91A TYR* 3.8 23.6 - - + -
96A ARG* 3.8 32.8 - - + +
99A ASP* 4.3 6.5 - - + -
100A ALA* 4.3 12.3 - - + +
103A LEU* 4.6 5.8 - - + -
122A ILE* 3.0 36.5 + - + +
123A ILE* 3.3 4.9 + - - +
125A ARG* 1.3 75.1 - - - +
127A TRP* 1.3 63.8 + - - +
129A ASP* 3.0 7.8 + - - +
132A ILE* 3.0 34.2 - - + +
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Residues in contact with TRP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 4.9 3.3 - - + +
80A ILE* 4.2 4.5 - - + -
123A ILE* 2.9 21.0 + - + +
124A GLN* 3.2 7.8 + - - +
126A LEU* 1.3 76.7 - - - +
128A LYS* 1.3 65.9 + - + +
129A ASP 3.4 0.5 + - - -
132A ILE* 4.2 9.2 - - + -
133A GLN* 2.7 56.5 + - - +
136A PHE* 3.8 46.2 - + + -
149A GLY* 4.0 7.9 - - - -
152A LEU* 3.6 47.8 - - + +
153A SER* 3.2 40.7 + - - +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.1 43.4 + - - +
125A ARG* 3.6 21.1 - - - +
126A LEU 3.2 0.4 - - - -
127A TRP* 1.3 81.3 - - + +
129A ASP* 1.3 62.6 + - - +
130A SER 3.6 1.9 + - - -
133A GLN* 5.1 2.1 - - - +
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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