Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 1TUB
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 GLY 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU* 5.1 4.0 - - - +
106A GLY* 2.3 34.3 + - - -
110A ILE* 1.3 76.2 - - - +
112A LYS* 1.2 65.0 + - - -
114A ILE* 2.9 2.4 + - - -
115A ILE* 2.8 25.6 + - - +
149A PHE* 4.2 17.0 - - - -
152A LEU* 3.8 3.8 - - - -
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Residues in contact with LYS 112 (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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106A GLY 3.2 1.4 + - - -
107A HIS* 3.2 8.7 - - - +
108A TYR* 1.8 71.9 + - - +
109A THR 3.3 5.3 + - - +
111A GLY* 1.2 75.8 - - - +
113A GLU* 1.4 64.2 + - + +
114A ILE 3.1 0.2 - - - -
115A ILE* 3.2 22.5 - - - +
116A ASP* 3.4 12.8 - - - +
152A LEU* 3.8 2.2 - - + +
156A ARG* 3.7 9.7 + - - +
411A GLU 5.1 2.0 + - - -
412A GLY* 5.7 1.6 - - - -
413A MET* 6.3 0.2 - - - +
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.7 13.5 - - - +
109A THR 3.8 15.7 - - - +
110A ILE* 3.5 14.1 - - - +
111A GLY 3.0 0.6 - - - -
112A LYS* 1.4 80.5 - - + +
114A ILE* 1.4 66.6 + - + +
115A ILE 3.7 0.2 - - - -
116A ASP* 4.5 10.7 - - - +
117A LEU* 4.9 3.8 + - - +
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Residues in contact with ILE 114 (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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68A VAL* 5.5 0.2 - - - +
70A LEU* 5.7 7.4 - - + -
93A ILE* 4.2 16.6 - - + -
95A GLY* 4.5 12.6 - - - -
97A GLU* 2.9 40.2 - - + +
110A ILE* 3.3 7.7 + - + +
111A GLY* 2.9 7.8 + - - -
113A GLU* 1.4 91.9 - - + +
115A ILE* 1.2 58.0 + - - +
116A ASP 3.3 1.8 - - - +
117A LEU* 4.7 20.2 - - + +
118A VAL* 3.1 22.7 - - + +
149A PHE* 4.0 10.6 - - - -
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Residues in contact with ILE 115 (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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111A GLY 2.8 3.2 + - - +
112A LYS 3.2 7.4 - - - +
114A ILE* 1.2 77.4 - - - +
116A ASP* 1.3 58.8 + - - +
118A VAL* 3.4 8.0 - - - +
119A LEU* 2.7 42.0 + - + +
149A PHE* 4.8 7.0 - - + +
152A LEU* 1.9 72.0 - - + +
153A LEU* 3.7 11.9 - - + +
156A ARG* 1.7 86.6 - - - +
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Residues in contact with ASP 116 (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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112A LYS 3.4 13.9 - - - +
113A GLU* 4.5 7.7 - - - +
115A ILE* 1.3 78.0 - - - +
117A LEU* 1.3 57.4 + - - +
118A VAL 2.6 4.9 + - - -
119A LEU* 2.1 40.6 + - + +
120A ASP* 2.7 16.6 + - - +
156A ARG* 2.5 33.4 + - - -
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Residues in contact with LEU 117 (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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113A GLU 4.9 2.4 + - - +
114A ILE* 4.7 20.8 - - + -
115A ILE 4.6 0.4 - - - +
116A ASP* 1.3 78.1 - - - +
118A VAL* 1.3 57.4 - - + +
120A ASP* 3.3 22.1 - - + +
121A ARG* 3.0 61.1 + - + +
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Residues in contact with VAL 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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7A ILE* 6.2 0.2 - - + -
66A VAL* 4.9 7.6 - - + -
68A VAL* 4.1 19.7 - - + -
93A ILE* 2.7 37.9 - - + -
114A ILE* 3.1 30.7 - - + +
115A ILE* 3.4 11.4 - - - +
116A ASP 2.6 0.6 + - - -
117A LEU* 1.3 75.5 - - - +
119A LEU* 1.3 67.2 + - - +
120A ASP 2.9 1.3 - - - -
121A ARG* 2.8 4.8 + - - +
122A ILE* 2.8 24.3 + - + +
149A PHE* 4.9 3.8 - - + -
153A LEU* 4.3 18.2 - - + -
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Residues in contact with LEU 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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115A ILE 2.7 24.8 + - - +
116A ASP* 2.1 28.2 + - - +
118A VAL* 1.3 68.4 - - - +
120A ASP* 1.3 58.3 + - - +
122A ILE* 2.3 29.3 - - + +
123A ARG* 2.8 13.4 + - - +
153A LEU* 4.2 10.8 - - + -
156A ARG* 3.3 52.7 - - + +
157A LEU* 4.1 20.4 - - + -
160A ASP* 4.5 12.1 - - - +
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Residues in contact with ASP 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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116A ASP* 2.7 17.9 + - - +
117A LEU* 3.3 25.0 + - + +
119A LEU* 1.3 79.6 - - - +
121A ARG* 1.3 65.9 + - + +
123A ARG* 3.4 10.6 + - - +
124A LYS* 3.1 41.4 + - - +
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Residues in contact with ARG 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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66A VAL* 5.0 6.5 - - + -
90A GLU 5.9 4.3 - - - -
91A GLN* 5.6 3.1 - - - +
92A LEU 3.2 8.6 + - - -
93A ILE* 1.5 81.4 - - - +
94A THR 5.2 0.2 - - - +
114A ILE* 6.1 0.2 - - - -
117A LEU* 3.0 42.7 + - + +
118A VAL* 2.8 6.0 + - - +
120A ASP* 1.3 78.8 - - + +
122A ILE* 1.3 52.0 + - - +
124A LYS* 3.3 7.1 + - - +
125A LEU* 2.4 53.3 + - + +
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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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5A ILE* 4.5 6.0 - - + +
7A ILE* 4.1 8.5 - - + -
66A VAL* 5.0 5.8 - - + +
118A VAL* 2.8 10.9 + - + +
119A LEU* 2.3 52.0 - - + +
121A ARG* 1.3 75.0 - - - +
123A ARG* 1.3 58.7 + - + +
125A LEU* 3.1 11.2 + - - +
126A ALA* 2.4 39.6 + - + +
135A PHE* 3.7 34.1 - - + -
153A LEU* 5.2 1.6 - - + -
157A LEU* 2.8 44.2 - - + -
161A TYR* 4.9 7.0 - - + -
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Residues in contact with ARG 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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119A LEU 2.8 16.5 + - - +
120A ASP* 3.6 11.5 + - - +
122A ILE* 1.3 80.7 - - + +
124A LYS* 1.3 57.3 + - + +
126A ALA* 2.9 9.9 + - - -
127A ASP* 2.3 48.6 + - - +
161A TYR* 4.0 12.1 - - + +
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Residues in contact with LYS 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 ASP* 3.1 27.3 + - - +
121A ARG* 3.7 6.3 - - - +
123A ARG* 1.3 78.3 - - + +
125A LEU* 1.3 62.4 + - + +
127A ASP* 3.0 24.2 + - - +
128A GLN* 3.3 24.2 + - + +
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Residues in contact with LEU 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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5A ILE* 5.1 6.9 - - + +
53A PHE* 3.9 31.0 - - + -
64A ARG* 4.8 9.1 + - - +
65A ALA* 3.8 4.9 - - + +
66A VAL* 2.6 41.7 - - + -
90A GLU 5.4 3.1 - - - +
91A GLN* 5.0 9.2 - - + -
121A ARG* 2.4 39.5 + - + +
122A ILE* 3.2 6.3 - - + +
124A LYS* 1.3 78.8 - - + +
126A ALA* 1.3 57.5 + - - +
127A ASP 2.9 9.7 + - - -
128A GLN* 3.8 14.2 + - + +
129A CYS* 5.4 0.2 - - - -
132A LEU* 4.6 5.7 - - - +
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Residues in contact with ALA 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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5A ILE* 3.8 13.7 - - + -
122A ILE* 2.4 30.9 + - + +
123A ARG 2.9 7.1 + - - +
125A LEU* 1.3 69.2 - - - +
127A ASP* 1.3 62.2 + - - +
129A CYS 6.0 0.2 - - - -
132A LEU* 2.4 40.9 - - + +
161A TYR* 3.3 28.0 - - + +
164A LYS* 4.6 1.0 + - - -
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Residues in contact with ASP 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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123A ARG* 2.3 42.6 + - - +
124A LYS* 3.3 9.8 - - - +
125A LEU 2.9 0.8 - - - -
126A ALA* 1.3 89.8 - - - +
128A GLN* 1.3 70.1 + - - +
129A CYS* 2.8 20.2 + - - +
161A TYR* 4.3 2.8 + - - -
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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