Contacts of the helix formed by residues 112 - 128 (chain A) in PDB entry 2ID7
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 THR 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.4 3.6 - - - -
110A PRO 5.8 0.4 - - - +
111A PHE* 1.3 81.9 - - - +
113A ALA* 1.3 64.4 + - - +
114A ALA* 3.5 9.2 + - - +
115A THR* 3.0 29.2 + - - +
116A LEU* 3.0 21.3 + - - +
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Residues in contact with ALA 113 (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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24A LEU* 3.8 17.6 - - + +
27A GLU* 3.6 26.2 - - + +
28A LEU* 3.9 21.0 - - + +
112A THR* 1.3 74.3 - - - +
114A ALA* 1.3 58.4 + - - +
116A LEU* 3.3 7.6 + - - +
117A GLU* 2.8 30.0 + - - +
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Residues in contact with ALA 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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112A THR* 3.2 8.9 + - - +
113A ALA* 1.3 79.6 - - - +
115A THR* 1.3 56.4 + - - +
117A GLU* 3.4 14.4 + - - +
118A GLU* 2.9 30.1 + - - +
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Residues in contact with THR 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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107A VAL* 3.7 26.2 - - + -
111A PHE* 4.2 9.8 - - + -
112A THR* 3.0 29.6 + - - +
114A ALA* 1.3 74.6 - - - +
116A LEU* 1.3 66.4 + - - +
118A GLU* 3.3 9.5 + - - +
119A LYS* 3.0 36.1 + - - +
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Residues in contact with LEU 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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21A VAL* 5.0 1.8 - - + +
24A LEU* 4.0 24.0 - - + -
25A LEU* 4.0 22.7 - - + +
28A LEU* 3.9 17.7 - - + -
55A ILE* 4.2 11.4 - - + -
84A LEU* 3.8 28.0 - - + -
107A VAL* 5.5 0.4 - - - -
111A PHE* 4.1 19.3 - - + -
112A THR 3.0 13.1 + - - +
113A ALA* 3.6 9.6 - - - +
115A THR* 1.3 78.7 - - - +
117A GLU* 1.3 57.9 + - - +
119A LYS* 3.2 4.1 + - - +
120A LEU* 2.8 48.3 + - + +
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Residues in contact with GLU 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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4A LYS* 5.9 0.9 + - - -
28A LEU* 3.6 30.9 - - + +
113A ALA 2.8 16.5 + - - +
114A ALA* 3.6 13.5 - - - +
116A LEU* 1.3 77.3 - - - +
118A GLU* 1.3 57.7 + - - +
120A LEU* 3.7 4.1 - - - +
121A ASN* 2.9 50.9 + - - +
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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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114A ALA 2.9 18.0 + - - +
115A THR* 3.6 8.4 - - - +
117A GLU* 1.3 77.3 - - - +
119A LYS* 1.3 72.0 + - + +
121A ASN* 3.4 7.1 + - - +
122A LYS* 3.0 32.7 + - + +
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Residues in contact with LYS 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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84A LEU* 4.4 20.2 - - + -
105A GLY* 5.6 0.2 - - - -
106A TYR* 2.8 38.1 + - - +
107A VAL* 3.3 23.8 - - + +
115A THR* 3.0 28.3 + - - +
116A LEU* 3.7 6.5 - - - +
118A GLU* 1.3 78.2 - - + +
120A LEU* 1.3 68.5 + - - +
122A LYS* 3.3 28.1 - - + +
123A ILE* 3.0 33.6 + - + +
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Residues in contact with LEU 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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8A PHE* 4.1 17.5 - - + -
25A LEU* 4.4 2.7 - - + -
28A LEU* 4.1 7.4 - - + -
30A PHE* 3.7 33.7 - - + -
53A PHE* 3.4 37.5 - - + -
55A ILE* 5.3 0.2 - - + -
84A LEU* 5.0 2.5 - - + -
116A LEU* 2.8 45.6 + - + +
117A GLU* 3.7 4.0 - - - +
119A LYS* 1.3 77.9 - - - +
121A ASN* 1.3 59.0 + - - +
123A ILE* 3.7 3.8 - - + +
124A PHE* 2.9 46.6 + - + -
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Residues in contact with ASN 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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2A ALA 5.4 5.0 + - - -
117A GLU* 2.9 41.2 + - - +
118A GLU* 3.8 6.5 - - - +
119A LYS 3.3 0.4 - - - -
120A LEU* 1.3 77.0 - - - +
122A LYS* 1.3 57.5 + - - +
124A PHE* 3.5 7.3 + - - +
125A GLU* 2.9 36.9 + - - +
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Residues in contact with LYS 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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104A SER 3.4 20.2 + - - -
105A GLY* 4.4 6.2 - - - -
118A GLU* 3.0 26.1 + - + +
119A LYS* 3.3 39.9 - - + +
121A ASN* 1.3 75.8 - - - +
123A ILE* 1.3 63.1 + - - +
125A GLU* 3.4 11.2 - - - +
126A LYS* 2.9 66.1 + - - +
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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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53A PHE* 3.8 36.3 - - + -
82A PRO* 4.1 9.2 - - + -
84A LEU* 4.4 15.5 - - + -
104A SER* 3.6 48.0 - - - +
105A GLY* 4.4 3.1 - - - +
119A LYS* 3.0 28.6 + - + +
120A LEU* 3.7 3.8 - - + +
122A LYS* 1.3 84.0 - - - +
124A PHE* 1.3 66.5 + - + +
126A LYS* 3.3 10.2 + - + +
127A LEU* 3.2 30.1 + - + +
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Residues in contact with PHE 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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2A ALA* 3.6 31.2 - - + +
6A LEU* 3.2 35.9 - - + -
8A PHE* 4.5 4.5 - + - -
30A PHE* 4.5 15.3 - + - -
53A PHE* 3.6 24.7 - + - -
82A PRO* 4.9 3.8 - - + -
120A LEU* 2.9 43.6 + - + +
121A ASN* 4.1 6.3 - - - +
123A ILE* 1.3 77.6 - - + +
125A GLU* 1.3 58.2 + - - +
127A LEU* 3.0 6.9 + - + +
128A GLY 2.9 24.3 + - - -
129A MET* 3.0 45.7 + - + +
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Residues in contact with GLU 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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121A ASN* 2.9 23.9 + - - +
122A LYS* 3.4 11.8 - - - +
124A PHE* 1.3 76.0 - - - +
126A LYS* 1.3 64.6 + - + +
128A GLY* 3.0 13.8 + - - +
129A MET* 4.4 3.8 + - - -
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Residues in contact with LYS 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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104A SER 4.7 4.1 + - - +
122A LYS* 2.9 58.9 + - - +
123A ILE* 3.3 8.0 + - - +
125A GLU* 1.3 76.7 - - + +
127A LEU* 1.3 62.6 + - + +
128A GLY 3.8 0.2 + - - -
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Residues in contact with LEU 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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80A ALA* 4.8 15.9 - - + +
82A PRO* 3.5 33.4 - - + -
104A SER* 6.0 0.4 - - - +
123A ILE* 3.2 21.0 + - + +
124A PHE* 3.0 10.8 + - + +
126A LYS* 1.3 79.7 - - + +
128A GLY* 1.3 64.7 + - - +
129A MET* 3.5 25.3 + - + +
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Residues in contact with GLY 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 PHE 2.9 4.0 + - - -
125A GLU* 3.0 11.0 + - - -
126A LYS 3.4 0.8 + - - -
127A LEU* 1.3 81.1 - - - +
129A MET* 1.3 62.3 + - - +
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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