Contacts of the helix formed by residues 115 - 139 (chain A) in PDB entry 2Q7M
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR* 4.8 4.4 - - - -
93A VAL* 4.0 24.0 - - - +
114A PHE* 1.3 77.3 - - - +
116A LYS* 1.3 64.1 + - - +
117A ARG* 3.0 4.5 - - - -
118A ILE* 2.7 24.5 + - - +
119A ILE* 3.2 12.4 + - - +
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Residues in contact with LYS 116 (chain A).
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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113A ILE* 4.1 13.7 - - + -
114A PHE* 3.1 3.6 - - - +
115A GLY* 1.3 75.3 - - - +
117A ARG* 1.3 62.7 + - + +
119A ILE* 3.4 3.7 - - - +
120A LEU* 2.9 31.4 + - - +
503A 2CS 2.7 88.7 + - + +
28B HIS* 6.0 1.0 + - - -
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Residues in contact with ARG 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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115A GLY* 2.8 2.7 + - - -
116A LYS* 1.3 84.5 - - + +
118A ILE* 1.3 59.9 + - + +
120A LEU* 3.3 14.8 - - - +
121A PHE* 2.7 31.4 + - - +
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Residues in contact with ILE 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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86A ALA* 3.0 45.3 - - + +
89A MET* 3.2 26.9 - - + -
90A TYR* 3.3 27.6 - - + +
93A VAL* 4.7 9.9 - - + -
115A GLY* 2.7 17.9 + - - +
117A ARG* 1.3 72.2 - - + +
119A ILE* 1.3 52.9 + - - +
121A PHE* 2.8 14.1 + - + +
122A LEU* 2.8 40.7 + - + +
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Residues in contact with ILE 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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66A THR 4.4 4.7 - - - +
67A PHE* 4.0 23.8 - - + -
70A VAL* 3.8 19.6 - - + +
90A TYR* 3.6 25.1 - - + -
114A PHE 3.6 9.0 - - - +
115A GLY 3.2 20.1 + - - +
116A LYS 3.4 2.5 - - - +
118A ILE* 1.3 75.1 - - - +
120A LEU* 1.3 57.2 + - - +
122A LEU* 4.3 0.9 - - - -
123A PHE* 2.8 32.2 + - - +
503A 2CS 2.8 61.6 - - + +
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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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116A LYS 2.9 22.0 + - - +
117A ARG* 3.3 17.3 - - - +
119A ILE* 1.3 79.4 - - - +
121A PHE* 1.3 63.6 + - + +
123A PHE* 3.1 5.5 - - - +
124A LEU* 2.8 63.3 + - + +
503A 2CS 3.3 49.4 - - + -
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Residues in contact with PHE 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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82A PRO* 4.3 11.2 - - + -
85A PHE* 6.5 0.4 - + - -
86A ALA* 3.2 34.3 - - + -
117A ARG 2.7 15.6 + - - +
118A ILE* 2.8 12.3 + - + +
120A LEU* 1.3 77.7 - - + +
122A LEU* 1.3 57.3 + - - +
124A LEU* 2.6 29.2 + - + +
125A MET* 3.1 44.2 + - + -
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Residues in contact with LEU 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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67A PHE* 4.0 20.6 - - + -
70A VAL* 3.4 32.1 - - + +
71A LEU* 3.5 28.3 - - + -
74A ALA* 2.8 30.0 - - + +
83A ALA* 3.7 10.3 - - - +
86A ALA* 2.9 38.1 - - + -
87A GLY* 4.1 1.1 - - - +
118A ILE* 2.8 24.2 + - + +
119A ILE* 4.8 0.7 - - - -
121A PHE* 1.3 75.5 - - + +
123A PHE* 1.3 60.8 + - - +
125A MET* 3.0 17.1 + - + -
126A SER* 2.9 5.4 + - - -
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Residues in contact with PHE 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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70A VAL* 3.7 7.8 - - + +
119A ILE 2.8 20.0 + - - +
120A LEU* 3.1 5.4 - - + +
121A PHE 3.0 0.2 - - - -
122A LEU* 1.3 76.1 - - - +
124A LEU* 1.3 85.4 + - + +
126A SER* 2.7 19.0 + - - -
127A VAL* 2.9 33.4 + - + +
503A 2CS 3.5 27.8 - - + -
17B LEU* 3.3 46.0 - - + -
18B ILE* 6.2 1.6 - - + -
20B VAL* 3.7 21.1 - - + -
21B VAL* 4.3 10.1 - - + -
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Residues in contact with LEU 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 LEU* 2.8 52.2 + - + +
121A PHE* 2.6 19.7 + - + +
123A PHE* 1.3 99.9 - - + +
125A MET* 1.3 58.3 + - - -
126A SER 3.3 0.2 - - - -
127A VAL* 3.0 15.4 - - + +
128A ALA* 2.9 25.5 + - - +
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Residues in contact with MET 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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74A ALA* 3.3 18.4 - - + +
77A LEU 3.7 0.2 - - - +
78A CYS* 3.3 30.1 - - - +
82A PRO* 3.4 23.6 - - - +
83A ALA* 3.0 43.1 - - + +
121A PHE* 3.1 44.4 + - + +
122A LEU* 3.0 13.4 + - + +
124A LEU* 1.3 74.9 - - - +
126A SER* 1.3 62.3 + - - +
128A ALA* 2.8 23.7 + - - +
129A GLY 3.1 6.9 + - - -
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Residues in contact with SER 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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73A SER* 2.9 48.5 + - - -
74A ALA* 3.7 1.0 - - - +
77A LEU* 3.4 5.9 - - - +
122A LEU 2.9 9.2 + - - -
123A PHE* 2.7 24.1 + - - -
125A MET* 1.3 77.2 - - - +
127A VAL* 1.3 55.2 + - - -
128A ALA 3.0 4.3 - - - -
130A ILE* 2.9 31.9 + - - +
17B LEU* 3.6 16.2 - - - +
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Residues in contact with VAL 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 PHE* 2.9 40.6 + - + +
124A LEU* 3.0 33.9 - - + +
126A SER* 1.3 75.8 - - - +
128A ALA* 1.3 61.6 + - - +
130A ILE* 2.9 28.2 - - + +
131A PHE* 3.5 9.2 + - + +
17B LEU* 4.9 3.7 - - + +
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Residues in contact with ALA 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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78A CYS* 4.6 7.4 - - - -
124A LEU 2.9 16.0 + - - +
125A MET* 2.8 17.7 - - - +
126A SER 3.0 0.8 - - - -
127A VAL* 1.3 76.0 - - - +
129A GLY* 1.3 68.1 + - - +
131A PHE* 2.9 19.0 + - - +
132A ASN* 2.9 15.0 + - - +
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Residues in contact with GLY 129 (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 LEU* 2.9 26.0 + - - -
78A CYS* 4.4 1.9 - - - +
125A MET 3.1 6.5 + - - -
128A ALA* 1.3 79.3 - - - +
130A ILE* 1.3 55.4 + - - +
132A ASN* 3.8 14.4 - - - +
133A TYR* 2.7 36.8 + - - +
6B VAL* 6.5 0.4 - - - -
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Residues in contact with ILE 130 (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 LEU* 3.7 22.1 - - + +
126A SER 2.9 15.3 + - - +
127A VAL* 2.9 35.4 - - + +
129A GLY* 1.3 75.8 - - - +
131A PHE* 1.3 67.5 + - + +
133A TYR* 3.7 10.7 - - - -
134A TYR* 3.4 18.4 - - + -
10B VAL* 3.5 38.1 - - + +
13B ALA* 4.6 4.0 - - + -
14B ILE* 4.0 21.1 - - + +
17B LEU* 5.2 3.8 - - + -
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Residues in contact with PHE 131 (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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127A VAL* 3.7 9.9 - - + +
128A ALA* 2.9 11.8 + - - +
130A ILE* 1.3 82.0 - - + +
132A ASN* 1.3 67.6 + - + -
133A TYR 2.7 5.2 + - - -
134A TYR* 2.5 45.8 + + + +
135A LEU* 3.0 50.8 + - + -
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Residues in contact with ASN 132 (chain A).
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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128A ALA 2.9 15.0 + - - +
129A GLY* 3.8 13.3 - - - +
131A PHE* 1.3 90.5 - - + +
133A TYR* 1.3 61.1 + - - +
135A LEU* 3.3 10.1 + - - +
136A ILE* 2.8 42.5 + - - +
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Residues in contact with TYR 133 (chain A).
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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129A GLY 2.7 19.7 + - - +
130A ILE* 3.7 8.7 - - - +
132A ASN* 1.3 77.3 - - - +
134A TYR* 1.3 112.2 + + - +
136A ILE* 3.1 13.9 + - + -
137A PHE* 2.9 37.6 + - + +
3B GLN* 3.1 47.3 + - - +
6B VAL* 4.2 17.7 - - + -
7B GLY* 3.4 35.4 + - - -
10B VAL* 3.6 14.7 - - + +
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Residues in contact with TYR 134 (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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130A ILE* 3.4 28.3 - - + -
131A PHE* 2.5 24.7 + + + +
133A TYR* 1.3 103.0 - + - +
135A LEU* 1.3 62.8 + - + +
137A PHE* 3.5 18.2 - + - +
138A PHE* 3.0 29.1 + - - +
10B VAL* 3.1 23.0 - - + +
11B LEU* 4.2 6.2 - - - +
14B ILE* 3.8 14.5 - - + +
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Residues in contact with LEU 135 (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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131A PHE* 3.0 51.3 + - + +
132A ASN* 3.6 10.1 - - - +
133A TYR 3.0 0.6 - - - -
134A TYR* 1.3 82.9 - - + +
136A ILE* 1.3 55.2 + - + +
137A PHE 2.9 3.4 - - - -
138A PHE* 2.8 7.1 + - + -
139A PHE* 2.3 69.5 + - + +
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Residues in contact with ILE 136 (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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132A ASN* 2.8 47.8 - - - +
133A TYR* 3.1 12.5 + - + +
135A LEU* 1.3 74.8 - - + +
137A PHE* 1.3 58.1 + - - +
139A PHE 4.2 15.2 - - - +
3B GLN* 3.4 30.6 + - + +
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Residues in contact with PHE 137 (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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133A TYR* 2.9 30.1 + - + +
134A TYR* 3.5 22.2 - + - +
136A ILE* 1.3 79.9 - - - +
138A PHE* 1.3 101.4 + + - +
3B GLN* 3.2 12.3 - - - +
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Residues in contact with PHE 138 (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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134A TYR 3.0 13.9 + - - +
135A LEU* 2.8 5.1 + - + +
137A PHE* 1.3 121.4 - + - +
139A PHE* 1.3 93.4 + + + +
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Residues in contact with PHE 139 (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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135A LEU* 2.3 62.0 + - + +
136A ILE* 4.2 14.0 - - - -
138A PHE* 1.3 106.8 - + + +
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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