Contacts of the helix formed by residues 126 - 147 (chain D) in PDB entry 1Q90
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 ARG 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 2.6 40.2 + - - -
106B LEU* 4.3 4.8 - - - +
108B GLY* 3.9 6.8 - - - +
110B PHE* 4.3 1.6 - - - -
111B LYS* 3.3 17.4 - - - +
115D GLU* 2.6 31.3 + - - -
118D ASN* 3.8 10.3 - - - +
120D PHE* 3.3 27.4 + - + -
121D GLN* 2.9 21.2 + - - +
122D ASN 3.2 13.3 + - - +
123D PRO* 3.0 13.7 + - + +
125D ARG* 1.3 84.2 - - - +
127D PRO* 1.3 59.5 - - - +
128D ILE 3.6 1.6 - - - -
129D ALA* 3.4 22.8 + - + +
130D THR* 2.9 29.5 + - - -
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Residues in contact with PRO 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ASN* 5.5 0.4 - - - +
123D PRO 4.0 1.1 - - - +
124D TYR 4.7 7.9 - - - +
125D ARG* 3.4 7.9 - - - +
126D ARG* 1.3 90.2 - - - +
128D ILE* 1.3 66.9 + - + +
130D THR* 3.3 7.2 + - - +
131D ILE* 3.1 31.2 + - + +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ARG 3.6 0.2 - - - -
127D PRO* 1.3 80.3 - - + +
129D ALA* 1.3 59.0 + - - +
131D ILE* 3.2 11.5 + - + +
132D LEU* 2.9 54.5 + - + +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 3.2 26.0 + - + +
115D GLU* 3.6 9.9 - - - +
126D ARG* 3.4 36.2 + - + +
127D PRO 3.3 0.4 - - - -
128D ILE* 1.3 79.0 - - - +
130D THR* 1.3 65.6 + - - +
132D LEU* 3.2 6.5 + - - +
133D PHE* 2.8 25.4 + - - +
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 5.6 1.1 - - - -
106B LEU* 5.7 1.8 - - - -
123D PRO* 2.8 37.5 + - - +
124D TYR* 6.1 2.0 - - + -
126D ARG* 2.9 6.4 + - - +
127D PRO* 3.5 9.6 - - - -
129D ALA* 1.3 76.3 - - - +
131D ILE* 1.3 64.8 + - + +
133D PHE* 3.2 5.4 + - - +
134D LEU* 2.9 36.6 + - + +
22G PHE* 3.5 33.2 - - + -
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO* 3.1 19.1 + - + +
128D ILE* 3.4 11.9 - - + +
130D THR* 1.3 79.1 - - + +
132D LEU* 1.3 63.1 + - + +
134D LEU* 3.6 7.5 - - + +
135D LEU* 2.5 49.1 + - + +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 2.9 52.9 + - + +
129D ALA* 3.7 6.1 - - - +
131D ILE* 1.3 82.2 - - + +
133D PHE* 1.3 54.8 + - - +
135D LEU* 3.9 16.4 - - + -
136D GLY* 2.6 32.7 + - - -
910D CLA 3.7 38.8 - - + +
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Residues in contact with PHE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 3.4 44.9 - + - -
105B TYR* 3.7 29.4 - + + -
106B LEU* 3.7 33.2 - - + -
129D ALA 2.8 20.7 + - - +
130D THR* 3.5 5.2 - - - +
132D LEU* 1.3 71.2 - - - +
134D LEU* 1.3 72.0 + - + +
136D GLY* 3.6 0.9 - - - -
137D THR* 2.8 36.9 + - - -
910D CLA 3.6 33.3 - + + +
953D LMG 4.5 1.4 - - + +
18G ILE* 3.8 24.2 - - + -
22G PHE* 4.5 7.9 - + - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 2.9 40.5 + - + +
131D ILE* 3.6 6.3 - - + +
133D PHE* 1.3 78.7 - - + +
135D LEU* 1.3 69.8 + - - +
137D THR* 2.9 16.2 + - + -
138D LEU* 3.0 20.4 + - + +
953D LMG 3.6 43.7 - - + -
18G ILE* 4.6 1.6 - - + -
22G PHE* 3.8 18.6 - - + -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 2.5 32.0 + - + +
132D LEU* 3.5 24.2 - - + +
134D LEU* 1.3 77.4 - - - +
136D GLY* 1.3 63.5 + - - +
138D LEU* 2.9 22.5 + - + +
139D VAL* 3.1 26.2 + - + +
910D CLA 5.2 7.2 - - + -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU 2.6 22.2 + - - -
133D PHE 3.6 1.6 - - - -
135D LEU* 1.3 73.3 - - - +
137D THR* 1.3 56.0 + - - +
139D VAL* 3.4 1.6 + - - +
140D ALA* 3.0 30.0 + - - +
910D CLA 3.5 37.8 - - - +
953D LMG 3.8 7.1 - - - +
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Residues in contact with THR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE* 2.8 35.3 + - - -
134D LEU* 2.9 12.8 + - + -
136D GLY* 1.3 70.0 - - - +
138D LEU* 1.3 68.4 + - + +
140D ALA* 3.4 1.0 + - - +
141D VAL* 2.9 36.1 + - + +
953D LMG 3.1 44.2 - - + +
14G VAL* 4.9 2.0 - - + -
18G ILE* 4.0 21.0 - - + +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU* 3.0 17.4 + - + +
135D LEU* 2.9 16.8 + - + +
137D THR* 1.3 77.7 - - + +
139D VAL* 1.3 56.6 + - + +
141D VAL* 3.2 4.8 + - - +
142D TRP* 2.6 42.0 + - + +
953D LMG 4.6 29.2 - - + -
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 3.2 29.4 - - + +
136D GLY 3.6 0.9 - - - +
138D LEU* 1.3 76.4 - - + +
140D ALA* 1.3 57.8 + - - +
142D TRP* 3.7 5.2 - - - +
143D LEU* 3.0 51.9 + - + +
910D CLA 3.4 36.3 - - + -
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO* 3.5 15.3 - - + +
136D GLY 3.0 17.2 + - - +
137D THR 3.9 3.1 - - - +
139D VAL* 1.3 75.9 - - - +
141D VAL* 1.3 63.1 + - - +
143D LEU* 4.7 0.2 - - - -
144D GLY* 3.0 17.7 + - - -
910D CLA 3.9 50.4 - - + +
953D LMG 3.9 14.9 - - + +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR* 2.9 34.1 + - + +
138D LEU* 3.7 4.0 - - - +
140D ALA* 1.3 74.8 - - - +
142D TRP* 1.3 58.3 + - - +
144D GLY* 3.3 1.7 + - - -
145D ILE* 2.9 41.2 + - + +
953D LMG 4.0 53.5 - - + +
11G LEU* 3.8 27.4 - - + -
14G VAL* 5.1 6.5 - - + -
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Residues in contact with TRP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 2.6 25.8 + - + +
139D VAL* 3.7 5.8 - - + +
141D VAL* 1.3 71.5 - - - +
143D LEU* 1.3 78.6 + - + +
145D ILE* 3.2 8.9 + - + +
146D GLY* 2.8 19.9 + - - -
154D SER 4.3 3.8 + - - -
155D LEU* 3.7 23.0 + - + +
156D THR* 3.9 19.5 - - - -
157D LEU* 3.6 36.7 - - + +
159D LEU* 4.6 11.2 - - + -
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO* 4.0 11.7 - - + +
86D GLN* 3.4 31.6 - - + +
87D ILE* 3.6 32.8 - - + +
90D VAL* 5.6 1.8 - - + -
139D VAL* 3.0 36.0 + - + +
140D ALA 3.9 2.9 - - - +
142D TRP* 1.3 83.3 - - + +
144D GLY* 1.3 65.3 + - - +
146D GLY* 3.0 3.7 + - - +
147D SER 2.9 18.7 + - - -
154D SER 6.1 0.2 - - - -
155D LEU* 4.2 19.1 - - + -
910D CLA 4.4 11.4 - - + -
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Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 3.7 26.5 - - - -
83D PRO* 3.9 8.5 - - - +
140D ALA 3.0 15.4 + - - -
141D VAL 3.6 3.8 - - - -
142D TRP 3.2 0.2 - - - -
143D LEU* 1.3 76.3 - - - +
145D ILE* 1.3 61.6 + - - +
147D SER* 2.6 23.4 + - - -
148D THR 4.0 0.7 + - - -
953D LMG 3.9 13.1 - - - +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL* 2.9 36.8 + - + +
142D TRP* 3.7 6.5 - - + +
144D GLY* 1.3 73.5 - - - +
146D GLY* 1.3 61.6 + - - +
148D THR* 2.5 28.4 + - - -
149D PHE* 3.1 23.4 - - + -
157D LEU* 3.8 17.9 - - + -
953D LMG 3.2 74.9 - - + +
11G LEU* 4.4 4.0 - - + -
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Residues in contact with GLY 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLN* 3.2 8.1 - - - -
142D TRP 2.8 13.1 + - - -
143D LEU* 3.0 4.9 + - - -
145D ILE* 1.3 72.9 - - - +
147D SER* 1.3 53.0 + - - +
148D THR 2.9 5.4 - - - -
149D PHE* 2.7 25.8 + - - +
154D SER* 3.1 25.3 - - - -
157D LEU* 3.4 20.6 - - - +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 4.0 8.3 - - - +
82D TYR* 3.3 35.3 - - - +
85D PHE* 3.3 39.7 - - - -
86D GLN* 3.1 15.6 + - - -
89D ARG* 3.7 9.4 + - - +
143D LEU 2.9 5.5 + - - -
144D GLY 2.6 19.5 + - - -
146D GLY* 1.3 75.1 - - - +
148D THR* 1.3 59.0 + - - +
149D PHE 3.3 2.9 + - - +
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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