Contacts of the helix formed by residues 129 - 150 (chain D) in PDB entry 2R7I
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 129 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D THR 4.9 3.8 - - - +
128D LEU* 1.3 78.3 - - - +
130D ASP* 1.3 65.8 + - - +
131D TYR* 3.3 10.9 + - - +
132D ASP* 2.8 42.1 + - - +
133D ILE* 3.1 10.7 + - - +
291D HIS* 5.6 2.9 - - - -
292D LEU* 4.0 3.4 - - - -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D THR* 1.3 73.2 - - - +
131D TYR* 1.3 63.2 + - - +
133D ILE* 3.7 6.0 + - - +
134D ARG* 3.1 62.5 + - - +
291D HIS* 3.3 25.7 - - - +
292D LEU* 3.2 36.3 - - - +
294D SER* 4.4 1.8 + - - -
323D TYR* 4.4 4.5 + - - -
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Residues in contact with TYR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D THR* 2.9 9.2 + - - +
130D ASP* 1.3 80.5 - - - +
132D ASP* 1.3 69.0 + - - +
134D ARG* 3.1 12.2 + - - +
135D PHE* 2.9 30.1 + + + -
169D ARG* 3.5 28.5 - - - -
326D THR* 3.7 32.1 + - + -
327D VAL* 4.1 28.8 + - + +
329D LYS 5.7 0.3 + - - -
330D ASP* 5.7 3.3 - - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D THR 5.4 0.2 - - - +
128D LEU* 3.7 22.5 - - + +
129D THR* 2.8 38.9 + - - +
131D TYR* 1.3 74.9 - - - +
133D ILE* 1.3 62.5 + - - +
135D PHE* 2.9 7.4 + - - +
136D TYR* 2.8 32.3 + - + -
166D HIS* 4.0 17.7 + - - -
169D ARG* 2.7 36.2 + - - -
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PHE* 5.4 0.2 - - - -
125D TYR* 5.5 2.9 - - + +
128D LEU* 4.0 25.7 - - + +
129D THR 3.1 10.3 + - - +
130D ASP* 3.8 8.3 - - - +
132D ASP* 1.3 76.3 - - - +
134D ARG* 1.3 63.4 + - - +
136D TYR* 3.8 2.3 - - - +
137D MET* 2.8 41.6 + - + +
222D LEU* 4.2 9.4 - - + -
225D MET* 3.9 43.3 - - + +
226D ILE* 4.3 9.0 - - + -
292D LEU* 4.3 21.8 - - + -
323D TYR* 3.4 17.5 - - - +
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP* 3.1 43.3 + - - +
131D TYR* 3.1 13.4 + - - +
133D ILE* 1.3 75.5 - - - +
135D PHE* 1.3 57.4 + - - +
138D TYR* 3.0 24.1 + - - +
294D SER* 3.4 27.1 + - - -
296D GLU* 4.1 19.0 + - - +
322D PRO 4.6 2.2 + - - -
323D TYR* 3.1 64.5 + - + +
324D PHE* 3.3 14.5 - - + -
325D TYR* 6.1 0.2 - - - +
326D THR* 4.5 17.4 + - - -
327D VAL* 4.0 14.4 - - + -
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 2.9 23.3 + + + +
132D ASP* 2.9 11.1 + - - +
134D ARG* 1.3 78.2 - - - +
136D TYR* 1.3 93.6 + + - +
138D TYR* 3.3 6.1 + - - +
139D GLU* 3.1 49.5 + - + +
169D ARG* 3.8 48.5 - - + +
327D VAL* 3.7 26.2 - - + -
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Residues in contact with TYR 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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121D PHE* 3.5 32.3 - + + -
124D LEU* 5.1 0.2 - - + -
128D LEU* 4.2 12.8 - - + -
132D ASP* 2.8 34.4 + - + +
133D ILE 4.2 0.7 - - - +
135D PHE* 1.3 95.7 - + - +
137D MET* 1.3 61.9 + - - +
138D TYR 3.2 1.6 - - - -
139D GLU* 3.1 5.3 + - + +
140D ILE* 2.9 36.0 + - - +
164D ILE* 3.7 23.6 - - + -
166D HIS* 2.7 47.8 + + - -
169D ARG* 3.7 22.5 - - - -
170D LYS 4.4 2.5 - - - -
171D LEU* 3.8 19.0 - - + +
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Residues in contact with MET 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 ILE* 2.8 31.9 + - + +
134D ARG* 3.7 4.9 - - - +
136D TYR* 1.3 77.7 - - + +
138D TYR* 1.3 59.4 + - - +
140D ILE* 3.3 9.5 + - - +
141D LEU* 2.9 35.4 + - - +
218D LEU* 3.5 44.2 - - + -
221D MET* 5.2 0.9 - - - -
222D LEU* 4.0 22.7 - - + -
225D MET* 3.5 32.1 - - + -
300D PHE* 3.9 23.6 - - + -
304D LEU* 4.9 0.4 - - + -
323D TYR* 4.9 0.2 - - + -
324D PHE* 3.8 11.0 - - + -
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ARG 3.0 14.1 + - - +
135D PHE 3.4 9.6 - - - +
136D TYR 3.2 0.4 - - - -
137D MET* 1.3 78.8 - - - +
139D GLU* 1.3 64.7 + - - +
141D LEU* 3.3 5.1 + - - +
142D LYS* 2.9 46.1 + - + +
316D ARG* 4.5 4.7 + - - -
319D MET* 3.4 58.2 + - + +
324D PHE* 3.7 30.5 - + + -
327D VAL* 4.2 19.1 - - + -
328D VAL* 4.3 21.6 - - + +
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Residues in contact with GLU 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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93D ASN* 2.7 33.7 + - - +
135D PHE* 3.1 51.1 + - + +
136D TYR* 3.1 12.4 + - + +
138D TYR* 1.3 85.9 - - - +
140D ILE* 1.3 63.8 - - - +
142D LYS* 3.1 35.0 + - - -
143D ALA* 3.2 5.5 + - - +
169D ARG 5.4 2.5 - - - +
171D LEU* 3.9 22.0 - - + +
327D VAL* 5.4 1.2 - - - +
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Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PHE* 3.9 24.0 - - + -
136D TYR 2.9 21.8 + - - +
137D MET* 3.7 9.9 - - - +
139D GLU* 1.3 75.7 - - - +
141D LEU* 1.3 52.3 + - - +
143D ALA* 3.0 6.4 + - - +
144D LEU* 2.7 45.6 + - + +
157D VAL* 4.9 8.7 - - + -
162D VAL* 4.2 12.8 - - + -
171D LEU* 3.9 19.3 - - + -
173D LEU* 5.1 8.5 - - + -
218D LEU* 3.8 26.2 - - + -
221D MET* 3.9 20.4 - - + -
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Residues in contact with LEU 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 MET* 2.9 22.4 + - + +
138D TYR* 3.7 4.9 - - - +
140D ILE* 1.3 73.8 - - - +
142D LYS* 1.3 60.0 + - - +
144D LEU* 4.3 4.5 - - + +
145D ASP* 2.8 32.7 + - - +
215D MET* 3.5 21.1 - - + -
218D LEU* 3.3 29.8 - - + -
300D PHE* 4.3 3.8 - - + -
315D ALA* 4.0 10.3 - - + +
318D ALA* 3.8 16.8 - - + -
319D MET* 3.6 22.5 - - + +
324D PHE* 3.5 36.1 - - + -
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Residues in contact with LYS 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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92D PRO* 3.8 30.6 - - + +
93D ASN* 3.7 9.8 + - - +
138D TYR* 2.9 41.6 + - + +
139D GLU* 3.1 30.5 + - - +
141D LEU* 1.3 76.0 - - - +
143D ALA* 1.3 57.8 + - - +
145D ASP* 4.3 1.5 - - - +
146D TYR* 3.2 26.5 + - - +
316D ARG* 5.9 0.4 - - - +
319D MET* 3.8 20.2 - - + -
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Residues in contact with ALA 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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92D PRO 3.4 21.5 + - - +
93D ASN* 3.7 22.0 - - + +
94D ILE* 4.0 9.6 - - + +
139D GLU 3.2 5.4 + - - +
140D ILE* 3.0 10.3 + - - +
142D LYS* 1.3 77.1 - - - +
144D LEU* 1.3 64.3 + - - +
146D TYR* 3.5 2.3 + - - +
147D CYS* 3.2 25.5 + - - +
171D LEU* 5.4 0.4 - - + -
173D LEU* 4.0 21.2 - - + +
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Residues in contact with LEU 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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140D ILE* 2.7 40.2 + - + +
141D LEU* 4.1 5.4 - - - +
143D ALA* 1.3 71.8 - - - +
145D ASP* 1.3 66.0 + - - +
147D CYS* 3.5 7.1 + - - -
148D HIS* 3.0 42.0 + - + +
154D HIS* 4.7 1.6 - - + -
157D VAL* 4.2 19.1 - - + -
173D LEU* 3.8 20.2 - - + -
214D ASP* 4.3 25.4 - - + +
215D MET* 4.5 11.2 - - - -
218D LEU* 4.4 22.0 - - + -
315D ALA* 4.4 6.1 - - + -
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Residues in contact with ASP 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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12D TYR* 2.7 32.2 + - - -
141D LEU 2.8 22.0 + - - +
142D LYS* 4.3 2.5 - - - +
144D LEU* 1.3 73.9 - - - +
146D TYR* 1.3 62.7 + - - +
148D HIS* 4.5 2.0 - - - -
149D SER* 2.9 26.9 + - - -
315D ALA* 3.6 15.8 + - + +
316D ARG* 3.3 47.4 + - - +
319D MET* 4.1 7.9 - - - -
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Residues in contact with TYR 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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87D ASN 4.4 6.6 + - - -
88D LEU* 3.9 21.5 + - + -
89D ARG 4.8 3.1 + - - -
90D GLY 5.2 0.2 - - - -
91D GLY* 3.3 24.4 + - - -
92D PRO* 3.7 22.9 - - + -
94D ILE* 3.5 21.3 - - + -
142D LYS 3.2 20.1 + - - +
143D ALA 3.6 4.5 - - - +
144D LEU 3.2 0.8 - - - -
145D ASP* 1.3 75.8 + - - +
147D CYS* 1.3 59.4 + - - +
149D SER* 2.5 28.3 + - - -
150D MET* 2.9 46.1 + - + +
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Residues in contact with CYS 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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88D LEU* 3.9 29.4 - - + -
94D ILE* 5.4 0.2 - - + -
143D ALA 3.2 17.9 + - - +
144D LEU* 3.6 16.8 - - - -
146D TYR* 1.3 80.1 - - + +
148D HIS* 1.3 67.4 + - - +
150D MET* 2.8 23.4 + - - +
151D GLY 3.1 0.5 + - - -
152D ILE* 2.9 35.2 + - + +
154D HIS 4.5 3.1 - - - -
176D TRP* 3.8 22.4 - - + -
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Residues in contact with HIS 148 (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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11D VAL* 6.4 1.1 - - + -
12D TYR* 3.4 32.0 - + + +
144D LEU* 3.0 38.4 + - + +
145D ASP* 3.9 3.1 - - - +
147D CYS* 1.3 78.0 - - - +
149D SER* 1.3 63.4 + - - +
151D GLY 3.0 10.4 + - - -
152D ILE 3.2 17.4 + - - -
153D MET* 4.6 0.4 - - - -
211D TYR* 3.4 48.6 + - + -
214D ASP* 3.0 35.5 + - + +
215D MET* 4.5 7.7 - - + -
315D ALA* 4.3 16.6 - - + -
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 3.4 33.7 - - - -
15D VAL* 3.9 18.7 - - - +
19D ARG* 5.8 0.2 + - - -
145D ASP* 2.9 18.2 + - - -
146D TYR* 2.5 25.8 + - - -
148D HIS* 1.3 75.6 - - - +
150D MET* 1.3 71.7 + - - +
151D GLY 3.3 2.6 + - - -
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 4.4 2.7 - - - -
16D ASN* 4.8 0.2 - - - -
19D ARG* 3.1 34.8 - - - +
23D TYR* 2.8 39.5 + - - +
87D ASN 4.4 7.9 - - - +
88D LEU* 3.6 14.4 - - + -
146D TYR* 2.9 55.1 + - + +
147D CYS 2.8 12.1 + - - +
149D SER* 1.3 88.8 - - - +
151D GLY* 1.3 58.7 + - - +
152D ILE* 3.4 3.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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