Contacts of the helix formed by residues 134 - 158 (chain D) in PDB entry 6SQ2
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 134 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 4.3 6.7 - - - +
132D ARG 5.2 0.2 - - - +
133D PHE* 1.3 77.4 - - - +
135D LEU* 1.3 65.8 + - - +
136D GLN* 3.6 7.1 + - - +
137D GLU* 2.9 42.9 + - - +
138D LEU* 3.1 18.5 + - - +
129E ASN* 3.8 43.3 - - + +
130E ARG 3.8 10.3 - - - +
131E PRO* 5.1 0.7 - - + -
133E PHE* 3.6 7.4 - - - -
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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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69B ARG 5.4 0.4 - - - +
70B PHE 6.5 0.2 - - - -
72B GLU* 4.0 25.4 - - + +
73B ILE* 3.9 33.0 - - + -
134D THR* 1.3 74.5 - - - +
136D GLN* 1.3 59.3 + - - +
138D LEU* 3.9 0.7 - - - +
139D ARG* 2.8 60.9 + - + +
130E ARG 4.6 0.4 + - - -
132E ARG* 4.0 29.6 - - - +
133E PHE* 3.7 19.8 - - + -
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 3.3 6.7 + - - +
135D LEU* 1.3 80.4 - - - +
137D GLU* 1.3 57.4 + - + +
139D ARG* 4.1 16.9 + - - +
140D ASP* 2.9 65.1 + - - +
143D GLN* 5.2 3.2 + - - +
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.9 31.6 - - + +
69A ARG* 2.4 44.3 + - - -
70A PHE* 4.9 0.2 - - - -
133D PHE* 3.5 13.0 - - + +
134D THR* 2.9 43.7 + - - +
136D GLN* 1.3 76.1 - - + +
138D LEU* 1.3 67.1 + - - +
140D ASP* 3.6 4.8 + - - +
141D VAL* 3.4 24.4 + - - +
138E LEU* 4.3 3.5 - - + +
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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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41B ILE* 4.2 6.3 - - + -
70B PHE* 3.9 13.9 - - + -
73B ILE* 3.9 13.0 - - + -
133D PHE* 5.4 1.5 - - + +
134D THR 3.1 4.9 + - - +
135D LEU 4.0 1.8 - - - +
137D GLU* 1.3 77.6 - - - +
139D ARG* 1.3 57.6 + - - +
141D VAL* 3.2 5.2 + - - +
142D LEU* 2.9 34.3 + - + +
133E PHE* 3.7 54.1 - - + -
137E GLU* 4.2 11.4 - - + +
138E LEU* 4.2 23.9 - - + +
141E VAL* 4.0 26.9 - - + -
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Residues in contact with ARG 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU* 2.9 39.2 + - - +
73B ILE* 3.9 24.6 - - + +
76B ALA* 4.7 9.7 - - - +
135D LEU* 2.8 44.7 + - + +
136D GLN* 3.7 18.1 + - - +
138D LEU* 1.3 78.4 - - - +
140D ASP* 1.3 60.8 + - - +
142D LEU* 3.6 8.2 - - + +
143D GLN* 2.7 55.8 + - - +
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Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 5.8 7.0 - - + +
136D GLN* 2.9 48.7 + - - +
137D GLU* 4.1 5.5 - - - +
138D LEU 3.3 0.2 - - - -
139D ARG* 1.3 75.4 - - - +
141D VAL* 1.3 64.9 + - + +
143D GLN* 4.0 14.0 - - - +
144D GLU* 3.2 22.5 + - - +
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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
----------------------------------------------------------
41A ILE* 4.0 23.1 - - + -
137D GLU 3.4 15.3 - - - +
138D LEU 3.2 6.3 + - - +
140D ASP* 1.3 75.8 - - + +
142D LEU* 1.3 60.3 + - - +
144D GLU* 3.3 7.2 + - - +
145D ARG* 2.8 28.1 + - - +
138E LEU* 4.0 11.9 - - + -
141E VAL* 3.5 31.2 - - + +
142E LEU* 3.9 26.0 - - + +
145E ARG* 4.3 13.4 - - + +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE 3.6 24.2 - - - +
42B GLY* 4.3 4.5 - - - -
43B ILE* 4.3 5.8 - - + +
73B ILE* 3.8 36.3 - - + -
138D LEU* 2.9 30.4 + - + +
139D ARG* 3.6 7.9 - - + +
141D VAL* 1.3 75.8 - - - +
143D GLN* 1.3 61.5 + - + +
145D ARG* 3.3 30.4 + - - +
146D ASN* 2.9 38.5 + - - +
141E VAL* 3.8 22.7 - - + -
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Residues in contact with GLN 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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77B TYR* 5.7 3.4 - - - +
136D GLN* 5.2 2.4 + - - +
139D ARG* 2.7 45.6 + - - +
140D ASP* 4.0 17.2 - - - +
142D LEU* 1.3 79.0 - - + +
144D GLU* 1.3 61.6 + - - +
146D ASN* 3.7 10.9 - - - +
147D LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 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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44A ASP* 5.3 0.8 - - - +
140D ASP 3.2 17.3 + - - +
141D VAL* 3.7 6.5 - - - +
143D GLN* 1.3 75.6 - - - +
145D ARG* 1.3 66.6 + - - +
147D LYS* 3.3 8.9 + - + +
148D LEU* 3.0 38.7 + - + +
145E ARG* 2.9 46.8 + - + +
149E LYS* 3.3 20.3 + - - -
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Residues in contact with ARG 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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41B ILE 5.4 0.8 + - - -
43B ILE* 2.7 33.3 + - - +
44B ASP* 3.9 18.8 + - - +
141D VAL 2.8 17.2 + - - +
142D LEU* 3.4 28.2 - - - +
144D GLU* 1.3 72.9 - - - +
146D ASN* 1.3 86.8 + - - +
148D LEU* 3.3 0.8 + - - +
149D LYS* 2.9 33.2 + - - +
141E VAL* 4.6 9.3 - - + +
144E GLU* 2.8 54.9 + - + +
145E ARG* 4.2 18.9 - - + +
148E LEU* 3.6 20.2 - - + +
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Residues in contact with ASN 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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43B ILE* 4.4 4.8 - - - +
45B PHE* 4.1 17.7 - - + -
62B TRP* 3.9 19.2 - - + -
77B TYR* 3.3 24.9 + - - -
142D LEU* 2.9 21.7 + - - +
143D GLN* 3.7 10.1 - - - +
145D ARG* 1.3 108.7 + - - +
147D LYS* 1.3 63.7 + - - +
149D LYS* 3.2 2.8 + - - +
150D SER* 3.0 27.4 + - - -
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Residues in contact with LYS 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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143D GLN 2.9 17.8 + - - +
144D GLU* 3.7 9.4 - - + +
146D ASN* 1.3 76.9 - - - +
148D LEU* 1.3 60.5 + - + +
150D SER* 3.3 6.4 + - - -
151D GLN* 2.9 64.0 + - - +
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Residues in contact with LEU 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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144D GLU* 3.0 43.8 + - + +
145D ARG 3.7 3.1 - - - +
147D LYS* 1.3 74.8 - - + +
149D LYS* 1.3 60.0 + - - +
151D GLN* 3.2 19.8 + - - +
152D LEU* 2.8 31.7 + - - +
145E ARG* 3.6 32.8 - - + +
148E LEU* 3.9 16.1 - - + +
149E LYS* 4.2 20.2 - - + +
152E LEU* 3.9 19.0 - - + +
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Residues in contact with LYS 149 (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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44B ASP* 3.5 16.7 + - - +
45B PHE* 2.4 59.5 + - + -
46B LYS* 3.8 18.5 - - - +
145D ARG* 2.9 18.9 + - - +
146D ASN 3.2 8.3 + - - +
148D LEU* 1.3 76.2 - - - +
150D SER* 1.3 62.4 + - - +
152D LEU* 3.2 3.8 + - + +
153D LEU* 3.1 36.1 + - + +
144E GLU* 4.6 6.3 - - - +
148E LEU* 3.7 34.2 - - + +
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Residues in contact with SER 150 (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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45B PHE* 3.7 15.9 - - - -
60B GLN* 5.2 5.4 + - - -
146D ASN 3.0 17.4 + - - -
147D LYS* 3.7 6.9 - - - -
149D LYS* 1.3 74.8 - - - +
151D GLN* 1.3 62.7 + - - +
153D LEU* 3.3 11.3 + - - +
154D VAL* 3.2 25.8 + - - +
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Residues in contact with GLN 151 (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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147D LYS* 2.9 53.5 + - + +
148D LEU* 3.7 17.5 - - - +
150D SER* 1.3 75.9 - - - +
152D LEU* 1.3 61.9 - - - +
154D VAL* 3.2 9.0 + - - +
155D VAL* 3.2 27.6 + - + +
152E LEU* 3.5 30.3 - - + +
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Residues in contact with LEU 152 (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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148D LEU 2.8 17.2 + - - +
149D LYS* 3.6 5.6 - - - +
151D GLN* 1.3 76.7 - - - +
153D LEU* 1.3 61.3 + - + +
155D VAL* 3.4 1.2 + - - -
156D GLN* 2.9 53.9 + - - +
148E LEU* 3.9 15.9 - - + +
151E GLN* 3.6 41.1 - - + +
152E LEU* 3.9 21.9 - - + +
155E VAL* 3.8 29.8 - - + -
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Residues in contact with LEU 153 (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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45B PHE* 4.3 13.9 - - + -
47B ILE* 3.8 31.9 - - + -
58B LYS* 6.1 4.5 - - - +
149D LYS* 3.1 24.1 + - + +
150D SER* 3.7 9.0 - - - +
151D GLN 3.2 0.4 - - - -
152D LEU* 1.3 80.6 - - + +
154D VAL* 1.3 65.0 + - + +
156D GLN* 3.4 21.3 - - - +
157D GLU* 3.1 35.5 + - + +
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Residues in contact with VAL 154 (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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150D SER 3.2 13.3 + - - +
151D GLN* 3.2 11.7 + - - +
153D LEU* 1.3 77.1 - - + +
155D VAL* 1.3 66.5 + - + +
157D GLU* 3.3 14.4 + - - +
158D GLU* 3.1 26.8 + - - +
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Residues in contact with VAL 155 (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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151D GLN* 3.2 17.6 + - + +
152D LEU 4.1 2.0 - - - +
154D VAL* 1.3 80.2 - - + +
156D GLN* 1.3 66.3 + - - +
158D GLU* 3.1 20.8 + - + +
159D LEU* 3.6 9.2 - - - +
152E LEU* 3.9 17.7 - - + -
155E VAL* 3.6 31.2 - - + +
156E GLN* 4.1 21.5 - - + +
158E GLU* 4.5 13.0 - - + +
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Residues in contact with GLN 156 (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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152D LEU* 2.9 42.8 + - + +
153D LEU* 3.4 26.9 - - - +
155D VAL* 1.3 76.9 - - - +
157D GLU* 1.3 63.2 + - + +
159D LEU* 3.3 21.1 + - - +
155E VAL* 3.8 25.5 - - + +
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Residues in contact with GLU 157 (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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4B THR* 5.8 4.6 - - - +
58B LYS* 4.3 17.9 + - - -
153D LEU* 3.1 22.6 + - + +
154D VAL* 3.6 13.6 - - - +
155D VAL 3.1 0.6 - - - -
156D GLN* 1.3 72.6 - - + +
158D GLU* 1.3 55.5 + - - +
159D LEU* 2.3 28.1 + - - -
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Residues in contact with GLU 158 (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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154D VAL* 3.1 20.1 + - - +
155D VAL* 3.1 18.0 + - + +
157D GLU* 1.3 74.3 - - - +
159D LEU* 1.3 72.7 + - + +
158E GLU* 4.2 11.8 - - - +
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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
------------------------------------------------------------
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