Contacts of the helix formed by residues 132 - 150 (chain D) in PDB entry 3T79
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 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PHE 2.8 14.2 - - - +
131D LYS* 1.3 93.7 - - + +
133D CYS* 1.3 64.0 + - - +
134D GLN* 2.7 33.9 + - + +
135D ASP* 3.1 33.4 + - - +
136D LYS 3.6 1.6 + - - -
208D LEU* 5.8 0.2 - - - +
360D ASP* 4.1 6.6 + - - -
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Residues in contact with CYS 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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118D TRP 4.8 3.1 - - - +
120D PRO* 4.0 32.3 - - - -
131D LYS 3.6 3.0 + - - -
132D THR* 1.3 68.1 - - - +
134D GLN* 1.3 66.4 + - - +
136D LYS* 3.5 12.9 + - - +
137D LEU* 2.9 27.5 + - + +
208D LEU* 5.3 1.6 - - + -
359D HIS* 3.7 27.8 - - + +
360D ASP* 3.0 46.6 + - + +
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Residues in contact with GLN 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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132D THR* 2.7 18.3 + - - +
133D CYS* 1.3 76.9 - - - +
135D ASP* 1.3 65.8 + - - +
137D LEU* 2.9 10.2 + - - +
138D LYS* 2.8 45.9 + - + +
205D TYR* 3.9 23.1 + - + -
208D LEU* 4.4 35.4 + - + +
209D ARG* 4.6 9.7 - - - +
217D TYR* 4.9 16.0 - - - -
220D ASP* 5.7 2.2 + - - -
235D ARG* 5.2 5.5 - - - +
360D ASP* 4.4 1.2 + - - -
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Residues in contact with ASP 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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129D HIS* 4.7 1.6 - - - -
130D PHE* 3.2 43.8 + - + +
131D LYS* 3.9 9.5 + - - -
132D THR* 3.1 29.6 + - - +
134D GLN* 1.3 77.9 - - - +
136D LYS* 1.3 65.2 + - - +
138D LYS* 3.0 25.7 + - + +
139D LEU* 3.0 23.6 + - - +
251D TRP* 5.7 1.1 - - - +
6F T 6.1 0.9 - - - -
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Residues in contact with LYS 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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117D LEU* 3.3 50.8 - - + +
118D TRP 4.9 0.9 - - - +
119D ASN 2.6 25.9 + - - +
120D PRO* 3.2 18.2 + - - +
122D THR* 2.9 30.7 - - - +
125D LEU* 5.6 2.9 - - + -
130D PHE* 3.2 41.7 - - + +
131D LYS 4.6 4.3 + - - -
132D THR 3.6 2.6 + - - +
133D CYS* 3.5 14.4 + - - +
134D GLN 3.3 0.4 - - - -
135D ASP* 1.3 78.4 - - - +
137D LEU* 1.3 59.3 + - - +
139D LEU* 3.4 1.4 + - - +
140D LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 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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117D LEU 4.4 7.2 - - - +
118D TRP* 3.3 37.9 - - + -
133D CYS 2.9 20.8 + - - +
134D GLN* 2.9 6.5 + - - +
136D LYS* 1.3 74.3 - - - +
138D LYS* 1.3 56.6 + - - +
140D LEU* 3.6 15.8 - - + +
141D LEU* 2.8 35.2 + - - +
201D THR* 4.3 5.3 - - + +
204D VAL* 3.3 37.7 - - + -
205D TYR* 3.9 24.1 - - + +
208D LEU* 4.9 3.4 - - + -
359D HIS* 4.3 11.0 - - + +
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Residues in contact with LYS 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 GLN* 2.8 30.8 + - + +
135D ASP* 3.0 30.9 + - + +
137D LEU* 1.3 72.3 - - - +
139D LEU* 1.3 65.4 + - - +
141D LEU* 3.1 6.3 + - - +
142D ASP* 3.0 20.0 + - - +
205D TYR* 2.4 53.9 + - + +
234D ILE* 4.3 21.3 - - + +
235D ARG* 3.1 32.3 + - - +
236D GLY* 5.4 0.7 - - - -
243D PRO* 5.7 0.7 - - + -
248D LEU* 6.1 1.8 - - + -
251D TRP* 6.2 4.0 - - + +
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Residues in contact with LEU 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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113D ILE* 6.0 0.2 - - + -
117D LEU* 3.7 21.1 - - + -
130D PHE* 4.1 13.2 - - + -
135D ASP 3.0 7.0 + - - +
136D LYS* 3.5 7.9 - - - +
138D LYS* 1.3 79.7 - - - +
140D LEU* 1.3 56.0 + - - +
142D ASP* 2.6 29.6 + - - +
143D PHE* 2.9 15.3 + - + +
248D LEU* 3.9 14.1 - - + +
251D TRP* 3.1 43.0 - - + -
252D TYR* 4.2 23.1 - - + -
255D ILE* 3.7 29.6 - - + -
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Residues in contact with LEU 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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113D ILE* 4.5 5.4 - - + -
114D SER* 2.9 49.6 - - - +
117D LEU* 3.6 19.4 - - + +
118D TRP* 3.9 16.2 - - + +
136D LYS 2.8 21.8 + - - +
137D LEU* 3.6 14.6 - - + +
138D LYS 3.3 0.2 - - - -
139D LEU* 1.3 73.3 - - - +
141D LEU* 1.3 56.5 + - - +
143D PHE* 4.4 6.7 - - + -
144D GLN* 2.9 42.0 + - + +
201D THR* 3.1 28.5 - - + -
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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 LEU 2.8 17.6 + - - +
138D LYS* 3.3 9.2 - - - +
140D LEU* 1.3 70.6 - - - +
142D ASP* 1.3 66.6 + - - +
144D GLN* 4.7 0.4 - - - -
145D TRP* 2.8 34.3 + - + +
187D LEU* 6.5 0.2 - - + -
198D PRO* 3.4 32.1 - - + +
201D THR* 4.4 10.7 - - - +
202D MET* 3.9 20.9 - - + +
205D TYR* 4.5 11.4 - - + -
233D ILE* 3.7 22.0 - - + +
234D ILE* 3.2 30.3 - - + -
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Residues in contact with ASP 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 LYS 3.0 9.8 + - - +
139D LEU* 2.6 17.7 + - - +
141D LEU* 1.3 72.9 - - - +
143D PHE* 1.3 62.9 + - - +
145D TRP* 2.8 20.9 + - - +
146D LYS* 2.9 12.8 + - - +
156D ARG* 2.6 45.8 + - - -
234D ILE* 5.2 3.8 - - + +
242D TYR* 3.5 12.2 + - + +
248D LEU* 3.3 21.1 - - + +
252D TYR* 3.0 27.2 + - + +
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Residues in contact with PHE 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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109D ILE* 4.3 3.1 - - + -
110D LEU* 3.6 24.9 - - + -
113D ILE* 3.0 46.0 - - + -
114D SER* 5.9 0.4 - - - -
117D LEU* 5.9 0.2 - - + -
139D LEU* 2.9 20.9 + - + +
140D LEU* 3.8 10.3 - - + +
142D ASP* 1.3 74.0 - - - +
144D GLN* 1.3 73.9 + - + +
146D LYS* 3.3 4.2 + - - +
147D PHE* 2.9 44.2 + + - +
252D TYR* 2.9 35.8 + + + +
255D ILE* 6.1 0.4 - - + -
256D PHE* 3.9 7.2 - + - -
268D TRP* 3.7 30.7 - + - -
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Residues in contact with GLN 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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110D LEU* 4.5 9.8 - - + +
114D SER* 2.1 36.7 + - - -
140D LEU* 2.9 36.7 + - + +
141D LEU* 4.0 1.8 - - - +
143D PHE* 1.3 85.4 - - + +
145D TRP* 1.3 57.5 + - - +
147D PHE* 3.7 4.9 - - - +
148D ASN* 2.9 33.6 + - - +
195D PHE 2.9 15.1 + - - -
196D THR* 3.7 10.5 - - - +
197D CYS 3.0 2.5 - - - +
198D PRO* 2.9 43.2 - - + +
201D THR* 2.9 11.0 + - - -
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Residues in contact with TRP 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 LEU* 2.8 29.6 + - + +
142D ASP* 2.8 11.8 + - - +
144D GLN* 1.3 77.0 - - - +
146D LYS* 1.3 62.6 - - - -
148D ASN* 3.2 0.7 + - - +
149D THR* 2.8 42.6 + - + +
151D VAL* 5.8 3.8 - - + -
156D ARG* 3.2 48.5 - - + -
159D VAL* 3.5 18.8 - - + -
185D PHE* 3.7 30.6 - + - -
187D LEU* 3.5 26.4 - - + +
198D PRO* 4.7 2.0 - - + -
233D ILE* 4.0 25.6 - - + -
234D ILE* 5.8 0.2 - - + -
242D TYR* 3.1 32.8 - + - -
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Residues in contact with LYS 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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142D ASP 2.9 13.0 + - - +
143D PHE* 3.6 8.5 - - - +
145D TRP* 1.3 72.2 - - - +
147D PHE* 1.3 62.0 + - - +
148D ASN 2.9 0.9 + - - -
149D THR* 2.9 6.2 + - - -
150D ASN* 2.5 58.0 + - - -
151D VAL 3.0 36.6 - - - +
156D ARG* 4.0 14.7 - - - +
252D TYR* 5.3 0.7 - - - +
267D HIS 2.7 29.4 + - - -
268D TRP* 3.7 32.9 - - + +
270D GLN 3.5 15.7 + - - -
271D VAL* 4.9 0.7 - - - +
272D ASN* 4.1 5.5 - - - +
275D TRP* 4.6 5.1 - - - -
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Residues in contact with PHE 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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103D TYR* 4.3 15.5 + + - -
106D VAL* 3.3 41.5 - - + -
107D ILE* 4.4 2.9 - - - -
109D ILE* 4.8 1.8 - - + -
110D LEU* 3.5 45.1 - - + -
143D PHE* 2.9 39.6 + + - +
144D GLN 3.7 4.5 - - - +
146D LYS* 1.3 78.1 - - - +
148D ASN* 1.3 59.5 + - - +
150D ASN* 4.3 11.1 + - - -
268D TRP* 3.9 13.0 - + + -
275D TRP* 4.2 16.0 - + - -
312D ARG* 2.4 50.2 + - - -
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Residues in contact with ASN 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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110D LEU* 5.6 0.6 - - - +
144D GLN* 2.9 18.7 + - - +
145D TRP 3.9 1.1 - - - +
146D LYS 2.9 0.6 + - - -
147D PHE* 1.3 79.9 - - - +
149D THR* 1.3 56.5 + - - +
187D LEU* 3.6 17.2 - - + +
188D VAL 4.7 2.4 + - - -
196D THR 5.4 2.5 + - - +
198D PRO* 3.6 27.1 - - + +
278D PHE* 4.5 2.6 - - - -
310D MET* 3.0 32.7 - - - +
311D ASN* 3.3 26.3 + - - +
312D ARG* 2.1 52.0 + - - +
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Residues in contact with THR 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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145D TRP* 2.8 54.8 + - + +
146D LYS* 3.8 1.6 - - - +
148D ASN* 1.3 74.0 - - - +
150D ASN* 1.3 69.1 + - - +
151D VAL* 3.0 29.3 - - + +
156D ARG* 5.9 0.2 - - + -
185D PHE* 3.0 36.2 - - - +
187D LEU* 4.8 3.6 - - - -
278D PHE* 4.1 12.1 + - - +
310D MET* 3.9 13.2 - - - +
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Residues in contact with ASN 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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103D TYR* 4.6 4.2 + - - -
146D LYS* 2.5 49.0 + - - -
147D PHE 4.3 6.7 + - - -
148D ASN 3.7 1.2 - - - -
149D THR* 1.3 74.4 - - - +
151D VAL* 1.3 56.9 + - - +
271D VAL* 4.3 17.7 - - + +
272D ASN* 4.0 9.2 + - - +
275D TRP* 2.9 48.1 - - - +
276D PRO* 3.5 30.8 + - - +
277D GLN* 4.8 9.0 - - - +
310D MET* 4.8 3.6 - - - -
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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