Contacts of the helix formed by residues 133 - 149 (chain D) in PDB entry 1S77
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D ASN 5.6 1.1 - - - -
132D THR* 1.3 75.4 - - - +
134D VAL* 1.3 66.6 + - - +
135D GLN* 3.5 19.2 + - - +
136D ALA* 3.3 9.8 + - - +
137D VAL* 3.1 25.8 + - - +
241D SER* 6.2 1.6 - - - -
242D GLU 2.8 21.8 - - - +
243D THR* 3.2 23.1 - - + -
244D ILE* 3.5 13.0 - - - +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D THR* 1.3 76.5 - - - +
135D GLN* 1.3 80.3 + - + +
137D VAL* 3.3 2.7 + - - +
138D ALA* 2.8 35.1 + - + +
214D VAL* 6.0 6.5 - - + -
217D ILE* 3.9 11.9 - - + +
229D LEU* 6.1 2.2 - - + -
241D SER* 5.3 6.5 - - - -
242D GLU* 4.3 29.4 - - + +
243D THR 5.3 0.2 - - - -
244D ILE* 4.1 20.4 - - + -
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Residues in contact with GLN 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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133D THR* 3.4 10.0 + - - +
134D VAL* 1.3 91.2 - - + +
136D ALA* 1.3 51.9 + - - +
138D ALA* 4.6 3.8 - - - -
139D SER* 2.5 42.3 + - - -
210D ILE* 4.7 11.6 - - + +
241D SER* 4.1 21.2 + - - +
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Residues in contact with ALA 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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125D CYS* 5.1 4.4 - - + -
132D THR* 4.2 18.6 - - + -
133D THR* 3.3 24.9 + - - +
134D VAL 3.2 0.2 - - - -
135D GLN* 1.3 78.6 - - - +
137D VAL* 1.3 63.4 + - - +
139D SER* 2.7 20.4 + - - -
140D ALA* 3.3 11.1 + - - +
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Residues in contact with VAL 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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121D THR 5.2 0.9 - - - +
122D THR* 4.1 23.1 - - + +
125D CYS* 5.1 13.0 - - + +
126D LEU* 5.7 0.2 - - + -
133D THR 3.1 15.6 + - - +
134D VAL 3.8 1.1 - - - +
136D ALA* 1.3 75.5 - - + +
138D ALA* 1.3 50.4 + - - +
140D ALA* 2.7 12.4 + - - +
141D ILE* 2.6 52.4 + - + -
217D ILE* 3.3 26.9 - - + -
227D VAL* 6.4 0.9 - - + -
244D ILE* 3.2 32.5 - - + -
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Residues in contact with ALA 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 VAL 2.8 21.4 + - - +
135D GLN* 4.0 2.9 - - - +
137D VAL* 1.3 72.4 - - - +
139D SER* 1.3 57.1 + - - +
140D ALA 2.9 0.3 + - - -
141D ILE* 4.3 0.9 - - - +
142D GLY* 2.8 31.5 + - - -
209D SER 3.5 6.0 - - - +
210D ILE* 3.3 31.0 - - + +
213D GLY* 3.8 10.1 - - - -
214D VAL* 3.8 15.7 - - + +
217D ILE* 3.4 6.7 - - + +
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Residues in contact with SER 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 GLN 2.5 29.3 + - - -
136D ALA* 2.7 18.0 + - - -
138D ALA* 1.3 72.1 - - - +
140D ALA* 1.3 50.5 + - - +
143D ARG* 2.8 32.2 - - - +
209D SER* 4.9 5.3 - - - -
210D ILE* 4.5 17.9 - - - +
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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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121D THR* 3.6 19.7 - - + -
125D CYS* 4.1 15.0 - - - -
136D ALA 3.3 10.6 + - - +
137D VAL 2.7 9.9 + - - +
139D SER* 1.3 79.7 - - - +
141D ILE* 1.3 55.2 + - - +
142D GLY 3.4 0.2 - - - -
143D ARG* 3.3 4.0 - - - +
144D ALA* 2.4 38.5 + - - +
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Residues in contact with ILE 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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117D ILE 5.0 0.4 - - - -
118D THR* 4.0 18.8 - - + +
121D THR* 3.8 14.5 - - + +
122D THR* 3.6 18.8 - - + -
137D VAL* 2.6 31.7 + - + +
140D ALA* 1.3 71.1 - - - +
142D GLY* 1.3 52.0 + - - +
144D ALA* 2.7 11.2 + - - +
145D ILE* 2.5 46.4 + - + +
213D GLY* 3.8 6.5 - - - -
216D CYS* 3.7 31.9 - - + -
217D ILE* 3.3 34.3 - - + -
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Residues in contact with GLY 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 ALA 2.8 11.9 + - - -
141D ILE* 1.3 74.3 - - - +
143D ARG* 1.3 62.1 + - - +
145D ILE* 3.1 21.7 + - - +
146D GLU* 3.2 18.7 + - - +
204D TRP* 4.7 1.4 - - - -
209D SER* 3.5 29.8 - - - -
212D VAL* 3.9 10.5 - - - -
213D GLY* 4.0 1.4 - - - -
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Residues in contact with ARG 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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138D ALA 4.0 0.8 + - - -
139D SER 2.8 26.9 + - - +
140D ALA* 3.0 7.5 + - - +
142D GLY* 1.3 75.5 - - - +
144D ALA* 1.3 56.2 + - - +
146D GLU* 3.4 22.6 + - - +
147D ASP* 2.8 39.6 + - - +
150D ARG* 5.9 1.8 - - - +
180D LYS* 5.2 4.9 - - - +
209D SER* 4.1 8.6 - - - +
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Residues in contact with ALA 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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117D ILE* 3.4 23.4 - - + +
121D THR* 3.9 16.4 - - + +
140D ALA 2.4 25.3 + - - +
141D ILE* 2.7 8.2 + - - +
143D ARG* 1.3 70.2 - - - +
145D ILE* 1.3 54.8 + - - +
146D GLU 2.4 22.6 - - - +
147D ASP* 4.5 3.3 - - - +
148D GLU* 3.7 12.8 - - - +
752D LEU* 4.7 9.3 - - + +
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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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106D LEU* 3.5 20.9 - - + -
109D ILE* 3.4 23.1 - - + +
114D VAL* 3.7 31.2 - - + +
117D ILE* 4.1 16.4 - - + -
118D THR* 4.6 0.2 - - - +
141D ILE* 2.5 42.0 + - + +
142D GLY 3.4 6.7 - - - +
144D ALA* 1.3 71.9 - - - +
146D GLU* 1.3 57.3 + - - +
148D GLU* 3.9 0.5 - - - +
149D ALA* 2.8 26.9 + - - +
204D TRP* 3.6 18.8 - - + -
212D VAL* 3.7 17.3 - - + -
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Residues in contact with GLU 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 GLY 3.2 12.7 - - - +
143D ARG* 3.5 18.7 + - - +
144D ALA 2.4 21.8 - - - +
145D ILE* 1.3 74.3 - - - +
147D ASP* 1.3 62.2 + - - +
148D GLU 2.3 22.6 + - - -
149D ALA* 3.4 11.0 - - - -
150D ARG* 2.6 41.0 + - - +
204D TRP* 2.8 46.1 - - + +
205D HIS 5.3 1.6 - - - +
209D SER* 2.8 27.5 + - - -
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Residues in contact with ASP 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 ARG* 2.8 35.9 + - - +
144D ALA* 4.5 3.1 - - - +
146D GLU* 1.3 76.2 - - - +
148D GLU* 1.3 58.7 + - + +
149D ALA 3.0 0.4 - - - -
150D ARG* 3.4 15.6 + - - +
151D PHE* 2.6 46.3 + - - +
152D GLY 3.1 2.6 + - - -
180D LYS* 1.8 41.5 + - - -
751D PHE* 3.5 23.1 - - + -
752D LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 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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109D ILE* 3.9 7.4 - - + +
117D ILE* 3.3 32.9 - - + +
144D ALA 3.7 2.0 - - - +
145D ILE 4.0 1.1 - - - +
146D GLU 2.3 22.7 + - - +
147D ASP* 1.3 70.3 - - - +
149D ALA* 1.3 55.0 + - - +
152D GLY* 2.7 31.8 - - - +
153D ARG 3.2 0.2 + - - -
749D LEU* 2.8 41.8 - - - +
750D MET* 2.4 40.1 - - - +
751D PHE* 4.1 3.8 - - + -
752D LEU* 3.5 26.2 + - + +
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Residues in contact with ALA 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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108D GLU* 4.6 6.8 - - + +
109D ILE* 3.4 20.4 - - + -
145D ILE 2.8 23.1 + - - +
146D GLU* 3.5 10.3 - - - -
148D GLU* 1.3 78.9 - - - +
150D ARG* 1.3 56.2 + - - +
153D ARG* 2.7 32.6 - - - +
201D TRP* 4.3 13.2 - - + -
204D TRP* 3.9 17.9 - - + -
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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