Contacts of the helix formed by residues 141 - 155 (chain D) in PDB entry 1SJB
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 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D MET* 3.1 6.3 - - - +
140D ASP* 1.4 84.8 + - - +
142D ILE* 1.3 72.9 + - - +
143D PRO* 2.9 30.7 - - + -
144D GLN* 2.9 19.1 + - + +
145D LEU* 3.0 13.3 + - - +
168D TRP* 3.8 9.2 - - - -
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Residues in contact with ILE 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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141D THR* 1.3 73.8 - - - +
143D PRO* 1.4 61.1 - - + -
145D LEU* 2.4 34.8 + - + -
146D LEU* 2.5 45.9 + - + -
168D TRP* 4.1 10.0 - - + -
171D GLU* 4.0 24.0 - - + +
172D PRO* 4.4 5.8 - - + -
175D ALA* 3.3 26.5 - - + -
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Residues in contact with PRO 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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141D THR* 2.9 25.1 - - + -
142D ILE* 1.4 88.1 - - + +
144D GLN* 1.3 54.9 + - - +
146D LEU* 3.9 12.1 - - + -
147D ASP* 2.5 45.6 + - - +
179D ARG* 5.4 4.7 - - - +
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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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139D MET* 3.7 19.7 - - + +
140D ASP* 3.0 30.2 + - - +
141D THR* 2.9 40.7 + - - +
142D ILE 2.8 0.8 + - - -
143D PRO* 1.3 85.1 - - - +
145D LEU* 1.3 62.8 + - - +
147D ASP* 3.2 6.0 - - - +
148D VAL* 2.8 26.3 + - + +
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Residues in contact with LEU 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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136D VAL* 3.7 24.9 - - + -
137D GLY 3.8 9.9 - - - +
139D MET* 3.3 27.3 - - + +
141D THR 3.0 4.7 + - - +
142D ILE* 2.4 19.1 + - - +
144D GLN* 1.3 73.5 - - - +
146D LEU* 1.3 69.5 + - + +
147D ASP 2.9 0.3 + - - -
148D VAL* 2.9 3.0 + - - +
149D VAL* 2.8 29.1 + - + +
162D LEU* 4.0 13.9 - - + -
168D TRP* 3.9 20.0 - - + +
172D PRO* 4.3 18.6 - - + +
175D ALA* 5.6 1.6 - - + -
176D VAL* 3.7 28.3 - - + -
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Residues in contact with LEU 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 ILE* 2.5 39.4 + - + +
143D PRO* 3.6 10.5 - - + +
145D LEU* 1.3 76.0 - - + +
147D ASP* 1.3 62.5 + - - +
149D VAL* 4.4 1.6 - - - -
150D GLY 3.0 18.0 + - - -
175D ALA* 3.5 27.1 - - + +
176D VAL* 3.8 15.5 - - + -
179D ARG* 3.2 54.3 - - + +
180D PHE* 3.3 24.5 - - + -
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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 PRO* 2.5 31.0 + - - +
144D GLN* 3.2 5.5 - - - +
146D LEU* 1.3 72.5 - - - +
148D VAL* 1.3 66.7 + - + +
149D VAL 3.2 0.3 + - - -
150D GLY* 3.2 1.4 + - - -
151D GLY* 3.0 18.9 + - - -
179D ARG* 5.0 8.0 + - - -
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Residues in contact with VAL 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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136D VAL* 4.1 4.0 - - + -
139D MET* 3.4 37.5 - - + -
144D GLN* 2.8 23.8 + - + +
145D LEU* 3.4 4.7 - - - +
147D ASP* 1.3 73.4 - - + +
149D VAL* 1.3 66.2 + - - +
151D GLY* 2.9 12.1 + - - -
152D TYR* 2.9 46.1 + - + +
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Residues in contact with VAL 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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136D VAL* 4.2 15.0 - - + -
145D LEU* 2.8 33.2 + - + +
146D LEU* 3.5 4.0 - - - +
148D VAL* 1.3 76.4 - - - +
150D GLY* 1.3 67.9 + - - +
152D TYR* 2.8 20.9 + - - +
153D LEU* 2.8 22.0 + - + +
160D ILE* 4.5 14.0 - - + +
162D LEU* 4.2 18.2 - - + -
176D VAL* 4.4 14.8 - - + -
180D PHE* 3.5 25.8 - - + -
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Residues in contact with GLY 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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146D LEU 3.0 9.5 + - - -
147D ASP 3.7 2.5 - - - -
149D VAL* 1.3 79.2 - - - +
151D GLY* 1.3 61.7 + - - +
153D LEU* 3.1 7.7 + - - +
154D ASP* 2.9 31.2 + - - -
180D PHE* 3.4 27.8 - - - -
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Residues in contact with GLY 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 ASP 3.0 9.4 + - - -
148D VAL 2.9 9.5 + - - -
150D GLY* 1.3 75.4 - - - +
152D TYR* 1.3 62.5 + - - +
154D ASP* 3.1 12.5 + - - +
155D GLU* 3.0 30.0 + - - +
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Residues in contact with TYR 152 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.8 26.9 - - + -
136D VAL* 3.8 24.5 - - + -
148D VAL* 2.9 48.2 + - + +
149D VAL* 2.8 9.5 + - - +
151D GLY* 1.3 71.8 - - - -
153D LEU* 1.3 64.1 + - - +
154D ASP 3.2 0.2 + - - -
155D GLU* 3.2 27.9 + - - -
157D TYR* 3.3 32.0 + + + -
160D ILE* 4.8 4.3 - - + -
322D ARG* 2.9 56.6 + - + -
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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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149D VAL* 2.8 19.9 + - + +
150D GLY* 3.1 9.8 + - - +
152D TYR* 1.3 76.6 - - - +
154D ASP* 1.3 65.8 - - - +
156D GLY* 3.1 17.2 + - - -
157D TYR* 3.7 19.4 - - - +
158D VAL 5.7 2.5 - - - +
160D ILE* 4.6 17.7 - - + -
180D PHE* 3.9 40.2 - - + +
184D VAL* 4.8 19.5 - - + -
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Residues in contact with ASP 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 GLY 2.9 17.7 + - - +
151D GLY* 3.1 12.1 + - - +
153D LEU* 1.3 76.4 - - - +
155D GLU* 1.3 54.3 + - + +
156D GLY* 2.6 17.0 + - - -
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Residues in contact with GLU 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 GLY* 3.0 19.3 + - - +
152D TYR* 3.2 25.4 + - - +
154D ASP* 1.3 73.0 - - + +
156D GLY* 1.4 55.8 + - - +
157D TYR* 3.6 25.3 + - + -
321D ASP* 4.7 12.8 - - - +
334D LEU* 3.5 18.3 - - + +
337D GLY 5.3 0.5 + - - -
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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