Contacts of the helix formed by residues 147 - 166 (chain J) in PDB entry 3SDI
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 147 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J VAL* 3.7 6.3 - - - +
9J GLN* 5.7 0.7 - - - -
10J ASP* 5.9 2.0 - - - -
145J ASP 4.8 3.4 - - - +
146J MET* 1.3 77.9 - - - +
148J THR* 1.3 64.2 + - - +
149J GLU* 3.2 8.9 + - - +
150J GLU* 3.2 36.3 + - + +
151J GLY 3.1 18.2 + - - -
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Residues in contact with THR 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J VAL* 4.1 8.9 - - - +
10J ASP* 5.0 5.5 - - - +
11J SER* 2.8 28.0 + - - +
13J ILE* 3.9 4.0 - - + +
147J THR* 1.3 74.8 - - - +
149J GLU* 1.3 56.8 + - - +
151J GLY* 3.5 1.6 + - - -
152J LEU* 3.1 30.4 + - + +
177J ILE* 3.7 30.9 - - + +
179J ASP* 5.6 1.2 + - - +
185J ARG* 3.9 14.6 + - - +
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Residues in contact with GLU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J THR* 3.2 8.6 + - - +
148J THR* 1.3 77.9 - - - +
150J GLU* 1.3 63.2 + - - +
152J LEU* 3.3 15.5 + - - +
153J ASP* 3.1 33.0 + - - +
193J GLN* 3.7 30.7 + - - +
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Residues in contact with GLU 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J ASP* 4.4 3.5 - - - +
146J MET* 3.6 40.4 - - + +
147J THR* 3.2 40.8 + - + +
149J GLU* 1.3 75.6 - - - +
151J GLY* 1.3 58.3 + - - +
153J ASP* 3.1 12.6 + - - +
154J LEU* 2.9 28.4 + - - +
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Residues in contact with GLY 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 4.9 5.7 - - - +
8J VAL* 3.7 26.2 - - - +
13J ILE* 3.7 11.4 - - - +
146J MET* 4.5 2.2 - - - +
147J THR 3.1 10.1 + - - -
148J THR 3.8 3.4 - - - -
150J GLU* 1.3 78.1 - - - +
152J LEU* 1.3 55.5 + - - +
154J LEU* 3.4 8.5 + - - +
155J LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 4.3 13.2 - - + -
148J THR* 3.1 25.6 + - + +
149J GLU* 3.7 23.3 - - - +
150J GLU 3.3 0.4 - - - -
151J GLY* 1.3 72.6 - - - +
153J ASP* 1.3 59.7 + - - +
155J LEU* 3.4 6.5 + - + +
156J LYS* 2.9 26.9 + - - +
175J VAL* 3.8 29.6 - - + -
177J ILE* 4.1 19.7 - - + -
187J VAL* 4.2 14.1 - - + -
190J PHE* 3.8 16.8 - - + -
193J GLN* 3.9 22.8 - - - +
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Residues in contact with ASP 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J GLU* 3.1 28.2 + - - +
150J GLU* 3.1 13.1 + - - +
152J LEU* 1.3 73.0 - - - +
154J LEU* 1.3 60.2 + - - +
156J LYS* 3.1 13.7 + - - +
157J LEU* 3.0 30.9 + - - +
193J GLN* 3.5 15.5 - - - +
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Residues in contact with LEU 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 4.5 7.6 - - + -
137J LEU* 5.8 2.0 - - + -
138J LEU* 3.5 24.5 - - + -
141J HIS* 3.3 33.9 - - + +
142J TYR* 3.7 24.9 - - + -
146J MET* 3.6 31.2 - - + -
150J GLU 2.9 15.2 + - - +
151J GLY* 3.5 7.2 - - - +
153J ASP* 1.3 76.6 - - - +
155J LEU* 1.3 60.4 + - - +
157J LEU* 3.4 15.3 + - + +
158J CYS* 3.2 23.4 + - - -
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.5 17.5 - - + -
6J ILE* 3.7 28.0 - - + +
13J ILE* 4.5 16.4 - - + +
15J ALA* 3.6 33.2 - - + +
151J GLY 2.9 17.5 + - - +
152J LEU* 3.5 9.4 - - - +
154J LEU* 1.3 73.4 - - - +
156J LYS* 1.3 65.9 + - - +
158J CYS* 3.1 10.2 + - + +
159J VAL* 3.0 30.6 + - + +
175J VAL* 4.4 4.7 - - + -
190J PHE* 3.6 21.3 - - + -
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Residues in contact with LYS 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J LEU 2.9 13.4 + - - +
153J ASP* 3.1 17.5 + - - +
155J LEU* 1.3 76.5 - - - +
157J LEU* 1.3 57.6 + - + +
159J VAL* 3.3 3.1 + - - +
160J GLN* 2.9 60.1 + - + +
190J PHE* 3.8 28.0 - - + +
192J ALA* 5.9 0.7 - - - +
193J GLN* 3.7 46.3 + - + +
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Residues in contact with LEU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J LEU* 3.6 9.5 - - + +
141J HIS* 4.2 36.3 - - + +
153J ASP 3.0 12.0 + - - +
154J LEU* 3.4 19.1 - - + +
155J LEU 3.2 0.2 - - - -
156J LYS* 1.3 76.5 - - + +
158J CYS* 1.3 62.4 + - - +
160J GLN* 3.4 21.6 + - - +
161J GLU* 3.1 24.3 + - - +
140Y SER* 4.3 21.8 - - - +
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Residues in contact with CYS 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.5 13.7 - - + -
6J ILE* 6.0 0.4 - - - -
134J THR* 4.1 18.7 - - + +
137J LEU* 3.6 18.2 - - - -
138J LEU* 3.7 37.0 - - - -
154J LEU* 3.2 16.5 + - - -
155J LEU* 3.1 15.5 + - + +
157J LEU* 1.3 77.3 - - - +
159J VAL* 1.3 58.0 + - - +
161J GLU* 3.4 3.6 + - - +
162J LEU* 3.1 33.1 + - - +
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Residues in contact with VAL 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.6 10.3 - - + -
155J LEU* 3.0 35.9 + - + +
156J LYS* 3.9 4.5 - - - +
158J CYS* 1.3 73.4 - - - +
160J GLN* 1.3 60.0 + - + +
162J LEU* 3.8 7.9 - - + +
163J GLU* 2.9 49.1 + - - +
170J PHE* 4.5 11.7 - - + -
172J GLY* 5.3 0.9 - - - -
173J VAL* 3.8 33.0 - - + +
190J PHE* 4.3 9.0 - - + -
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Residues in contact with GLN 160 (chain J).
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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156J LYS* 2.9 51.2 + - + +
157J LEU* 3.4 30.9 - - - +
158J CYS 3.3 0.2 - - - -
159J VAL* 1.3 77.9 - - + +
161J GLU* 1.3 56.6 + - - +
163J GLU* 3.3 14.3 + - - +
164J LYS* 3.0 29.0 + - - +
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Residues in contact with GLU 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TYR* 4.1 19.4 - - + -
134J THR* 6.1 0.2 - - + -
137J LEU* 4.0 12.6 - - + -
157J LEU 3.1 11.3 + - - +
158J CYS 3.6 8.7 - - - +
160J GLN* 1.3 79.8 - - - +
162J LEU* 1.3 58.5 + - + +
164J LYS* 3.1 7.1 + - - +
165J ARG* 2.9 38.6 + - - +
135Y TYR* 3.0 19.0 - - - +
136Y GLY* 3.4 15.4 + - - +
139Y ASP* 2.9 46.8 - - - +
140Y SER* 4.7 2.4 + - - -
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ILE* 3.9 33.7 - - + -
4J LEU* 4.0 9.2 - - + -
130J SER* 4.0 16.6 - - - -
133J TYR* 3.8 36.8 - - + -
134J THR* 4.0 17.0 - - + -
158J CYS 3.1 22.1 + - - +
159J VAL* 3.4 6.7 + - + +
161J GLU* 1.3 75.1 - - + +
163J GLU* 1.3 63.7 + - - +
165J ARG* 5.5 0.4 - - - -
166J MET* 3.0 41.5 + - + +
170J PHE* 3.9 18.1 - - + -
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Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J VAL* 2.9 34.8 + - - +
160J GLN* 3.7 12.7 - - - +
162J LEU* 1.3 76.2 - - - +
164J LYS* 1.3 51.1 + - - +
166J MET 4.6 3.1 - - - +
170J PHE* 3.7 17.9 - - + -
172J GLY* 4.3 19.4 + - - -
169X ASP* 3.8 8.6 - - - +
171X LYS* 2.7 28.3 + - - -
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Residues in contact with LYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J GLN 3.0 13.7 + - - +
161J GLU* 3.1 12.1 + - - +
163J GLU* 1.3 77.0 - - - +
165J ARG* 1.3 86.3 + - + +
166J MET 5.0 0.2 - - - -
26X VAL* 3.9 9.4 - - - +
29X ASP* 3.4 25.3 + - - +
171X LYS* 2.9 24.8 + - - +
124Y ILE* 5.8 4.3 - - - -
139Y ASP* 4.0 27.8 - - + +
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Residues in contact with ARG 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TYR* 3.4 33.7 + - + +
161J GLU* 2.9 36.0 + - - +
164J LYS* 1.3 98.3 + - + +
166J MET* 1.3 64.3 + - - +
25X SER* 3.6 1.7 - - - +
26X VAL* 2.8 54.1 + - - +
27X LEU 4.1 11.3 + - - -
28X LYS* 5.5 1.2 - - - +
29X ASP* 6.3 0.4 - - - -
124Y ILE* 4.5 17.6 + - - +
135Y TYR* 3.4 33.9 - - + -
139Y ASP* 2.9 32.7 + - - +
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Residues in contact with MET 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1J MET* 4.8 16.4 - - + +
2J ILE* 4.4 18.4 - - + -
129J TYR* 4.2 27.6 - - + -
130J SER 4.2 7.6 - - - -
133J TYR* 3.4 26.5 - - + -
162J LEU* 3.0 40.5 + - + +
163J GLU 4.6 5.9 - - - +
164J LYS 4.8 0.3 - - - +
165J ARG* 1.3 79.5 - - - +
167J PRO* 1.3 81.1 - - + +
168J MET* 3.4 24.5 + - + +
170J PHE* 5.2 3.1 - - + -
24X ILE* 5.7 0.4 - - - -
26X VAL* 3.9 5.4 - - - +
169X ASP* 4.7 5.7 - - - +
171X LYS* 5.1 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