Contacts of the helix formed by residues 153 - 170 (chain J) in PDB entry 2ONK
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 ASP 153 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J GLY* 3.7 5.6 - - - -
148J SER* 3.3 12.6 + - - +
149J ASN 2.9 12.9 + - - +
150J PRO 3.6 6.7 - - - +
152J ASP* 1.3 74.6 - - - +
154J PRO* 1.3 64.6 - - - +
155J CYS* 3.2 9.8 - - - +
156J GLY* 2.8 22.2 + - - -
157J TYR* 3.5 5.3 + - - -
216J SER 3.4 18.8 - - - +
217J MET* 4.3 0.7 - - - -
218J GLU* 2.7 27.7 + - - +
702J WO4 2.0 53.1 + - - -
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Residues in contact with PRO 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J SER* 3.5 18.2 - - - +
90J ALA* 4.4 0.4 - - + -
91J ASP* 3.9 7.0 - - + +
94J LEU* 3.3 30.5 - - + -
152J ASP 4.2 0.9 - - - +
153J ASP* 1.3 90.9 - - - +
155J CYS* 1.3 57.6 + - - +
156J GLY 2.8 6.1 + - - -
157J TYR* 3.0 24.4 + - + +
158J ARG* 2.7 52.3 + - - +
236J TYR* 3.9 0.7 - - - -
702J WO4 3.2 13.9 - - - +
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Residues in contact with CYS 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ILE* 4.0 12.8 - - - -
148J SER* 3.5 2.2 - - - +
153J ASP* 3.2 12.1 - - - +
154J PRO* 1.3 73.2 - - - +
156J GLY* 1.3 52.3 + - - +
158J ARG* 4.0 5.8 - - - -
159J SER* 2.5 41.4 + - - -
218J GLU* 3.4 13.5 - - + +
234J PHE 3.8 21.8 - - - -
235J ILE* 4.0 11.4 - - - -
236J TYR* 3.2 24.6 + - + -
702J WO4 2.7 22.9 + - - +
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Residues in contact with GLY 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J PHE* 4.7 0.5 - - - -
148J SER* 2.8 38.9 + - - +
150J PRO* 3.9 8.9 - - - +
153J ASP 2.8 8.6 + - - -
154J PRO 2.8 2.8 - - - -
155J CYS* 1.3 80.7 - - - +
157J TYR* 1.3 59.7 + - - -
159J SER* 3.3 10.7 + - - -
160J LEU* 3.3 16.5 + - - +
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Residues in contact with TYR 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J ALA* 5.9 0.4 - - + -
91J ASP* 2.4 32.1 + - - -
94J LEU* 3.3 21.4 - - + +
150J PRO* 3.5 40.6 - - + +
153J ASP 3.5 5.0 + - - -
154J PRO* 3.3 34.8 - - + +
156J GLY* 1.3 72.9 - - - +
158J ARG* 1.3 65.3 + - + +
160J LEU* 3.3 5.1 + - - +
161J MET* 2.7 48.5 + - + +
270J VAL* 4.3 19.5 - - + +
272J LEU* 3.6 23.1 - - + -
278J VAL* 3.6 22.2 - - + +
279J THR 6.1 0.2 - - - -
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Residues in contact with ARG 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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90J ALA* 2.7 34.5 + - - +
91J ASP* 3.5 25.6 + - - +
115J ILE* 4.0 11.2 - - + +
154J PRO* 2.7 23.0 + - - +
155J CYS* 3.8 5.8 - - - +
157J TYR* 1.3 87.8 - - + +
159J SER* 1.3 57.3 + - - +
161J MET* 3.3 6.6 + - - +
162J ALA* 2.9 30.0 + - - +
236J TYR* 2.9 26.9 + - - -
256J LEU* 3.6 24.1 - - + +
281J LYS* 5.3 3.2 + - - +
282J PRO 4.6 2.4 + - - -
283J ILE* 3.4 48.8 - - - +
284J VAL 3.8 2.8 - - - +
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Residues in contact with SER 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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115J ILE* 4.6 5.2 - - - +
147J PHE* 4.0 18.0 - - - +
148J SER 5.0 0.3 + - - -
155J CYS* 2.5 26.1 + - - -
156J GLY* 3.4 6.9 - - - -
158J ARG* 1.3 73.6 - - - +
160J LEU* 1.3 67.9 + - - +
162J ALA* 3.2 7.1 + - - +
163J ILE* 3.0 28.5 + - - +
234J PHE* 3.3 40.8 + - - +
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Residues in contact with LEU 160 (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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147J PHE* 3.8 30.3 - - + -
150J PRO* 3.4 29.8 - - + -
156J GLY 3.3 8.3 + - - +
157J TYR* 3.8 7.2 - - - +
159J SER* 1.3 80.7 - - - +
161J MET* 1.3 64.7 + - - +
163J ILE* 3.2 8.2 + - + +
164J GLN* 3.1 21.8 + - - +
176J PHE* 3.8 23.6 - - + -
180J VAL* 4.1 13.7 - - + -
186J LEU* 4.4 12.6 - - + -
188J PHE* 3.7 8.8 - - + -
197J LEU* 3.9 20.9 - - + -
199J MET* 4.8 2.2 - - - -
270J VAL* 5.1 3.8 - - + -
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Residues in contact with MET 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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157J TYR* 2.7 36.4 + - + +
158J ARG* 3.4 15.7 - - - +
160J LEU* 1.3 72.7 - - - +
162J ALA* 1.3 53.3 + - - +
164J GLN* 3.0 4.0 + - - +
165J LEU* 2.7 39.2 + - + +
188J PHE* 4.5 4.9 - - - -
256J LEU* 4.1 11.4 - - + -
268J VAL* 3.8 23.1 - - + +
270J VAL* 4.0 16.6 - - + +
278J VAL* 3.1 48.2 - - + +
279J THR* 3.7 2.0 - - - +
280J GLY* 3.7 26.7 - - - +
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Residues in contact with ALA 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ILE* 4.4 18.8 - - + -
134J TRP* 4.9 1.7 - - + -
158J ARG 2.9 18.2 + - - +
159J SER 3.2 5.6 + - - +
161J MET* 1.3 77.4 - - - +
163J ILE* 1.3 62.8 + - + +
165J LEU* 3.8 3.8 - - - +
166J ALA* 3.1 21.5 + - - +
234J PHE* 5.6 2.9 - - + -
250J LEU* 4.9 10.8 - - + -
254J ILE* 3.6 34.7 + - + +
256J LEU* 4.6 0.4 - - + +
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Residues in contact with ILE 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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134J TRP* 4.6 6.5 - - + -
145J PHE* 4.7 6.3 - - + -
147J PHE* 5.2 2.0 - - + -
159J SER* 3.0 19.7 + - - +
160J LEU* 3.2 14.3 + - + +
162J ALA* 1.3 75.6 - - - +
164J GLN* 1.3 61.8 + - - +
166J ALA* 3.3 18.3 - - - +
167J GLU 3.6 3.1 + - - -
175J ILE* 4.1 16.1 - - + +
176J PHE* 3.5 34.6 + - + +
179J LEU* 4.6 11.2 - - + -
180J VAL* 4.0 20.9 - - + -
234J PHE* 3.6 40.6 - - + -
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Residues in contact with GLN 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 LEU 3.1 3.4 + - - +
161J MET 3.0 5.0 + - - +
163J ILE* 1.3 74.4 - - - +
165J LEU* 1.3 56.9 + - - +
166J ALA 2.9 4.9 - - - -
167J GLU* 2.7 49.2 + - - +
168J LEU* 3.7 4.0 + - + +
176J PHE* 3.4 23.1 - - + +
188J PHE* 3.3 51.1 - - + +
195J TYR* 3.9 29.4 - - + -
268J VAL* 3.5 19.3 - - + -
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Residues in contact with LEU 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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161J MET 2.7 24.2 + - - +
162J ALA 3.8 0.9 - - - +
164J GLN* 1.3 73.6 - - - +
166J ALA* 1.3 61.8 + - - +
168J LEU* 3.3 14.6 + - + +
169J TYR* 3.2 15.8 + - - +
253J GLU 4.9 1.8 - - - +
254J ILE* 3.2 43.3 - - + +
256J LEU* 4.1 7.9 - - + -
264J LEU* 3.3 28.3 - - + +
265J TYR* 4.0 22.7 - - + -
267J LYS* 4.5 4.5 - - + -
268J VAL* 3.5 34.1 - - + +
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Residues in contact with ALA 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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134J TRP* 4.0 12.6 - - + -
162J ALA 3.1 12.9 + - - +
163J ILE 3.3 13.9 - - - +
164J GLN 2.9 0.6 - - - -
165J LEU* 1.3 76.2 - - - +
167J GLU* 1.3 66.0 + - - +
169J TYR* 4.2 0.7 - - - +
170J TYR* 2.9 51.7 + - + +
175J ILE* 3.7 9.4 - - + +
254J ILE* 3.8 14.4 - - + -
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Residues in contact with GLU 167 (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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163J ILE 3.6 0.4 + - - +
164J GLN* 2.7 38.3 + - - +
166J ALA* 1.3 79.1 - - - +
168J LEU* 1.3 59.3 + - + +
171J ASN* 3.2 6.4 + - - -
172J ASP 3.0 43.9 + - - +
173J PRO* 3.0 16.8 - - + +
175J ILE* 4.0 4.7 - - + +
176J PHE* 3.3 32.3 + - + +
177J ASP* 3.0 11.1 - - - +
195J TYR* 4.6 5.9 + - - -
706J MG 2.5 30.4 - - - -
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Residues in contact with LEU 168 (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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164J GLN 4.3 8.5 - - - +
165J LEU* 3.3 16.5 + - + +
166J ALA 3.1 0.6 - - - -
167J GLU* 1.3 82.3 - - + +
169J TYR* 1.3 61.8 + - - +
171J ASN* 3.9 8.3 + - - +
193J GLY 5.5 0.2 - - - +
195J TYR* 3.4 49.4 - - + +
267J LYS* 3.8 35.0 - - + +
268J VAL* 5.6 0.7 - - + -
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Residues in contact with TYR 169 (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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132J GLN* 5.8 2.9 - - - -
165J LEU 3.2 13.7 + - - +
166J ALA 3.0 5.0 + - - +
168J LEU* 1.3 79.8 - - - +
170J TYR* 1.3 91.9 + + + +
171J ASN* 3.3 3.0 - - - +
251J PRO* 4.0 16.2 - - + +
253J GLU* 3.3 55.5 + - + +
254J ILE* 4.1 11.4 - - + -
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Residues in contact with TYR 170 (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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131J SER 3.3 13.3 + - - -
132J GLN* 4.7 15.5 - - + -
134J TRP* 3.2 21.9 + - - -
135J TYR* 3.7 41.1 + + + +
166J ALA* 2.9 43.8 + - + +
169J TYR* 1.3 102.6 - + - +
171J ASN* 1.3 72.6 + - - +
172J ASP* 3.2 3.9 + - + +
175J ILE* 4.0 7.6 - - + -
251J PRO* 3.0 22.6 - - + +
254J ILE* 4.4 4.7 - - + -
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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