Contacts of the helix formed by residues 152 - 168 (chain J) in PDB entry 2QJK
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 GLY 152 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J PHE* 4.6 2.5 - - - -
150J PRO 3.4 2.7 - - - -
151J TRP* 1.3 76.5 - - - +
153J GLN* 1.3 66.0 + - - -
155J SER* 3.1 7.9 + - - -
156J PHE 2.9 17.7 + - - -
279J ASN* 3.1 20.2 - - - -
281J ILE 3.2 13.9 - - - -
282J GLU* 4.4 0.7 - - - -
283J ALA* 3.3 12.2 - - - +
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Residues in contact with GLN 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J GLY* 1.3 71.0 - - - +
154J MET* 1.3 70.4 + - + +
155J SER 2.9 1.4 + - - -
156J PHE* 3.1 8.5 + - - +
157J TRP* 3.3 30.7 + - - -
278J ASP* 3.2 11.6 + - + +
279J ASN* 3.2 2.6 + - - -
281J ILE* 3.0 39.7 + - + +
282J GLU 3.7 3.6 - - - +
283J ALA* 3.6 0.5 - - - +
284J ASN* 2.8 37.5 + - - +
287J ARG* 3.3 29.1 + - - +
289J PRO* 3.4 31.9 - - + +
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Residues in contact with MET 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J TYR* 3.4 30.5 - - + +
153J GLN* 1.3 77.7 - - - +
155J SER* 1.3 56.5 + - - +
157J TRP* 5.2 0.4 - - - -
158J GLY* 2.9 29.1 + - - +
276J HIS* 3.6 44.2 - - + +
278J ASP* 3.6 21.7 + - + -
279J ASN* 2.9 15.5 + - - +
289J PRO* 3.7 27.8 - - + -
292J ILE* 3.8 29.2 - - + -
293J VAL 3.9 8.1 - - - +
503J SMA 4.0 8.5 - - - +
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Residues in contact with SER 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J TYR* 2.7 26.6 + - - -
148J VAL* 3.3 31.3 + - - +
150J PRO* 4.2 1.0 - - - +
151J TRP* 3.7 4.2 + - - -
152J GLY 3.2 24.0 + - - -
153J GLN 2.9 1.8 + - - -
154J MET* 1.3 78.7 - - - +
156J PHE* 1.3 63.8 + - - +
158J GLY* 4.1 0.2 - - - -
159J ALA* 3.2 19.8 + - - +
279J ASN* 2.9 19.7 + - - +
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Residues in contact with PHE 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLY 5.2 4.0 - - - -
151J TRP* 3.9 24.9 - + + -
152J GLY 2.9 15.3 + - - +
153J GLN 3.8 2.7 - - - +
155J SER* 1.3 72.7 - - - +
157J TRP* 1.3 106.8 + + + +
159J ALA* 2.8 18.3 + - - +
160J THR* 2.9 17.4 + - - -
185J ALA* 6.1 0.9 - - + -
186J VAL* 3.2 50.5 - - + -
283J ALA* 3.8 15.2 - - + +
284J ASN 4.1 3.1 - - - -
285J PRO* 3.3 44.9 - - + -
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Residues in contact with TRP 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I PRO* 5.0 4.7 - - + -
133I GLY 4.1 7.0 - - - -
134I CYS* 3.9 22.7 - - - -
135I SER* 4.3 9.6 - - - -
153J GLN* 3.3 21.7 + - - +
156J PHE* 1.3 89.9 - + - +
158J GLY* 1.3 66.9 + - - +
160J THR* 2.8 35.4 + - + -
161J VAL* 2.9 16.8 + - - +
284J ASN 3.3 22.7 + - - -
285J PRO 3.6 17.3 - - - -
287J ARG 2.6 32.1 + - - -
288J THR* 3.2 24.2 - - + -
289J PRO* 3.5 21.8 - - + -
292J ILE* 3.7 21.1 - - + -
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Residues in contact with GLY 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J PHE* 4.4 3.8 - - - -
147J TYR* 6.2 0.2 - - - -
154J MET* 2.9 21.3 + - - +
155J SER 4.1 0.4 - - - -
157J TRP* 1.3 77.9 - - - +
159J ALA* 1.3 55.2 + - - +
161J VAL* 3.3 2.1 + - - +
162J ILE* 2.9 35.9 + - - +
292J ILE* 4.9 0.2 - - - +
503J SMA 3.4 30.6 + - - -
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Residues in contact with ALA 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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144J PHE* 3.8 16.4 - - + -
148J VAL* 4.1 21.5 - - + -
155J SER 3.2 13.2 + - - +
156J PHE* 2.8 11.2 + - - +
158J GLY* 1.3 71.0 - - - +
160J THR* 1.3 58.9 + - - +
162J ILE* 3.8 0.3 - - - +
163J THR* 2.8 39.5 + - + +
186J VAL* 4.1 16.8 - - + -
190J THR* 5.8 0.9 - - + -
194J PHE* 4.5 7.0 - - + -
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Residues in contact with THR 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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132I LEU 3.7 6.1 - - - +
133I GLY* 4.2 22.2 - - - +
134I CYS 4.8 0.2 - - - +
156J PHE* 2.9 21.0 + - - -
157J TRP* 2.8 39.3 + - + -
159J ALA* 1.3 77.2 - - - +
161J VAL* 1.3 58.6 + - + +
163J THR* 2.7 19.5 + - - -
164J GLY* 3.1 9.5 + - - -
177J GLN* 4.4 1.7 + - - -
186J VAL* 3.6 20.2 - - + +
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Residues in contact with VAL 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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132I LEU* 4.0 35.8 - - + +
134I CYS* 3.8 27.4 - - - -
151I CYS* 4.5 0.4 - - - -
152I HIS* 4.1 2.9 - - + -
157J TRP 2.9 12.9 + - - +
158J GLY 3.6 7.2 - - - +
160J THR* 1.3 76.7 - - - +
162J ILE* 1.3 63.7 + - + +
163J THR 3.2 0.2 - - - -
164J GLY* 2.9 14.9 + - - -
165J LEU* 3.0 15.0 + - + +
292J ILE* 5.5 0.4 - - + -
503J SMA 3.4 49.6 - - + +
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Residues in contact with ILE 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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144J PHE* 3.5 47.3 - - + -
158J GLY 2.9 14.2 + - - +
159J ALA 3.2 0.2 + - - -
161J VAL* 1.3 77.0 - - + +
163J THR* 1.3 66.0 + - - +
165J LEU* 3.4 16.6 + - + +
166J PHE* 3.3 17.7 - - - -
298J PHE* 5.0 0.4 - - + -
503J SMA 3.5 87.5 - - + +
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Residues in contact with THR 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J PHE* 5.3 1.8 - - + -
159J ALA 2.8 17.4 + - - +
160J THR* 2.7 25.8 + - - -
162J ILE* 1.3 76.7 - - - +
164J GLY* 1.3 61.8 + - - +
166J PHE* 3.1 23.8 + - - +
167J GLY 3.6 0.7 + - - -
177J GLN* 3.1 20.1 + - - +
180J LEU* 4.4 20.1 - - + +
181J LEU* 3.5 34.9 - - + +
186J VAL* 4.1 1.1 - - + +
190J THR* 4.8 1.1 - - + -
194J PHE* 4.4 20.4 - - + -
503J SMA 5.7 0.9 - - + -
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Residues in contact with GLY 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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132I LEU* 3.8 22.9 - - - +
160J THR 3.1 11.9 + - - -
161J VAL 2.9 9.9 + - - -
163J THR* 1.3 73.2 + - - +
165J LEU* 1.3 56.7 + - - +
166J PHE 2.9 2.7 - - - -
167J GLY* 2.5 29.5 + - - -
168J ALA 3.2 3.5 + - - -
177J GLN* 3.0 14.6 - - - -
329J LYS* 5.5 0.7 - - - -
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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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132I LEU* 3.9 27.8 - - + +
161J VAL* 3.0 11.0 + - + +
162J ILE* 3.6 28.5 - - + +
163J THR 3.4 0.4 - - - -
164J GLY* 1.3 73.7 - - - +
166J PHE* 1.3 68.3 + - + +
168J ALA* 3.1 18.9 + - - +
169J ILE* 4.1 3.6 + - - +
305J LEU* 4.0 20.6 - - + -
333J VAL* 4.1 18.6 - - + +
336J MET* 3.7 26.5 - - + -
337J PHE* 4.6 15.7 - - + -
503J SMA 4.4 15.9 - - + +
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Residues in contact with PHE 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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162J ILE* 3.3 21.8 - - + -
163J THR 3.5 8.5 - - - +
164J GLY 2.9 1.4 - - - -
165J LEU* 1.3 78.4 - - + +
167J GLY* 1.3 63.2 + - - +
168J ALA 2.9 5.6 + - - -
169J ILE* 2.8 35.8 + - + +
173J GLY* 3.3 12.7 - - - -
176J ILE* 3.6 29.8 - - + +
177J GLN 4.8 2.9 - - - +
180J LEU* 4.1 17.9 - - + -
337J PHE* 4.6 16.2 - + - -
503J SMA 3.8 39.9 - - + -
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Residues in contact with GLY 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J THR 3.6 2.6 + - - -
164J GLY 2.5 19.6 + - - -
166J PHE* 1.3 73.2 - - - +
168J ALA* 1.3 57.5 + - - -
169J ILE 3.4 7.1 + - - +
173J GLY 3.5 17.8 + - - -
174J HIS* 4.6 3.0 + - - -
177J GLN* 4.2 16.5 - - - +
329J LYS* 5.3 5.1 - - - -
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Residues in contact with ALA 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I LEU* 5.5 0.7 - - + -
164J GLY 3.2 3.7 + - - +
165J LEU* 3.1 17.4 + - - +
166J PHE 2.9 0.6 - - - -
167J GLY* 1.3 76.6 - - - +
169J ILE* 1.3 68.0 + - - +
170J PRO* 3.2 8.7 - - - +
329J LYS* 4.4 20.0 - - + +
330J PHE* 3.5 23.8 - - + +
333J VAL* 3.5 26.0 - - + -
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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