Contacts of the helix formed by residues 154 - 165 (chain J) in PDB entry 5GJQ
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 LEU 154 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151J ILE* 3.2 33.2 - - + -
152J GLY 3.5 1.0 - - - -
153J GLY* 1.3 87.1 - - - +
155J ASP* 1.3 55.6 + - - +
157J GLN* 3.3 26.9 - - + +
158J ILE* 2.3 43.3 + - - +
194J THR 4.1 5.6 - - - +
195J GLY* 2.8 30.1 - - - +
199J LEU* 3.6 7.4 - - + -
317J PHE* 2.9 36.1 - - + -
318J PRO* 4.5 4.0 - - + -
501J ADP 3.9 9.9 - - - +
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Residues in contact with ASP 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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152J GLY* 4.9 3.6 - - - -
153J GLY* 4.1 11.4 + - - -
154J LEU* 1.3 79.9 + - - +
156J LYS* 1.3 65.6 + - + +
157J GLN* 2.9 1.7 + - - +
158J ILE* 2.1 44.2 + - - +
159J LYS* 2.5 24.8 + - + +
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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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408I ARG* 5.2 12.5 - - - +
155J ASP* 1.3 80.4 + - + +
157J GLN* 1.3 71.5 + - - +
159J LYS* 3.4 34.3 + - - +
160J GLU* 2.8 32.5 + - + +
315J ILE* 5.3 0.2 - - - -
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Residues in contact with GLN 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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153J GLY 4.8 0.7 - - - +
154J LEU* 3.3 49.3 - - + +
155J ASP 2.7 4.6 + - - -
156J LYS* 1.3 79.4 - - - +
158J ILE* 1.3 51.4 + - - +
160J GLU* 2.6 7.0 + - - +
161J ILE* 2.5 39.5 + - + +
188J LEU* 5.5 0.4 - - + -
199J LEU* 3.5 13.9 - - + -
315J ILE* 3.8 22.9 - - + +
316J GLU 2.9 30.1 + - - +
317J PHE* 3.6 17.8 - - + +
318J PRO* 3.8 15.1 - - - +
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Residues in contact with ILE 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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148J TYR* 4.0 26.7 - - + +
151J ILE* 5.2 6.7 - - + -
154J LEU* 2.3 35.4 - - + +
155J ASP* 2.1 29.4 + - - +
157J GLN* 1.3 72.9 - - - +
159J LYS* 1.3 50.9 + - + +
161J ILE* 2.8 13.4 + - + +
162J LYS* 2.4 66.0 + - + +
199J LEU* 3.4 21.3 - - + -
203J VAL* 5.3 0.4 - - + -
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Residues in contact with LYS 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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408I ARG* 4.2 20.2 - - - +
155J ASP* 2.5 18.6 + - + +
156J LYS* 3.4 50.0 - - - +
158J ILE* 1.3 73.3 - - + +
160J GLU* 1.3 52.0 + - - +
162J LYS* 3.0 12.2 + - + +
163J GLU* 2.6 45.4 + - + +
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Residues in contact with GLU 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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408I ARG* 2.0 43.8 + - - -
156J LYS* 2.8 24.2 + - + +
157J GLN* 2.6 9.5 + - - +
159J LYS* 1.3 71.8 - - - +
161J ILE* 1.3 48.4 + - - -
163J GLU* 3.0 8.3 + - - +
164J VAL* 2.7 37.4 + - - +
313J ARG* 1.7 53.1 + - - -
315J ILE* 2.3 47.8 - - + -
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Residues in contact with ILE 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 GLN* 2.5 17.8 + - + +
158J ILE* 2.8 15.0 + - - +
160J GLU* 1.3 70.9 - - - +
162J LYS* 1.3 51.8 + - - +
164J VAL* 2.9 9.8 + - + +
165J ILE* 2.4 60.7 + - + +
186J VAL* 5.6 3.8 - - + -
188J LEU* 4.9 13.7 - - + -
199J LEU* 3.0 55.2 - - + +
203J VAL* 3.4 28.5 - - + -
292J ILE* 5.5 3.8 - - + -
315J ILE* 4.5 7.9 - - + -
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Residues in contact with LYS 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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148J TYR* 3.5 24.9 - - - +
158J ILE* 2.4 42.8 + - + +
159J LYS* 3.2 13.9 - - + +
161J ILE* 1.3 66.9 - - - +
163J GLU* 1.3 58.6 + - + +
166J GLU* 2.1 62.3 + - + +
167J LEU* 2.5 33.1 + - + +
96R GLY* 5.7 1.5 - - - -
98R SER* 4.8 3.0 - - - -
99R GLU* 2.8 39.8 + - - -
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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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404I LEU* 3.9 30.9 - - + +
407I LEU* 5.6 2.7 - - + +
408I ARG* 2.6 63.1 + - - +
159J LYS* 2.6 28.5 + - + +
160J GLU* 3.2 14.4 - - - +
162J LYS* 1.3 74.5 - - + +
164J VAL* 1.3 56.9 + - - +
167J LEU* 4.2 13.2 - - + -
168J PRO* 3.0 18.5 - - - +
175J PHE* 3.4 14.4 - - + -
313J ARG* 4.6 2.0 - - - -
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Residues in contact with VAL 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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404I LEU* 5.4 2.2 - - + -
160J GLU 2.7 19.8 + - - +
161J ILE* 3.0 20.9 - - - +
163J GLU* 1.3 70.7 - - - +
165J ILE* 1.3 69.4 + - + +
168J PRO* 3.0 16.8 - - - +
183J PRO* 3.5 31.2 - - + +
184J LYS 6.2 0.2 - - - -
186J VAL* 3.5 35.0 - - + -
290J LYS* 3.9 5.9 + - - +
312J ASP* 4.2 3.6 - - + -
313J ARG* 3.8 28.0 - - + +
315J ILE* 5.1 1.1 - - + -
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Residues in contact with ILE 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 ILE* 2.4 43.4 + - + +
164J VAL* 1.3 85.0 - - + +
166J GLU* 1.3 70.0 + - - +
168J PRO* 2.8 11.3 - - - +
169J VAL* 3.0 26.0 + - + +
186J VAL* 4.5 5.6 - - + -
203J VAL* 3.8 19.1 - - + -
207J THR* 4.0 9.4 - - + +
209J CYS* 6.1 0.2 - - - -
245J ILE* 3.9 22.9 - - + -
290J LYS* 3.8 23.6 - - + -
292J ILE* 4.0 29.2 - - + -
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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