Contacts of the helix formed by residues 148 - 159 (chain g) in PDB entry 5JPQ
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 148 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144g LEU* 3.1 22.9 - - - -
145g GLY 3.2 5.5 + - - -
146g GLN 2.9 3.2 + - - -
147g ASN* 1.3 77.1 - - - +
149g THR* 1.3 57.2 + - - +
151g LEU* 3.1 10.4 + - - +
152g LYS* 2.9 28.5 + - - +
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Residues in contact with THR 149 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144g LEU 3.7 0.4 + - - -
146g GLN* 2.9 15.4 + - - -
147g ASN* 3.1 7.6 - - - -
148g GLY* 1.3 76.1 - - - +
150g THR* 1.3 52.8 + - - +
152g LYS* 3.0 11.7 + - - +
153g ALA* 2.8 34.8 + - - +
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Residues in contact with THR 150 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142g ARG 4.7 5.4 - - - -
143g LEU 4.2 10.3 - - - -
144g LEU 3.7 11.6 + - - -
145g GLY* 4.5 6.9 - - - -
146g GLN 4.7 0.6 + - - +
148g GLY 3.4 0.4 - - - -
149g THR* 1.3 76.1 - - - +
151g LEU* 1.3 52.1 + - - +
153g ALA* 3.1 10.6 + - - +
154g LEU* 2.8 35.5 + - - +
194g PRO* 6.0 5.4 - - - -
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Residues in contact with LEU 151 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143g LEU 4.1 6.2 + - - +
144g LEU* 3.4 23.7 + - + +
148g GLY* 3.1 12.9 + - - +
150g THR* 1.3 77.7 - - - +
152g LYS* 1.3 57.4 + - - +
154g LEU* 3.1 11.1 + - - +
155g GLU* 2.9 28.2 + - - +
162g ILE* 5.4 9.3 - - + +
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Residues in contact with LYS 152 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148g GLY 2.9 11.7 + - - +
149g THR* 3.2 12.6 - - - +
151g LEU* 1.3 73.7 - - - +
153g ALA* 1.3 55.2 + - - +
155g GLU* 3.1 11.8 + - - +
156g LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 153 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149g THR 2.8 14.9 + - - +
150g THR* 3.1 14.1 + - - +
152g LYS* 1.3 70.7 - - - +
154g LEU* 1.3 63.8 + - - +
156g LEU* 3.1 9.4 + - - +
157g LEU* 3.0 25.1 + - - +
198g ILE* 5.7 9.9 - - + -
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Residues in contact with LEU 154 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150g THR 2.8 15.7 + - - +
151g LEU* 3.1 13.2 - - - +
153g ALA* 1.3 71.3 - - - +
155g GLU* 1.3 57.8 + - - +
157g LEU* 3.0 6.9 + - - +
158g THR* 2.9 34.3 + - - -
162g ILE* 6.1 3.6 - - + -
184g VAL* 6.1 5.4 - - + -
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Residues in contact with GLU 155 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151g LEU 2.9 11.6 + - - +
152g LYS* 3.3 13.7 - - - +
154g LEU* 1.3 74.3 - - - +
156g LEU* 1.3 56.4 + - - +
158g THR* 5.4 0.4 - - - -
159g GLN* 3.0 24.3 + - - -
160g THR* 3.2 31.4 + - - +
161g TYR* 5.3 0.7 - - - -
162g ILE* 5.1 11.1 - - + +
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Residues in contact with LEU 156 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152g LYS 2.9 14.0 + - - +
153g ALA* 3.1 8.5 + - - +
155g GLU* 1.3 75.8 - - - +
157g LEU* 1.3 59.3 + - - +
159g GLN* 4.2 5.8 + - - +
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Residues in contact with LEU 157 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153g ALA 3.0 15.1 + - - +
154g LEU* 3.8 4.9 - - - +
156g LEU* 1.3 79.8 - - - +
158g THR* 1.3 59.0 + - - +
159g GLN* 3.5 1.2 - - - +
198g ILE* 5.7 2.2 - - - +
201g LEU* 4.0 32.5 - - + +
202g MET* 5.4 1.3 - - - +
205g ARG* 5.9 6.4 - - + +
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Residues in contact with THR 158 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154g LEU 2.9 15.1 + - - -
155g GLU* 5.4 0.2 - - - -
157g LEU* 1.3 75.7 - - - +
159g GLN* 1.3 71.6 + - - +
160g THR* 3.3 9.8 + - - -
174g GLY 5.5 1.7 + - - -
177g GLY* 3.5 43.8 - - - -
180g GLU* 4.7 10.5 - - - -
181g VAL* 5.0 6.7 - - - -
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Residues in contact with GLN 159 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155g GLU 3.0 12.4 + - - -
156g LEU 4.2 5.3 - - - +
157g LEU 3.5 3.9 - - - +
158g THR* 1.3 80.1 - - - +
160g THR* 1.3 58.3 + - - +
172g MET 4.7 0.2 - - - +
173g GLY* 4.5 8.7 - - - -
174g GLY 4.8 2.4 + - - -
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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