Contacts of the helix formed by residues 148 - 159 (chain h) 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 h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144h LEU* 3.1 22.2 - - - -
145h GLY 3.2 5.3 + - - -
146h GLN 2.9 3.0 + - - -
147h ASN* 1.3 76.3 - - - +
149h THR* 1.3 58.6 + - - +
151h LEU* 3.1 11.1 + - - +
152h LYS* 2.9 28.9 + - - +
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Residues in contact with THR 149 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144h LEU 3.7 0.2 + - - -
146h GLN* 2.9 15.8 + - - -
147h ASN* 3.1 7.6 - - - -
148h GLY* 1.3 74.5 - - - +
150h THR* 1.3 53.1 + - - +
152h LYS* 3.0 11.6 + - - +
153h ALA* 2.8 34.4 + - - +
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Residues in contact with THR 150 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142h ARG 4.7 5.2 - - - -
143h LEU 4.2 9.9 - - - -
144h LEU 3.7 11.2 + - - -
145h GLY* 4.5 7.4 - - - -
146h GLN 4.7 0.6 + - - -
148h GLY 3.4 0.6 - - - -
149h THR* 1.3 75.3 - - - +
151h LEU* 1.3 52.8 + - - +
153h ALA* 3.1 10.1 + - - +
154h LEU* 2.8 34.8 + - - +
194h PRO* 6.0 5.8 - - - -
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Residues in contact with LEU 151 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143h LEU 4.1 5.8 + - - +
144h LEU* 3.4 23.5 + - + +
148h GLY* 3.1 12.7 + - - +
150h THR* 1.3 77.7 - - - +
152h LYS* 1.3 56.8 + - - +
154h LEU* 3.1 11.6 + - - +
155h GLU* 2.9 28.2 + - - +
162h ILE* 5.4 9.0 - - + +
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Residues in contact with LYS 152 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148h GLY 2.9 12.6 + - - +
149h THR* 3.2 12.8 - - - +
151h LEU* 1.3 74.9 - - - +
153h ALA* 1.3 56.1 + - - +
155h GLU* 3.1 11.3 + - - +
156h LEU* 2.9 29.6 + - - +
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Residues in contact with ALA 153 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149h THR 2.8 15.7 + - - +
150h THR* 3.2 14.4 - - - +
152h LYS* 1.3 70.6 - - - +
154h LEU* 1.3 63.7 + - - +
156h LEU* 3.1 9.2 + - - +
157h LEU* 3.0 25.6 + - - +
198h ILE* 5.7 9.2 - - + -
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Residues in contact with LEU 154 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150h THR 2.8 14.8 + - - +
151h LEU* 3.1 13.9 - - - +
153h ALA* 1.3 71.1 - - - +
155h GLU* 1.3 56.0 + - - +
157h LEU* 3.0 6.4 + - - +
158h THR* 2.9 34.5 + - - -
198h ILE* 6.4 0.2 - - - +
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Residues in contact with GLU 155 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151h LEU 2.9 12.0 + - - +
152h LYS* 3.1 14.1 + - - +
154h LEU* 1.3 73.6 - - - +
156h LEU* 1.3 55.7 + - - +
158h THR* 5.4 0.7 - - - -
159h GLN* 3.0 24.1 + - - -
160h THR* 3.2 31.1 + - - +
161h TYR* 5.3 0.2 - - - -
162h ILE* 5.1 11.8 - - + +
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Residues in contact with LEU 156 (chain h).
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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152h LYS 2.9 14.9 + - - +
153h ALA* 3.1 8.0 + - - +
155h GLU* 1.3 76.0 - - - +
157h LEU* 1.3 60.5 + - - +
159h GLN* 4.2 6.0 + - - +
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Residues in contact with LEU 157 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153h ALA 3.0 16.0 + - - +
154h LEU* 3.0 4.9 + - - +
156h LEU* 1.3 80.0 - - - +
158h THR* 1.3 59.5 + - - +
159h GLN* 3.5 0.8 - - - +
198h ILE* 5.7 2.2 - - - +
201h LEU* 4.0 32.7 - - + +
202h MET* 5.4 1.3 - - - +
205h ARG* 5.9 7.0 - - + +
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Residues in contact with THR 158 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154h LEU 2.9 15.1 + - - -
157h LEU* 1.3 76.1 - - - +
159h GLN* 1.3 71.2 - - - +
160h THR* 3.2 9.6 + - - -
174h GLY 5.5 2.3 + - - -
177h GLY* 3.5 43.3 - - - -
180h GLU* 4.7 9.6 - - - -
181h VAL* 5.0 6.7 - - - -
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Residues in contact with GLN 159 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155h GLU 3.0 12.4 + - - -
156h LEU* 4.2 4.9 - - - +
157h LEU 3.5 3.4 - - - +
158h THR* 1.3 81.1 - - - +
160h THR* 1.3 57.3 + - - +
173h GLY* 4.5 8.8 - - - -
174h GLY 4.8 2.6 + - - -
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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