Contacts of the helix formed by residues 174 - 190 (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 174 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118g GLY 5.2 4.9 - - - -
158g THR 5.5 1.2 + - - -
159g GLN 4.8 4.6 + - - -
160g THR* 5.4 0.6 - - - -
173g GLY* 1.3 74.9 - - - -
175g TYR* 1.3 59.3 + - - -
176g LYS 3.4 2.0 - - - -
177g GLY* 3.3 7.2 + - - -
178g LEU* 2.9 27.7 + - - +
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Residues in contact with TYR 175 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120g ALA* 4.7 12.0 - - + +
173g GLY 3.9 1.0 + - - -
174g GLY* 1.3 70.4 - - - -
176g LYS* 1.3 58.3 + - - +
178g LEU* 3.1 9.7 + - - +
179g LYS* 3.0 28.3 + - - +
23w PHE* 5.8 9.2 - - + +
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Residues in contact with LYS 176 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9042 G 4.6 15.8 + - - +
174g GLY 3.4 0.6 - - - -
175g TYR* 1.3 74.3 - - - +
177g GLY* 1.3 63.9 + - - +
179g LYS* 3.1 10.2 + - - +
180g GLU* 3.0 22.3 + - - +
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Residues in contact with GLY 177 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158g THR* 3.5 37.7 - - - -
160g THR* 5.1 5.2 - - - -
174g GLY* 3.3 9.2 + - - -
176g LYS* 1.3 77.4 - - - +
178g LEU* 1.3 55.6 + - - +
180g GLU* 3.3 6.2 + - - +
181g VAL* 2.9 28.9 + - - +
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Residues in contact with LEU 178 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120g ALA* 5.8 4.5 - - + +
121g CYS 5.6 3.4 - - - +
122g ASP* 4.7 20.2 - - + +
171g VAL* 5.5 7.6 - - + -
172g MET 6.2 0.2 - - - +
173g GLY 5.4 5.4 - - - +
174g GLY 2.9 14.1 + - - +
175g TYR* 3.1 12.5 + - - +
177g GLY* 1.3 76.7 - - - +
179g LYS* 1.3 57.3 + - - +
181g VAL* 3.3 8.1 + - - +
182g ARG* 2.9 30.2 + - - +
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Residues in contact with LYS 179 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9042 G 4.0 20.6 - - - +
175g TYR 3.0 11.7 + - - +
176g LYS* 3.3 11.4 - - - +
178g LEU* 1.3 74.0 - - - +
180g GLU* 1.3 57.4 + - - +
182g ARG* 3.2 7.5 + - - +
183g ARG* 2.9 30.0 + - - +
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Residues in contact with GLU 180 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9042 G 5.0 3.2 + - - +
158g THR* 4.7 9.0 - - - -
176g LYS 3.0 12.0 + - - +
177g GLY* 3.5 11.4 - - - +
179g LYS* 1.3 74.3 - - - +
181g VAL* 1.3 55.6 + - - +
183g ARG* 3.3 8.1 + - - +
184g VAL* 2.9 30.4 + - - +
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Residues in contact with VAL 181 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158g THR* 5.0 7.1 - - - -
160g THR* 5.7 4.3 - - - -
162g ILE* 6.2 3.1 - - + -
171g VAL* 4.7 16.4 - - + -
177g GLY 2.9 15.1 + - - +
178g LEU* 3.3 12.1 + - - +
180g GLU* 1.3 74.8 - - - +
182g ARG* 1.3 57.8 + - - +
184g VAL* 3.2 7.3 + - - +
185g VAL* 2.8 33.1 + - - +
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Residues in contact with ARG 182 (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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124g ILE* 5.5 6.3 - - - -
178g LEU 2.9 17.0 + - - +
179g LYS* 3.2 7.4 + - - +
181g VAL* 1.3 75.0 - - - +
183g ARG* 1.3 59.1 + - - +
185g VAL* 3.9 4.1 - - - +
186g GLU* 2.9 34.7 + - - +
129w LYS 5.4 0.2 - - - -
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Residues in contact with ARG 183 (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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179g LYS 2.9 12.7 + - - +
180g GLU* 3.5 11.2 - - - +
182g ARG* 1.3 76.2 - - - +
184g VAL* 1.3 56.7 + - - +
187g ASP* 2.9 35.0 + - - +
129w LYS* 3.7 25.6 - - + +
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Residues in contact with VAL 184 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154g LEU* 6.1 4.3 - - + -
180g GLU 2.9 17.4 + - - +
181g VAL* 3.6 7.4 - - - +
183g ARG* 1.3 76.8 - - - +
185g VAL* 1.3 56.5 + - - +
187g ASP* 3.8 3.3 - - - +
188g THR* 2.9 31.4 + - - -
192g ILE 5.2 0.2 - - - +
194g PRO* 5.4 9.7 - - + +
197g LEU* 4.7 21.1 - - + -
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Residues in contact with VAL 185 (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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124g ILE* 5.2 9.0 - - + -
126g ILE* 6.2 0.2 - - - +
143g LEU* 5.9 4.5 - - + -
169g VAL* 5.1 15.9 - - + -
181g VAL 2.8 19.6 + - - +
182g ARG* 4.0 5.2 - - - +
184g VAL* 1.3 73.9 - - - +
186g GLU* 1.3 61.6 + - - +
188g THR* 3.1 9.0 + - - -
189g MET* 3.0 24.2 + - - +
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Residues in contact with GLU 186 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182g ARG 2.9 19.2 + - - +
183g ARG 4.1 1.8 - - - +
185g VAL* 1.3 76.1 - - - +
187g ASP* 1.3 62.8 + - - +
189g MET* 3.3 9.9 + - - +
190g ASN* 3.2 21.0 + - - +
127w ARG* 5.9 5.6 - - + -
128w LYS* 5.8 4.3 - - + +
129w LYS 4.4 18.2 - - - +
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Residues in contact with ASP 187 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183g ARG 2.9 20.4 + - - +
184g VAL* 3.9 3.6 - - - +
186g GLU* 1.3 76.0 - - - +
188g THR* 1.3 58.9 + - - +
190g ASN* 3.1 14.6 + - - +
192g ILE* 2.9 42.3 + - + +
129w LYS 4.1 12.2 + - - +
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Residues in contact with THR 188 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139g ARG* 3.9 18.2 - - - +
142g ARG* 5.8 1.1 - - - -
143g LEU* 4.6 24.0 - - - -
184g VAL 2.9 18.8 + - - -
185g VAL* 3.1 8.9 + - - -
187g ASP* 1.3 75.4 - - - +
189g MET* 1.3 59.8 + - - +
191g ASN* 3.3 13.5 + - - -
192g ILE 3.4 15.2 + - - -
194g PRO* 5.0 11.2 - - - -
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Residues in contact with MET 189 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126g ILE* 5.0 17.0 - - + +
129g MET* 3.8 35.1 - - + +
130g VAL* 5.5 3.6 - - - +
139g ARG* 4.6 14.3 - - + +
185g VAL 3.0 11.9 + - - +
186g GLU* 3.6 11.2 - - - +
188g THR* 1.3 77.3 - - - +
190g ASN* 1.3 55.9 + - - +
191g ASN 3.3 3.2 + - - -
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Residues in contact with ASN 190 (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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129g MET* 5.7 1.3 - - + -
186g GLU 3.2 10.3 + - - +
187g ASP* 3.1 12.1 + - - +
189g MET* 1.3 75.4 - - - +
191g ASN* 1.3 69.6 + - - +
192g ILE* 3.3 4.2 + - + +
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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
------------------------------------------------------------
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