Contacts of the helix formed by residues 234 - 250 (chain N) in PDB entry 5G04
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 ARG 234 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183N VAL* 4.8 0.2 - - - +
190N LYS* 4.2 24.3 - - + +
233N CYS* 1.3 72.7 - - + +
235N GLN* 1.3 60.0 + - - +
236N ALA* 3.1 1.8 - - - +
237N LEU* 3.0 37.5 + - + +
238N GLU* 3.3 21.5 + - - +
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Residues in contact with GLN 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N LEU* 3.5 29.7 - - - +
232N TRP 6.1 1.1 - - - +
233N CYS 2.5 11.8 + - - +
234N ARG* 1.3 72.1 - - - +
236N ALA* 1.3 58.9 + - - +
238N GLU* 3.4 26.2 + - - +
239N GLN* 2.9 51.4 + - + +
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Residues in contact with ALA 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N VAL* 3.9 32.1 - - + -
232N TRP* 4.7 6.0 - - + +
233N CYS 3.3 17.4 + - - +
235N GLN* 1.3 76.1 - - - +
237N LEU* 1.3 50.9 + - - +
239N GLN* 3.2 13.6 + - - +
240N PHE* 2.6 53.8 + - + -
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Residues in contact with LEU 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N PHE* 4.3 9.2 - - + -
183N VAL* 3.6 27.8 - - + -
184N TYR* 4.7 16.8 - - + -
187N SER* 4.6 16.8 - - - -
190N LYS* 4.8 4.3 - - - +
234N ARG* 3.0 23.3 + - + +
236N ALA* 1.3 73.8 - - - +
238N GLU* 1.3 60.1 + - - +
240N PHE* 3.7 8.1 - - - +
241N HIS* 3.1 33.3 + - + +
302N LYS* 3.7 23.7 + - - +
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Residues in contact with GLU 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N ARG* 3.4 12.9 - - - +
235N GLN* 3.4 39.2 + - + +
237N LEU* 1.3 74.0 - - + +
239N GLN* 1.3 66.3 + - + +
241N HIS* 3.2 6.8 + - - +
242N GLN* 3.0 30.5 + - - +
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Residues in contact with GLN 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N LEU* 3.0 34.1 + - - +
112N LEU* 3.7 18.5 - - + +
113N ASP* 3.6 19.6 - - - +
235N GLN* 2.9 48.5 + - + +
236N ALA* 3.4 11.3 + - - +
238N GLU* 1.3 75.6 - - + +
240N PHE* 1.3 60.6 + - + +
242N GLN* 3.1 26.0 + - - +
243N LEU* 3.1 23.4 + - - +
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Residues in contact with PHE 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N LEU* 5.4 13.9 - - + -
176N LEU* 3.3 40.8 - - + -
179N CYS* 4.7 4.0 - - + -
180N PHE* 3.5 62.6 - + + -
183N VAL* 4.8 2.2 - - + -
232N TRP* 6.5 0.2 - + - -
236N ALA* 2.6 45.6 + - + +
237N LEU* 3.6 5.1 + - - +
238N GLU 3.2 0.2 - - - -
239N GLN* 1.3 72.9 - - + +
241N HIS* 1.3 61.3 + - - +
242N GLN 3.2 0.7 - - - -
243N LEU* 3.3 25.4 + - + +
244N SER* 3.0 28.2 + - - -
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Residues in contact with HIS 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N PHE* 5.1 1.0 - + - -
237N LEU 3.1 16.1 + - - +
238N GLU* 3.2 5.1 + - - +
240N PHE* 1.3 75.1 + - - +
242N GLN* 1.3 64.1 + - - +
244N SER* 4.2 8.1 - - - +
245N GLN* 3.3 24.0 + - - +
302N LYS* 3.3 56.3 - - + +
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Residues in contact with GLN 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238N GLU* 3.0 24.4 + - - +
239N GLN* 3.1 30.1 + - - +
241N HIS* 1.3 77.6 - - - +
243N LEU* 1.3 52.7 + - - -
245N GLN* 3.4 12.4 + - - +
246N VAL* 2.9 38.3 + - + +
249N ARG* 6.2 0.2 - - - +
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Residues in contact with LEU 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N GLY* 5.5 14.4 - - - -
119N GLU* 5.5 8.3 - - + -
173N ILE* 6.5 0.2 - - + -
176N LEU* 5.2 13.0 - - + -
177N TYR* 4.0 33.2 - - + +
180N PHE* 5.1 1.1 - - + -
239N GLN 3.1 13.3 + - - +
240N PHE* 3.3 34.3 + - + +
242N GLN* 1.3 75.3 - - - +
244N SER* 1.3 58.2 + - - +
246N VAL* 3.3 11.7 + - + +
247N LEU* 3.0 46.7 + - + +
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Residues in contact with SER 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N TYR* 4.1 9.4 + - - -
180N PHE* 4.3 13.2 - - - -
240N PHE 3.0 17.1 + - - -
241N HIS* 4.9 8.7 - - - -
243N LEU* 1.3 73.6 - - - +
245N GLN* 1.3 61.2 + - - +
247N LEU* 4.0 5.4 - - - +
248N HIS* 3.0 30.7 + - - +
253N LEU* 4.6 3.8 - - - +
302N LYS 4.7 4.5 - - - -
303N VAL* 3.8 40.0 - - - +
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Residues in contact with GLN 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N HIS* 3.3 21.1 + - - +
242N GLN* 3.4 10.6 + - - +
243N LEU 3.3 0.4 - - - -
244N SER* 1.3 74.4 - - - +
246N VAL* 1.3 63.9 + - - +
248N HIS* 3.3 5.2 + - - +
249N ARG* 3.0 65.6 + - + +
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Residues in contact with VAL 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N GLY* 5.1 2.5 - - - +
119N GLU* 4.3 15.5 - - + +
120N SER* 4.0 35.9 - - - +
123N ASP* 4.7 4.3 - - + -
242N GLN* 2.9 23.9 + - + +
243N LEU* 3.4 14.4 - - + +
245N GLN* 1.3 75.0 - - - +
247N LEU* 1.3 68.6 + - + +
249N ARG* 3.3 51.4 - - - +
250N LEU* 3.8 9.4 + - - +
251N SER* 4.7 4.8 + - - +
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Residues in contact with LEU 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N GLU* 5.6 6.1 - - + -
173N ILE* 5.1 3.1 - - + -
177N TYR* 3.3 28.7 - - + +
243N LEU* 3.0 31.3 + - + +
244N SER* 4.1 3.4 - - - +
246N VAL* 1.3 78.0 - - + +
248N HIS* 1.3 61.5 + - - +
249N ARG 3.1 5.5 + - - -
250N LEU 3.4 3.3 + - - -
251N SER* 4.3 13.2 - - - +
252N LEU* 3.0 27.6 + - - +
253N LEU* 3.6 19.5 - - + +
256N VAL* 3.8 26.7 - - + -
257N SER* 3.7 19.5 - - - +
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Residues in contact with HIS 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N SER 3.0 20.2 + - - +
245N GLN* 4.1 3.4 - - - +
247N LEU* 1.3 73.2 - - - +
249N ARG* 1.3 64.9 + - - +
252N LEU* 3.9 13.5 - - + +
253N LEU* 3.6 28.5 + - + +
303N VAL 5.1 1.6 - - - +
304N PHE* 4.1 31.5 + + - +
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Residues in contact with ARG 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N SER* 4.6 8.9 + - - -
123N ASP* 4.0 20.2 - - - +
124N PRO* 5.0 6.5 - - - +
154N HIS* 5.9 0.9 + - - -
245N GLN* 3.0 54.0 + - + +
246N VAL* 3.3 42.5 - - - +
248N HIS* 1.3 80.3 - - - +
250N LEU* 1.3 77.1 + - + +
252N LEU* 4.3 4.5 - - - +
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Residues in contact with LEU 250 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N ASP* 3.7 50.3 - - + +
126N LEU* 5.4 1.6 - - + -
127N ARG* 4.4 14.8 - - + +
130N GLU* 5.4 10.5 - - + -
154N HIS* 4.4 15.7 - - + +
157N LEU* 4.5 22.0 - - + +
246N VAL 3.8 3.8 + - - +
247N LEU 3.4 4.2 + - - -
248N HIS 3.5 0.2 - - - -
249N ARG* 1.3 105.0 - - + +
251N SER* 1.3 83.9 + - - +
252N LEU* 3.0 17.9 - - - +
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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