Contacts of the helix formed by residues 230 - 242 (chain G) in PDB entry 5UQ9
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 SER 230 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G ILE* 5.1 0.3 - - - +
224G ASN* 3.4 9.2 + - - +
228G LEU 3.0 8.3 + - - -
229G ASP* 1.3 78.6 + - - +
231G PHE* 1.3 62.1 + - - +
232G LEU* 3.2 9.1 + - - +
233G ILE* 2.7 31.4 + - - +
234G GLU* 3.2 17.7 + - - +
331G LYS* 4.2 14.8 + - - -
368G ILE 6.1 0.2 - - - -
369G ARG 3.8 1.6 - - - -
370G SER* 3.5 22.7 - - - +
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Residues in contact with PHE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLU* 4.1 13.2 - - - -
230G SER* 1.3 70.1 - - - +
232G LEU* 1.3 61.1 + - - +
234G GLU* 3.3 22.8 + - - +
235G ILE* 3.0 62.1 + - + +
367G ILE* 3.7 23.3 - - + +
369G ARG* 2.9 69.1 + - + +
370G SER* 4.5 0.2 - - - +
449H TYR* 5.3 3.4 - + - -
450H PHE* 3.7 25.4 - - + -
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Residues in contact with LEU 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G GLU* 5.0 1.6 - - + +
194G ASP* 3.6 37.5 - - + +
195G MET* 4.2 25.8 - - + -
198G ILE* 3.6 16.0 - - + +
230G SER* 3.2 7.0 + - - +
231G PHE* 1.3 78.2 - - - +
233G ILE* 1.3 56.9 + - - +
235G ILE* 3.3 24.8 - - + +
236G THR* 2.9 32.9 + - - +
331G LYS* 6.0 1.3 - - - +
367G ILE* 4.2 19.0 + - + +
368G ILE* 4.9 10.1 - - + -
369G ARG 4.6 0.4 + - - -
446H GLN* 4.5 9.1 + - - +
450H PHE* 4.5 12.1 - - + -
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Residues in contact with ILE 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G ILE* 3.8 22.0 - - + -
220G PHE* 3.2 54.9 - - + +
223G TRP* 4.4 2.7 - - + -
224G ASN* 3.6 19.7 + - + +
228G LEU* 3.3 25.4 - - + +
230G SER* 2.7 28.1 + - - +
232G LEU* 1.3 72.8 - - - +
234G GLU* 1.3 62.5 + - - +
236G THR* 3.2 14.7 - - - +
237G ALA* 3.3 11.8 + - - +
327G LEU* 4.6 11.4 - - + -
331G LYS* 6.1 0.2 - - - +
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Residues in contact with GLU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G ASN* 3.2 19.6 - - - +
230G SER 3.2 9.4 + - - +
231G PHE* 3.6 29.8 - - - +
232G LEU 3.2 0.4 - - - -
233G ILE* 1.3 78.0 - - - +
235G ILE* 1.3 65.6 + - + +
237G ALA* 3.4 4.7 + - - +
238G ASN* 3.2 39.9 + - - +
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Residues in contact with ILE 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G PHE* 3.0 42.6 + - + +
232G LEU* 3.3 30.1 - - + +
234G GLU* 1.3 80.1 - - + +
236G THR* 1.3 68.5 + - - +
238G ASN* 3.5 5.7 + - - +
239G ILE* 3.0 29.4 + - + +
446H GLN* 4.4 13.7 - - + +
449H TYR* 3.5 35.7 - - + -
450H PHE* 3.6 32.8 - - + -
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Residues in contact with THR 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G ILE* 3.9 8.2 - - + +
220G PHE* 3.8 23.6 - - + -
232G LEU 2.9 21.7 + - - +
233G ILE* 3.2 15.7 - - - +
235G ILE* 1.3 79.1 - - - +
237G ALA* 1.3 64.2 + - - +
239G ILE* 3.2 11.0 + - - +
240G LEU* 3.0 34.6 + - - +
442H LEU* 3.5 28.1 - - - +
446H GLN* 4.0 13.5 - - - -
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Residues in contact with ALA 237 (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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217G ALA* 3.6 15.7 - - - +
220G PHE* 3.8 11.0 - - + -
221G GLU* 3.6 31.2 - - + +
233G ILE 3.3 14.4 + - - +
234G GLU* 3.8 5.2 - - - +
235G ILE 3.3 0.2 - - - -
236G THR* 1.3 82.5 - - - +
238G ASN* 1.3 62.5 + - - +
240G LEU* 3.3 5.6 + - - -
241G LYS* 3.1 28.8 + - - +
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Residues in contact with ASN 238 (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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221G GLU* 4.5 10.6 - - - +
234G GLU* 3.2 34.4 + - - +
235G ILE* 3.8 6.8 - - - +
236G THR 3.3 0.2 - - - -
237G ALA* 1.3 77.0 - - - +
239G ILE* 1.3 58.0 + - - +
241G LYS* 3.3 10.0 + - - +
242G PHE* 2.8 35.0 + - + +
449H TYR* 3.6 28.0 + - + +
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Residues in contact with ILE 239 (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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235G ILE* 3.0 23.9 + - + +
236G THR* 3.5 8.3 - - - +
237G ALA 3.2 0.2 - - - -
238G ASN* 1.3 74.1 - - - +
240G LEU* 1.3 65.8 + - - +
241G LYS 3.4 0.2 + - - -
242G PHE* 3.4 21.0 + - - +
249G HIS* 5.8 0.2 - - - +
250G LEU* 5.8 0.3 - - - +
251G LEU* 3.6 39.0 + - + +
254G ILE* 5.9 0.4 - - + -
442H LEU* 4.0 3.8 - - + -
445H ALA* 3.4 42.8 - - + +
446H GLN* 3.7 20.0 - - + +
449H TYR* 4.0 21.3 - - + -
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G TYR* 3.6 19.3 - - + -
213G GLN* 3.2 56.9 - - + +
216G MET* 4.6 2.9 - - + +
217G ALA* 3.5 24.5 - - + +
220G PHE* 3.8 32.1 - - + -
236G THR* 3.0 33.5 + - - +
237G ALA* 3.3 2.7 + - - +
239G ILE* 1.3 76.5 - - - +
241G LYS* 1.3 60.9 + - - +
249G HIS* 3.4 11.6 - - - +
251G LEU* 3.6 20.1 - - + +
442H LEU* 5.0 1.8 - - + -
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Residues in contact with LYS 241 (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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214G ASP* 4.5 21.4 + - - +
217G ALA* 3.4 15.0 - - + +
218G GLN* 4.1 10.1 + - - -
221G GLU* 3.5 34.6 + - - +
237G ALA 3.1 17.4 + - - +
238G ASN* 3.8 11.4 - - - +
239G ILE 3.2 0.2 - - - -
240G LEU* 1.3 77.1 - - - +
242G PHE* 1.3 64.1 + - - +
243G GLN* 3.0 15.2 + - - +
249G HIS* 3.6 9.7 + - - -
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Residues in contact with PHE 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G ASN* 2.8 23.1 + - + +
239G ILE* 3.4 18.1 + - - +
241G LYS* 1.3 70.9 - - - +
243G GLN* 1.3 76.5 + - - +
244G ASP* 4.9 4.0 - - + -
249G HIS* 4.0 3.5 - - - +
250G LEU* 3.2 35.0 + - + +
449H TYR* 5.5 11.4 - + - -
467H THR* 3.7 31.2 - - + -
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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