Contacts of the helix formed by residues 236 - 249 (chain G) in PDB entry 5JLH
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 236 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233G GLU* 4.0 21.1 - - + +
234G LEU* 2.6 11.6 + - - +
235G GLU* 1.3 69.1 - - - +
237G GLN* 1.3 58.5 + - - +
238G LEU 3.0 5.4 - - - -
239G LEU* 3.0 59.9 + - + +
240G GLN* 3.6 6.7 + - - +
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Residues in contact with GLN 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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235G GLU* 4.3 15.6 + - + +
236G ARG* 1.3 79.6 - - - +
238G LEU* 1.3 59.9 + - - +
239G LEU 3.1 0.9 - - - -
240G GLN* 2.9 10.4 + - + +
241G ALA* 2.8 28.6 + - - +
354G VAL* 5.1 3.5 - - + +
355G LEU* 3.6 36.2 - - + +
462G ALA 3.1 27.4 + - - +
463G LEU* 3.3 33.0 - - + +
464G ASP* 4.6 1.6 + - - +
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Residues in contact with LEU 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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205G THR* 5.5 0.9 - - - +
209G LYS* 5.8 4.7 - - + -
212G ILE* 3.7 39.0 - - + -
235G GLU* 3.2 35.1 + - + +
236G ARG 3.0 0.8 - - - -
237G GLN* 1.3 78.8 - - - +
239G LEU* 1.3 59.3 + - + +
241G ALA* 3.5 20.2 + - + +
242G ASN* 3.7 12.9 + - - +
266G ILE* 5.3 9.9 - - + -
268G ILE* 6.1 2.2 - - + -
279G ALA* 5.5 11.0 - - + -
281G ILE* 4.5 21.8 - - + -
463G LEU* 4.5 19.1 - - + -
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Residues in contact with LEU 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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209G LYS* 3.2 48.2 - - + +
235G GLU 5.7 0.2 - - - +
236G ARG* 3.0 52.8 + - + +
238G LEU* 1.3 80.7 - - - +
240G GLN* 1.3 60.1 + - - +
242G ASN* 3.3 16.8 + - - +
243G PRO* 3.3 16.6 - - - +
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Residues in contact with GLN 240 (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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236G ARG* 3.6 5.4 + - - +
237G GLN* 2.9 23.1 + - + +
239G LEU* 1.3 79.8 - - - +
241G ALA* 1.3 60.9 + - - +
243G PRO* 3.2 22.7 - - - +
244G ILE* 3.6 10.3 - - - +
347G GLU* 4.1 10.0 + - - +
350G GLU* 5.2 3.2 - - - +
351G SER* 2.8 50.2 - - - +
354G VAL* 3.5 23.4 - - + +
355G LEU* 4.0 8.7 - - + -
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Residues in contact with ALA 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G GLN 2.8 10.4 + - - +
238G LEU* 3.5 20.6 - - + +
239G LEU 3.2 0.2 - - - -
240G GLN* 1.3 76.3 - - - +
242G ASN* 1.3 66.4 + - - +
244G ILE* 3.1 20.3 + - - +
245G LEU* 3.1 23.4 + - + +
264G LYS* 6.0 0.9 - - - +
281G ILE* 5.7 6.1 - - + -
355G LEU* 5.0 2.9 - - - -
459G LEU* 4.3 22.0 - - + -
463G LEU* 6.5 0.7 - - + -
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Residues in contact with ASN 242 (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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205G THR* 3.2 35.8 + - - +
206G GLU* 6.0 2.4 - - - +
209G LYS* 4.8 8.3 - - - +
238G LEU 3.7 11.5 + - - +
239G LEU* 3.4 18.0 + - - +
240G GLN 3.2 0.2 - - - -
241G ALA* 1.3 77.0 - - - +
243G PRO* 1.3 67.4 - - + +
245G LEU* 4.3 0.4 - - - +
246G GLU* 2.7 41.7 + - + +
264G LYS* 3.5 20.1 + - - +
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Residues in contact with PRO 243 (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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239G LEU 3.3 9.4 - - - +
240G GLN* 3.2 32.1 - - - +
242G ASN* 1.3 98.5 - - + +
244G ILE* 1.3 55.4 + - - +
246G GLU* 3.9 12.6 - - + +
247G ALA* 2.9 31.0 + - - +
347G GLU* 5.5 8.3 - - + +
348G THR* 4.2 11.8 + - - +
351G SER* 4.1 10.8 - - - +
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Residues in contact with ILE 244 (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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240G GLN 3.6 13.9 - - - +
241G ALA* 3.1 8.5 + - - +
243G PRO* 1.3 76.5 - - - +
245G LEU* 1.3 61.1 + - + +
247G ALA* 3.0 6.5 + - - +
248G PHE* 2.9 33.9 + - + +
348G THR* 4.1 5.8 - - + +
351G SER* 3.1 34.3 - - - +
352G LEU* 3.4 34.3 - - + +
355G LEU* 3.8 14.8 - - + -
455G LEU* 3.5 37.2 - - + -
459G LEU* 5.1 4.9 - - + -
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Residues in contact with LEU 245 (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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241G ALA* 3.1 17.1 + - + +
242G ASN 4.3 1.3 - - - +
244G ILE* 1.3 76.3 - - + +
246G GLU* 1.3 58.7 + - - +
248G PHE* 4.6 1.8 - - - +
249G GLY* 2.6 36.8 + - - +
262G PHE* 3.5 24.3 - - + -
264G LYS* 4.0 28.3 - - + +
281G ILE* 4.3 23.8 - - + -
283G THR* 4.8 4.9 - - + -
452G PHE* 4.4 17.9 - - + -
455G LEU* 4.0 24.9 - - + -
456G VAL* 5.4 6.5 - - + -
459G LEU* 4.6 18.8 - - + -
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Residues in contact with GLU 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G ASN* 2.7 34.6 + - - +
243G PRO* 3.8 9.0 - - - +
245G LEU* 1.3 78.4 - - - +
247G ALA* 1.3 58.0 + - - +
250G ASN* 3.0 55.5 + - - +
258G ASN* 2.8 30.6 + - - +
262G PHE* 5.3 0.4 - - - -
302G HIS* 3.6 8.0 - - + -
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Residues in contact with ALA 247 (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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243G PRO 2.9 20.4 + - - +
244G ILE* 3.0 4.9 + - - +
246G GLU* 1.3 80.6 - - - +
248G PHE* 1.3 69.1 + - + +
250G ASN 4.1 0.2 - - - +
302G HIS* 3.4 12.3 + - - -
303G ILE* 2.8 28.9 + - + +
306G GLN* 3.1 31.2 - - - +
348G THR* 4.3 9.4 - - + -
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Residues in contact with PHE 248 (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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244G ILE* 2.9 20.8 + - + +
245G LEU 4.2 0.7 - - - +
247G ALA* 1.3 77.6 - - + +
249G GLY* 1.3 56.6 + - - +
301G PHE* 3.1 22.7 - - - +
303G ILE* 3.6 37.0 - - + -
348G THR* 6.4 1.1 - - + -
352G LEU* 6.2 2.7 - - + -
365G MET* 3.8 24.9 - - + -
366G LEU* 5.7 4.3 - - + -
369G VAL* 4.5 13.7 - - + -
448G TYR* 2.6 30.2 + + - +
451G LEU* 3.9 30.5 - - + -
452G PHE* 4.1 22.4 - + + -
455G LEU* 3.5 29.4 - - + -
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Residues in contact with GLY 249 (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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245G LEU 2.6 21.8 + - - -
248G PHE* 1.3 74.7 - - - +
250G ASN* 1.3 62.5 + - - +
261G ARG* 3.5 16.1 + - - +
262G PHE* 3.5 19.5 - - - -
286G LEU* 5.1 2.9 - - - +
301G PHE* 3.2 20.5 - - - -
448G TYR* 6.1 0.2 - - - -
452G PHE* 4.3 6.0 - - - -
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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