Contacts of the helix formed by residues 233 - 244 (chain M) in PDB entry 5GJQ
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 LYS 233 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225M MET* 4.2 10.6 - - + +
226M TYR* 4.1 20.6 - - - +
227M GLY 3.8 2.6 + - - +
228M PRO 3.2 23.8 + - - +
231M THR* 4.3 4.0 - - - +
232M GLY* 1.3 74.0 - - - +
234M THR* 1.3 69.0 + - - +
235M LEU 3.0 2.2 - - - +
236M LEU* 2.9 21.9 + - - +
237M ALA* 3.2 6.8 + - - +
284M PHE* 4.8 2.5 - - - -
331M ALA* 4.2 22.4 - - + -
332M THR 3.8 2.6 + - - +
333M ASN* 3.6 36.8 - - - +
354M PHE* 2.8 36.8 - - + -
501M ADP 3.2 27.4 + - - +
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Residues in contact with THR 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308H GLY* 4.2 5.8 - - - -
309H PHE* 3.4 33.2 - - + +
233M LYS* 1.3 78.7 - - - +
235M LEU* 1.3 56.0 + - - +
237M ALA* 3.3 4.5 - - - +
238M ARG* 2.8 50.8 + - - +
284M PHE* 4.4 10.4 - - + -
286M ASP* 4.0 15.6 + - - +
501M ADP 2.2 37.8 + - - -
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Residues in contact with LEU 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M GLU* 3.1 38.6 - - - +
187M ASP 5.6 0.2 - - - +
188M ILE* 4.2 14.8 - - + -
232M GLY* 5.0 2.9 - - - -
233M LYS* 4.1 4.7 - - - +
234M THR* 1.3 73.3 - - - +
236M LEU* 1.3 57.6 + - + +
238M ARG* 2.8 35.6 + - - +
239M ALA* 2.2 40.3 + - - +
501M ADP 3.5 68.0 - - + +
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Residues in contact with LEU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M TYR* 5.5 1.8 - - + -
188M ILE* 3.6 24.7 - - + -
191M LEU* 3.5 11.7 - - + -
194M GLN* 5.6 0.7 - - + -
195M ILE* 3.7 28.7 - - + -
198M LEU* 4.4 13.0 - - + +
225M MET* 3.8 12.8 - - + -
232M GLY 3.6 8.1 - - - +
233M LYS* 2.9 8.4 + - - +
235M LEU* 1.3 77.6 - - - +
237M ALA* 1.3 57.4 + - - +
239M ALA* 3.0 8.6 + - + +
240M CYS* 2.8 35.2 + - - +
354M PHE* 2.7 49.8 - - + -
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Residues in contact with ALA 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H PHE* 3.9 6.1 - - + -
198M LEU* 6.4 0.2 - - - -
225M MET* 4.9 3.5 - - + +
233M LYS 3.2 3.4 + - - +
234M THR 3.3 4.9 - - - +
236M LEU* 1.3 75.0 - - - +
238M ARG* 1.3 53.5 + - - +
240M CYS* 2.9 9.2 + - - +
241M ALA* 2.6 35.0 + - - +
248M PHE* 4.7 4.6 - - + -
284M PHE* 2.5 52.7 - - + -
329M ILE* 5.8 9.0 - - + -
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Residues in contact with ARG 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H GLY* 5.4 0.6 - - - -
309H PHE* 3.5 31.0 - - + +
310H ASP 5.0 3.8 - - - +
311H PRO* 6.4 1.7 - - - +
181M PRO* 3.6 31.4 - - + +
183M GLU* 4.1 23.4 + - + +
234M THR* 2.8 46.7 + - - +
235M LEU* 2.8 38.0 + - - +
237M ALA* 1.3 69.8 - - - +
239M ALA* 1.3 59.8 + - - +
241M ALA* 3.3 4.3 + - - +
242M ALA* 3.1 20.6 + - - +
501M ADP 5.0 12.3 + - - -
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Residues in contact with ALA 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M GLU* 4.3 4.4 - - + +
184M GLN 3.8 17.0 - - - +
185M TYR* 3.7 29.2 - - + -
188M ILE* 4.7 4.7 - - + -
235M LEU 2.2 27.4 + - - +
236M LEU* 3.1 14.1 - - - +
238M ARG* 1.3 68.9 - - - +
240M CYS* 1.3 59.1 + - - +
242M ALA* 3.2 0.6 + - - -
243M GLN* 2.9 39.2 + - - +
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Residues in contact with CYS 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M TYR* 4.1 11.9 - - - -
198M LEU* 2.7 40.8 - - - -
199M VAL* 5.2 2.9 - - - -
202M ILE* 4.8 6.5 - - - -
203M VAL* 5.4 1.8 - - - -
236M LEU 2.8 13.4 + - - +
237M ALA* 2.9 8.5 + - - +
239M ALA* 1.3 75.2 - - - +
241M ALA* 1.3 56.2 + - - +
243M GLN* 4.3 2.7 - - - -
244M THR* 2.2 61.5 + - + +
248M PHE* 5.4 0.7 - - + -
282M ILE* 4.6 9.0 - - + -
329M ILE* 5.1 4.5 - - + -
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Residues in contact with ALA 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309H PHE* 3.9 4.5 - - + -
180M ARG* 1.7 46.1 + - - +
181M PRO* 3.4 27.4 - - + -
237M ALA 2.6 19.8 + - - +
238M ARG 3.4 3.8 - - - +
239M ALA 3.2 0.2 - - - -
240M CYS* 1.3 72.1 - - - +
242M ALA* 1.3 50.5 + - - +
244M THR* 4.0 2.9 - - - -
248M PHE* 3.7 33.1 - - + -
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Residues in contact with ALA 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M ARG* 3.7 9.9 + - - +
181M PRO* 3.3 29.8 - - - +
182M THR* 4.2 1.6 - - - -
183M GLU 4.2 11.2 - - - +
184M GLN 5.0 0.9 - - - +
238M ARG 3.1 12.4 + - - +
239M ALA 3.8 5.8 - - - +
241M ALA* 1.3 75.1 - - - +
243M GLN* 1.3 76.2 + - - +
245M LYS* 5.6 0.5 - - - +
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Residues in contact with GLN 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M GLN* 3.8 29.9 - - - +
185M TYR* 3.5 35.0 - - + +
203M VAL* 5.8 3.1 - - + -
239M ALA 2.9 30.7 + - - +
240M CYS* 3.9 2.0 - - - +
242M ALA* 1.3 88.9 + - - +
244M THR* 1.3 57.6 + - + +
245M LYS* 2.5 29.3 + - - +
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Residues in contact with THR 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M ARG* 2.9 10.6 + - - -
202M ILE* 4.7 1.3 - - + -
203M VAL* 4.0 27.3 - - + +
240M CYS* 2.2 50.2 + - + +
241M ALA* 3.8 3.8 + - - -
243M GLN* 1.3 72.1 - - + +
245M LYS* 1.3 53.2 + - - +
246M ALA* 2.7 32.2 + - - +
248M PHE* 5.2 1.9 - - - +
282M ILE* 3.3 35.9 - - + +
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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