Contacts of the helix formed by residues 233 - 240 (chain M) in PDB entry 1JH0
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 233 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117H ARG* 5.8 2.7 - - - -
122H GLU* 2.7 49.5 + - - +
130H LYS* 4.5 16.2 - - - +
131H ILE* 4.5 8.2 - - - +
173H GLU* 5.1 3.1 - - - +
177H ARG* 3.8 51.2 - - - +
178H PHE* 5.4 0.8 - - - -
227H LEU* 4.3 4.3 - - - +
230H GLU* 2.6 43.5 + - - -
226L THR* 4.9 1.6 - - - -
230M GLY* 3.6 24.5 - - - +
231M GLY 2.9 4.2 + - - -
232M GLU* 1.3 76.7 - - + +
234M GLU* 1.3 65.0 + - - +
235M LEU 3.2 3.5 + - - -
236M GLU* 3.2 12.8 + - + -
237M GLN* 3.2 11.9 + - + +
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Residues in contact with GLU 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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190L HIS* 3.2 11.4 - - - -
194L VAL* 3.4 13.9 - - + +
226L THR* 6.1 0.3 - - - -
230L HIS* 2.8 15.1 + - - -
219M HIS* 2.9 13.3 - - - -
223M ILE* 3.6 8.1 - - + +
231M GLY 3.3 14.6 + - - +
232M GLU 2.8 12.9 + - - +
233M ARG* 1.3 73.5 - - - +
235M LEU* 1.3 58.4 + - + +
237M GLN* 2.8 25.8 + - - +
238M ILE* 2.9 17.8 + - + +
262M MET* 4.1 13.6 - - + +
266M HIS* 2.8 20.8 + - + -
856M FE 2.0 31.8 - - - -
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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
----------------------------------------------------------
194L VAL* 3.8 14.6 - - + +
197L ALA* 3.7 17.0 - - + -
198L ALA* 3.7 39.3 - - + +
206L MET* 3.7 25.2 - - + +
207L ARG 4.1 4.5 - - - +
208L THR* 4.0 3.4 - - - -
209L PRO* 3.8 27.1 - - + -
212L GLU* 3.3 28.5 - - - +
233M ARG 3.2 1.4 + - - -
234M GLU* 1.3 76.2 - - - +
236M GLU* 1.3 58.9 + - - +
238M ILE* 3.0 27.4 + - + +
239M ALA* 3.2 5.0 + - - +
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Residues in contact with GLU 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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70H ARG* 4.6 4.5 + - - -
117H ARG* 3.3 22.0 + - - +
118H ARG* 2.5 32.1 + - - +
122H GLU* 3.6 47.7 - - + +
123H LEU 5.5 0.7 + - - +
227H LEU* 3.6 11.4 - - + +
206L MET* 5.8 1.9 - - - +
233M ARG* 3.2 8.0 + - + +
235M LEU* 1.3 74.4 - - - +
237M GLN* 1.3 55.8 + - - +
238M ILE 3.1 5.4 - - - -
239M ALA* 4.5 7.6 - - - +
240M ASP* 2.9 22.8 + - - -
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Residues in contact with GLN 237 (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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38H GLU* 5.0 1.4 - - - +
117H ARG* 3.9 16.4 - - - +
231H ASP* 4.9 0.2 + - - -
229M PHE 3.9 6.7 + - - -
230M GLY 3.6 17.3 + - - +
231M GLY 4.4 0.7 - - - +
233M ARG* 3.2 16.2 + - + +
234M GLU 2.8 11.3 + - - +
236M GLU* 1.3 76.0 - - - +
238M ILE* 1.3 60.5 + - - +
240M ASP 4.0 4.5 - - - -
241M ARG* 3.4 19.6 - - - +
242M GLY* 2.8 35.9 + - - -
244M ALA* 3.4 26.2 - - - +
245M ALA* 3.4 16.1 + - - +
262M MET* 3.6 30.0 - - + +
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Residues in contact with ILE 238 (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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38H GLU* 3.9 14.0 - - - +
64H PHE* 4.0 30.8 - - + -
73H LEU* 3.7 10.2 - - - +
194L VAL* 5.6 4.9 - - + -
198L ALA* 4.8 8.1 - - + -
206L MET* 5.0 4.0 - - + -
234M GLU* 2.9 16.7 + - + +
235M LEU* 3.0 22.9 - - + +
237M GLN* 1.3 80.2 - - - +
239M ALA* 1.3 64.1 + - - +
240M ASP 3.6 0.2 + - - -
241M ARG 4.5 0.7 + - - -
262M MET* 3.1 23.3 - - + +
263M GLU* 3.0 47.1 - - + +
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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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64H PHE* 5.7 0.2 - - + -
66H LEU* 3.6 37.4 - - + +
73H LEU* 3.1 31.9 - - - +
118H ARG* 5.0 5.0 + - - +
206L MET* 4.3 10.1 - - + -
235M LEU 3.2 9.6 + - - +
236M GLU* 4.3 8.7 - - - +
238M ILE* 1.3 81.0 - - - +
240M ASP* 1.3 62.3 + - + +
241M ARG 4.0 0.4 - - - -
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Residues in contact with ASP 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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116H ALA 4.9 0.7 - - - +
117H ARG* 3.0 45.9 + - - +
118H ARG* 2.8 59.1 + - - +
227H LEU* 3.7 5.8 - - + +
236M GLU 2.9 14.6 + - - +
237M GLN* 4.0 1.0 - - - -
239M ALA* 1.3 80.5 - - - +
241M ARG* 1.3 69.0 + - - +
242M GLY 3.2 0.3 + - - -
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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