Contacts of the helix formed by residues 232 - 237 (chain M) in PDB entry 5PRC
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 GLU 232 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190L HIS* 3.1 15.6 - - - -
194L ILE* 3.2 21.7 - - + +
212L GLU* 5.6 0.8 + - - -
230L HIS* 2.8 17.3 + - - -
217M HIS* 3.1 13.0 + - - -
221M ILE* 3.7 5.4 - - - +
229M GLY 3.5 18.6 - - - +
230M ASP 2.9 12.2 + - - +
231M ARG* 1.3 69.1 - - - +
233M ILE* 1.3 67.8 + - - +
235M GLN* 3.0 8.8 + - - +
236M ILE* 2.9 28.3 + - - +
260M ILE* 3.8 15.0 - - + +
264M HIS* 3.2 8.7 + - + -
500M FE2 2.0 31.9 - - - -
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Residues in contact with ILE 233 (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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194L ILE* 3.9 27.6 - - + +
197L VAL* 3.5 30.1 - - + -
198L ALA* 4.5 5.4 - - + +
206L VAL* 3.9 18.2 - - + -
207L LYS 3.8 17.7 - - - +
208L THR* 5.0 5.4 - - - -
209L ALA* 5.1 1.1 - - - +
212L GLU* 3.2 26.2 - - - +
231M ARG 3.4 0.2 - - - -
232M GLU* 1.3 76.2 - - - +
234M GLU* 1.3 76.4 + - - +
236M ILE* 3.0 29.7 + - + +
237M THR* 3.2 8.6 + - + +
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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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71H PRO* 5.9 2.4 - - - +
120H ARG* 2.7 31.7 + - - +
125H ASP* 3.9 20.5 - - - +
133H LYS* 3.3 24.6 + - - -
232H LEU* 5.4 7.0 - - + -
207L LYS 4.5 5.4 - - - +
208L THR* 4.7 9.2 - - - +
209L ALA* 4.8 6.1 + - - +
231M ARG* 3.3 20.0 + - + +
232M GLU 3.3 0.4 - - - -
233M ILE* 1.3 95.1 - - - +
235M GLN* 1.3 57.4 + - - +
236M ILE 3.2 1.6 - - - -
237M THR* 3.9 10.1 - - - +
238M ASP* 3.0 20.6 + - + +
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Residues in contact with GLN 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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39H GLU* 5.2 0.5 - - - +
120H ARG* 3.3 24.1 - - - +
236H ASP* 5.1 0.8 + - - -
227M PHE 3.8 5.9 + - - -
228M GLY 3.7 14.9 + - - +
229M GLY 4.3 6.3 - - - +
231M ARG* 3.1 18.6 + - + +
232M GLU* 3.0 11.3 + - - +
234M GLU* 1.3 76.3 - - - +
236M ILE* 1.3 62.6 + - - +
238M ASP 4.1 1.8 - - - -
239M ARG* 3.2 22.9 + - - +
240M GLY* 3.0 30.9 + - - +
242M ALA* 3.7 22.2 - - - +
243M VAL* 3.4 30.0 + - + +
260M ILE* 3.6 11.3 - - + +
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Residues in contact with ILE 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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39H GLU* 3.9 16.5 - - - +
68H PHE* 3.7 36.0 - - + -
78H VAL* 5.4 1.9 - - - +
194L ILE* 3.8 25.8 - - + -
198L ALA* 3.7 26.9 - - + -
232M GLU* 2.9 17.8 + - + +
233M ILE* 3.0 15.0 - - - +
235M GLN* 1.3 78.0 - - - +
237M THR* 1.3 63.5 + - + +
238M ASP 3.1 4.5 + - - -
239M ARG 4.2 0.9 + - - -
260M ILE* 3.7 20.0 - - + +
261M GLU* 3.9 26.2 - - + +
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Residues in contact with THR 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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68H PHE* 4.1 25.4 - - + -
70H LEU* 3.8 29.8 - - + +
71H PRO* 6.0 0.2 - - + -
76H VAL* 3.6 28.1 - - - +
80H ARG* 5.3 1.4 + - - -
206L VAL* 4.1 22.0 - - + -
233M ILE* 3.2 13.9 + - - +
234M GLU* 3.9 12.8 + - - +
236M ILE* 1.3 79.3 - - + +
238M ASP* 1.3 64.0 + - - +
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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