Contacts of the helix formed by residues 235 - 240 (chain L) 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 ILE 235 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L LEU* 4.5 2.2 - - + -
200L SER* 3.6 15.0 - - - +
232L MET* 4.2 14.4 - - + +
234L GLU* 1.3 73.4 - - - +
236L ASP* 1.3 50.9 + - - +
237L ALA* 2.7 10.3 + - - -
238L ILE* 3.0 9.5 + - + -
239L GLY* 1.8 51.6 + - - +
260L LEU* 5.6 3.6 - - + -
277L MET* 3.1 53.6 - - + -
278L ALA 2.6 33.6 + - - +
279L THR* 5.0 1.8 - - - -
285L LEU* 4.8 12.6 - - + -
289L LEU* 4.9 9.6 - - + -
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Residues in contact with ASP 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L GLU* 4.2 7.8 - - - +
235L ILE* 1.3 78.1 + - - +
237L ALA* 1.3 65.3 + - - +
239L GLY* 3.5 5.6 - - - -
240L GLY* 3.2 10.3 + - - +
279L THR* 2.9 35.7 + - - -
280L ASN* 4.1 3.3 + - - +
281L ARG* 3.3 1.8 + - - +
284L THR* 3.1 28.6 + - + +
285L LEU* 4.1 8.9 - - - +
295M ARG* 3.4 35.5 + - - +
304M ARG* 4.7 8.5 + - - -
307M GLN* 6.2 0.6 - - - +
311M LEU* 3.8 8.1 - - + +
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Residues in contact with ALA 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L SER 2.7 26.7 - - - +
201L SER* 4.1 10.5 - - - +
204L VAL* 5.6 1.8 - - + -
235L ILE 2.7 4.2 + - - +
236L ASP* 1.3 82.1 - - - +
238L ILE* 1.3 61.6 + - - +
239L GLY 2.7 5.5 + - - -
240L GLY* 3.0 8.0 + - - -
253L ILE* 4.1 6.2 - - - +
304M ARG* 4.7 2.9 - - - -
308M ARG* 3.7 40.7 + - + +
311M LEU* 3.7 8.7 - - + +
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Residues in contact with ILE 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L SER* 2.3 38.8 + - - +
203L ILE* 5.2 6.3 - - + -
204L VAL* 5.7 4.8 - - + +
232L MET* 5.2 3.1 - - - -
235L ILE* 3.8 8.1 - - + +
237L ALA* 1.3 79.3 - - - +
239L GLY* 1.3 64.8 + - - +
240L GLY* 3.2 0.7 + - - -
253L ILE* 3.4 15.9 - - + +
256L THR* 3.2 13.5 - - + +
257L LEU* 2.1 77.1 - - + +
260L LEU* 3.4 24.0 - - + -
308M ARG* 5.0 0.2 - - - +
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Residues in contact with GLY 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L ILE* 1.8 45.7 + - - -
236L ASP 3.7 0.2 - - - -
237L ALA 2.7 1.4 - - - -
238L ILE* 1.3 70.8 - - - +
240L GLY* 1.3 70.0 + - - +
257L LEU* 3.7 12.7 - - - +
285L LEU* 3.5 19.7 - - - +
286L ASP* 4.0 6.9 + - - +
289L LEU* 4.6 3.5 - - - +
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Residues in contact with GLY 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L ASP* 3.2 8.6 + - - +
237L ALA 3.0 13.0 + - - -
238L ILE 3.1 3.3 - - - -
239L GLY* 1.3 85.5 - - - +
241L ARG* 1.3 63.0 + - - -
253L ILE* 5.8 2.5 - - - -
254L GLN* 5.1 4.0 - - - -
257L LEU* 5.1 2.5 - - - -
284L THR* 3.0 19.9 + - - +
285L LEU* 3.3 6.6 - - - -
286L ASP* 3.5 0.4 + - - -
304M ARG* 3.8 20.2 - - - -
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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