Contacts of the helix formed by residues 236 - 249 (chain c) in PDB entry 3J7Y
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 ASN 236 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234c ILE* 4.9 0.2 - - - -
235c ILE* 1.3 88.1 - - + +
237c PRO* 1.3 70.9 - - - +
238c MET* 3.6 10.4 + - - +
239c GLY* 3.6 23.3 + - - +
240c LEU* 4.0 11.6 + - - +
298c ARG* 5.9 0.2 - - - +
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Residues in contact with PRO 237 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234c ILE* 4.0 23.8 - - + -
235c ILE* 3.9 1.5 - - - -
236c ASN* 1.3 88.2 - - - +
238c MET* 1.3 61.7 + - + +
239c GLY 3.2 0.4 - - - -
240c LEU* 3.2 6.4 + - + +
241c LEU* 2.9 34.1 + - - +
294c GLU* 4.1 28.0 - - + +
297c ALA* 4.1 18.4 - - + -
298c ARG* 4.2 23.6 - - + +
301c LEU* 4.2 10.8 - - + -
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Residues in contact with MET 238 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236c ASN* 3.3 9.8 - - - +
237c PRO* 1.3 82.8 - - + +
239c GLY* 1.3 57.5 + - - +
241c LEU* 3.2 25.8 + - - +
242c VAL* 2.9 45.3 + - + +
253c PRO* 4.8 14.8 - - + +
255c SER* 5.6 6.1 - - - -
274c LEU* 4.4 15.3 - - + -
293c GLU* 5.0 17.3 - - + +
294c GLU* 5.6 4.0 - - + -
297c ALA* 4.1 11.9 - - + -
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Residues in contact with GLY 239 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236c ASN* 3.6 16.8 + - - -
237c PRO 3.2 0.4 - - - -
238c MET* 1.3 78.1 - - - +
240c LEU* 1.3 58.2 + - - +
242c VAL* 3.2 10.1 + - - +
243c GLU* 2.9 34.7 + - - +
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Residues in contact with LEU 240 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151c GLU* 5.9 2.2 - - - +
232c TRP* 4.8 15.5 - - + -
234c ILE* 3.5 42.0 - - + -
235c ILE 5.3 1.8 - - - +
236c ASN 4.0 10.1 + - - +
237c PRO 3.2 9.4 + - - +
239c GLY* 1.3 74.6 - - - +
241c LEU* 1.3 57.4 + - - +
243c GLU* 3.2 20.2 + - - +
244c GLU* 2.9 35.7 + - + +
301c LEU* 4.4 14.6 - - + -
305c TYR* 5.0 8.1 - - - +
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Residues in contact with LEU 241 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237c PRO 2.9 29.9 + - - +
238c MET* 3.3 20.4 - - + +
240c LEU* 1.3 76.1 - - - +
242c VAL* 1.3 55.2 + - + +
244c GLU* 3.2 4.7 + - - +
245c LEU* 2.8 39.1 + - + +
253c PRO* 5.1 8.7 - - + -
274c LEU* 3.5 18.8 - - + -
281c ILE* 5.3 4.9 - - + -
297c ALA* 3.0 51.4 - - + +
300c ALA* 4.4 7.0 - - + -
301c LEU* 3.2 27.4 - - + +
304c LEU* 5.0 4.1 - - + +
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Residues in contact with VAL 242 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238c MET* 2.9 25.1 + - + +
239c GLY* 3.4 11.2 - - - +
241c LEU* 1.3 78.8 - - - +
243c GLU* 1.3 60.0 - - + +
245c LEU* 3.2 9.2 + - - +
246c LYS* 2.9 59.0 + - + +
251c SER 5.5 2.0 - - - +
252c ALA* 5.6 3.6 - - + -
253c PRO* 4.1 26.2 - - + -
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Residues in contact with GLU 243 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239c GLY 2.9 19.0 + - - +
240c LEU* 3.2 22.3 + - - +
242c VAL* 1.3 78.0 - - + +
244c GLU* 1.3 59.9 + - + +
246c LYS* 3.2 13.3 + - + +
247c LYS* 2.9 45.4 + - - +
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Residues in contact with GLU 244 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147c ASP 5.1 1.8 - - - +
149c PRO* 4.1 14.9 - - - +
240c LEU* 2.9 19.0 + - + +
241c LEU* 3.5 9.2 - - - +
243c GLU* 1.3 79.0 - - + +
245c LEU* 1.3 55.3 + - - +
247c LYS* 3.2 23.0 + - - +
248c ARG* 2.9 53.3 + - - +
301c LEU* 4.6 2.2 - - + -
304c LEU* 3.9 18.5 - - + +
305c TYR* 2.6 45.3 + - + +
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Residues in contact with LEU 245 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241c LEU* 2.8 21.0 + - + +
242c VAL* 3.4 6.5 - - - +
244c GLU* 1.3 72.6 - - - +
246c LYS* 1.3 56.3 + - - +
248c ARG* 4.5 4.9 - - + -
249c ASN* 2.8 41.8 + - + +
250c VAL 3.3 3.5 + - - -
251c SER* 3.5 32.8 - - - +
252c ALA 3.7 2.9 - - - -
253c PRO* 3.5 34.8 - - + -
276c CYS* 3.7 27.4 - - + -
281c ILE* 4.4 15.0 - - + -
304c LEU* 5.4 13.0 - - + -
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Residues in contact with LYS 246 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242c VAL* 2.9 40.1 + - + +
243c GLU* 3.2 14.3 + - + +
245c LEU* 1.3 75.9 - - - +
247c LYS* 1.3 65.6 + - + +
250c VAL* 3.4 31.9 + - + +
251c SER 4.2 12.3 - - - +
252c ALA* 6.0 3.8 - - - -
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Residues in contact with LYS 247 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149c PRO* 6.0 4.2 - - - +
243c GLU* 2.9 29.6 + - - +
244c GLU* 3.4 26.8 + - - +
246c LYS* 1.3 77.6 - - + +
248c ARG* 1.3 67.7 + - + +
250c VAL* 5.5 0.9 - - - +
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Residues in contact with ARG 248 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147c ASP* 3.8 47.5 + - - +
244c GLU* 2.9 35.9 + - - +
245c LEU* 3.7 5.8 - - + +
247c LYS* 1.3 83.2 - - + +
249c ASN* 1.3 75.7 + - - +
250c VAL* 3.7 2.9 - - - +
304c LEU* 4.7 23.3 + - + +
305c TYR* 6.1 0.4 - - - -
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Residues in contact with ASN 249 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245c LEU* 2.8 19.5 + - + +
248c ARG* 1.3 87.2 - - - +
250c VAL* 1.3 70.8 + - - +
251c SER* 3.4 21.2 + - - +
276c CYS* 5.8 5.5 - - - +
277c ASP* 5.5 5.5 + - - +
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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