Contacts of the helix formed by residues 236 - 246 (chain C) in PDB entry 3JXI
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 CYS 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C LEU* 3.9 20.9 - - + -
191C GLY* 3.5 21.3 - - - -
231C ALA* 2.9 16.5 + - - +
234C ARG 4.1 3.1 - - - +
235C ARG* 1.3 75.9 - - - +
237C LYS* 1.3 64.5 + - - +
238C HIS* 3.1 9.0 + - - -
239C TYR* 3.2 38.9 + - + +
240C VAL* 3.1 21.3 + - - +
283C GLN* 4.6 0.2 + - - -
286C ILE* 4.6 0.8 - - - +
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Residues in contact with LYS 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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235C ARG 3.9 3.4 + - - -
236C CYS* 1.3 73.4 - - - +
238C HIS* 1.3 52.8 + - - +
240C VAL* 3.1 8.5 + - + +
241C GLU* 2.8 60.5 + - + +
285C HIS* 3.7 31.2 + - + +
286C ILE* 4.0 19.5 - - + +
289C TYR* 3.1 34.8 - - + +
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Residues in contact with HIS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ARG* 3.6 46.0 + - - +
236C CYS* 3.1 8.7 + - - -
237C LYS* 1.3 79.2 - - - +
239C TYR* 1.3 92.2 + + - +
241C GLU* 3.5 12.4 - - - +
242C LEU* 3.0 34.8 + - + +
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Residues in contact with TYR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.9 26.0 - - + -
188C LEU* 3.8 18.6 - - + -
191C GLY 3.7 17.5 - - - -
192C ARG* 3.3 12.6 - - - -
193C ASN 2.9 28.2 + - - -
194C ASP* 4.2 3.8 + - - -
196C ILE* 3.9 32.1 - - + -
197C PRO* 4.8 4.9 - - + +
231C ALA* 4.2 8.1 - - + -
236C CYS* 3.2 25.7 + - - +
238C HIS* 1.3 100.4 - + - +
240C VAL* 1.3 61.0 + - - +
242C LEU* 3.8 13.5 - - + -
243C LEU* 2.9 38.2 + - + +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 4.2 16.8 - - + -
231C ALA* 3.7 29.4 - - + +
232C ILE* 3.8 14.6 - - + -
236C CYS 3.1 14.1 + - - +
237C LYS* 3.3 9.9 - - + +
239C TYR* 1.3 77.6 - - - +
241C GLU* 1.3 63.8 + - - +
243C LEU* 3.8 0.9 - - - +
244C VAL* 2.9 27.9 + - - +
286C ILE* 3.9 29.2 - - + -
289C TYR* 4.2 19.3 - - + -
290C LEU* 4.3 8.7 - - + -
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LYS* 2.8 54.8 + - + +
238C HIS* 3.5 13.0 - - - +
240C VAL* 1.3 74.1 - - - +
242C LEU* 1.3 58.1 + - - +
244C VAL 3.3 0.2 + - - -
245C GLU* 2.8 45.6 + - - +
289C TYR* 3.3 38.5 + - + +
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Residues in contact with LEU 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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196C ILE* 4.2 7.4 - - + -
197C PRO* 4.5 15.9 - - + -
200C LEU* 3.7 27.6 - - + -
238C HIS* 3.0 26.0 + - + +
239C TYR* 3.9 27.1 - - + +
240C VAL 3.4 0.2 - - - -
241C GLU* 1.3 73.7 - - - +
243C LEU* 1.3 64.2 + - + +
245C GLU* 3.4 20.6 + - - +
246C LYS* 3.1 43.8 + - + +
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Residues in contact with LEU 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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181C LEU* 3.8 32.3 - - + -
185C LEU* 4.1 8.1 - - + -
196C ILE* 5.5 2.5 - - + -
200C LEU* 4.2 18.2 - - + -
213C ILE* 3.9 16.9 - - + +
227C ALA* 3.8 31.6 - - + +
228C LEU* 4.0 6.7 - - + +
231C ALA* 3.8 14.1 - - + -
239C TYR* 2.9 28.4 + - + +
240C VAL 3.9 2.2 - - - +
242C LEU* 1.3 78.1 - - + +
244C VAL* 1.3 58.5 + - - +
246C LYS 3.4 2.3 + - - -
247C GLY 3.2 5.7 + - - -
248C ALA* 2.8 34.8 + - + +
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Residues in contact with VAL 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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228C LEU* 4.2 13.2 - - + -
240C VAL 2.9 21.0 + - - +
243C LEU* 1.3 73.6 - - - +
245C GLU* 1.3 64.6 + - - +
247C GLY* 3.1 13.9 + - - -
248C ALA* 4.0 7.3 + - + +
250C VAL* 4.0 17.5 - - + -
289C TYR* 3.8 15.3 - - + +
290C LEU* 4.0 26.0 - - + -
293C ASN* 3.9 13.0 - - - +
295C HIS* 4.4 5.9 - - + +
296C LYS* 3.6 35.3 + - + +
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Residues in contact with GLU 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 GLU* 2.8 40.5 + - - +
242C LEU* 3.4 26.2 + - - +
244C VAL* 1.3 72.7 - - - +
246C LYS* 1.3 64.0 + - + +
247C GLY 3.7 0.5 + - - -
289C TYR* 3.9 4.4 + - - +
295C HIS* 3.5 46.7 + - + +
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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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197C PRO* 5.0 3.4 + - - +
200C LEU* 4.0 19.1 - - + +
201C ASP* 4.5 11.1 + - - +
204C GLU* 4.1 14.0 + - - -
209C MET* 3.0 44.1 - - + +
210C ARG* 3.6 15.3 - - - +
213C ILE* 3.7 22.6 - - + +
242C LEU* 3.1 29.2 + - + +
243C LEU 3.4 2.4 + - - -
244C VAL 3.1 0.2 - - - -
245C GLU* 1.3 82.8 - - + +
247C GLY* 1.3 56.7 + - - +
248C ALA 3.8 0.2 - - - -
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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