Contacts of the helix formed by residues 240 - 252 (chain C) in PDB entry 2J2M
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 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ARG* 2.7 33.3 + - - +
102C HIS* 5.1 2.4 - - - -
105C GLU* 3.1 13.8 - - - +
238C ASP* 3.0 14.0 + - - +
239C PHE* 1.3 106.0 - - - +
241C HIS* 1.3 55.3 + - - +
243C SER* 4.7 2.9 - - - -
244C ASN* 3.0 27.4 + - - +
99D HIS* 5.9 0.3 - - - -
156D ASN 4.3 5.9 - - - +
157D ILE* 3.8 38.7 - - + +
158D GLN 5.6 0.4 - - - +
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Residues in contact with HIS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLU* 3.2 31.0 + - - +
106C THR* 3.4 26.1 - - + +
187C PRO 4.3 6.3 + - - -
188C ALA 2.7 31.4 + - - -
189C SER* 5.1 1.1 - - - -
226C LEU* 4.3 7.6 - - + +
234C VAL* 3.6 24.9 - - + -
238C ASP* 3.5 24.3 + - + +
239C PHE 3.5 2.8 + - - -
240C ASN* 1.3 76.3 - - - +
242C ALA* 1.3 69.4 + - + +
244C ASN* 3.4 1.4 + - - +
245C ASP* 2.9 31.8 + - + +
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Residues in contact with ALA 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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105C GLU* 3.0 15.7 + - + +
111C ARG* 6.2 1.1 - - - +
187C PRO 5.9 0.7 - - - +
189C SER* 4.2 7.6 - - - -
190C TYR* 3.7 39.0 - - + +
241C HIS* 1.3 95.1 + - + +
243C SER* 1.3 60.0 + - - +
245C ASP* 3.5 1.0 + - - +
246C THR* 2.7 37.8 + - - -
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Residues in contact with SER 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ARG* 4.1 8.6 + - - -
59C GLY 3.8 7.7 + - - -
60C PHE* 3.5 31.1 - - - +
105C GLU* 2.7 36.6 + - - -
190C TYR* 3.7 4.9 - - - -
240C ASN* 3.9 7.0 - - - -
242C ALA* 1.3 73.3 - - - +
244C ASN* 1.3 56.1 + - - +
247C PHE* 2.9 32.1 + - - +
306C TYR* 6.4 0.7 - - - -
155D THR 5.0 10.2 - - - +
156D ASN* 5.7 3.8 + - - -
157D ILE* 4.9 3.1 - - - -
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Residues in contact with ASN 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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238C ASP* 3.2 21.9 + - - +
240C ASN 3.0 19.3 + - - +
241C HIS 3.6 4.9 - - - +
243C SER* 1.3 75.2 - - - +
245C ASP* 1.3 63.6 + - - +
247C PHE* 3.8 3.3 - - - +
248C GLN* 3.0 38.5 + - - +
157D ILE* 3.6 26.7 - - + +
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Residues in contact with ASP 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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189C SER* 2.7 30.3 + - - +
191C ARG* 2.7 37.4 + - - -
192C LYS* 5.6 1.5 + - - -
241C HIS* 2.9 20.6 + - + +
242C ALA 3.8 3.1 - - - +
244C ASN* 1.3 77.4 - - - +
246C THR* 1.3 57.0 + - - +
248C GLN* 3.4 4.9 + - - +
249C ALA* 2.9 28.8 + - - +
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Residues in contact with THR 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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60C PHE* 3.3 33.2 - - + -
94C PHE* 5.2 5.8 - - + -
189C SER* 3.5 8.1 + - - -
190C TYR* 3.5 21.2 - - + +
191C ARG* 3.6 23.1 - - + +
242C ALA 2.7 24.3 + - - -
243C SER 4.2 0.2 - - - -
245C ASP* 1.3 72.0 - - - +
247C PHE* 1.3 67.7 + - - +
249C ALA* 3.7 0.9 - - - +
250C ILE* 3.4 24.0 + - + +
256C PRO* 4.4 11.7 - - + -
258C TRP* 5.9 0.2 - - + -
299C LEU* 5.9 1.1 - - + -
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Residues in contact with PHE 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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60C PHE* 3.9 11.8 - + + -
243C SER 2.9 19.6 + - - +
244C ASN* 3.8 5.6 - - - +
246C THR* 1.3 76.9 - - - +
248C GLN* 1.3 77.1 + - + +
250C ILE 3.3 2.6 + - - -
251C GLU* 3.1 28.3 + - + +
302C ASN* 3.1 56.1 + - + -
303C VAL* 5.4 1.3 - - + -
154D ARG* 3.7 51.8 - - + -
155D THR* 3.5 40.8 - - + +
157D ILE* 6.1 1.1 - - + -
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Residues in contact with GLN 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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244C ASN* 3.0 32.8 + - - +
245C ASP* 3.9 4.7 - - - +
247C PHE* 1.3 90.8 - - + +
249C ALA* 1.3 59.5 + - - +
251C GLU* 3.4 9.4 + - - +
252C ASN* 2.8 58.3 + - - +
155D THR* 5.4 2.4 - - - +
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Residues in contact with ALA 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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191C ARG* 3.7 33.0 - - - +
245C ASP 2.9 18.5 + - - +
246C THR 3.7 5.8 - - - +
247C PHE 3.3 0.2 - - - -
248C GLN* 1.3 78.2 - - - +
250C ILE* 1.3 56.5 + - - +
252C ASN* 3.3 3.3 + - - +
253C GLY 3.3 2.6 + - - -
254C ASP* 2.8 51.1 + - + +
256C PRO* 4.8 3.4 - - + -
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Residues in contact with ILE 250 (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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60C PHE* 4.4 6.5 - - + -
62C ALA* 3.6 31.0 - - + -
246C THR* 3.4 14.3 + - + +
247C PHE 3.3 2.3 + - - +
249C ALA* 1.3 74.5 - - - +
251C GLU* 1.3 58.5 + - - +
253C GLY 2.9 17.0 + - - -
254C ASP 4.7 0.4 - - - -
255C PHE* 3.4 18.2 - - + -
256C PRO* 3.7 13.5 - - + -
299C LEU* 3.6 28.3 - - + +
300C ASN* 3.9 6.5 - - - +
301C LYS* 3.6 23.8 - - - +
302C ASN* 3.5 28.3 - - - +
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Residues in contact with GLU 251 (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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247C PHE* 3.1 25.2 + - + +
248C GLN* 3.8 14.8 - - - +
250C ILE* 1.3 77.2 - - - +
252C ASN* 1.3 61.9 + - - +
253C GLY 3.2 1.1 + - - -
302C ASN* 2.8 23.7 + - - +
154D ARG* 2.6 34.3 + - - -
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Residues in contact with ASN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLN* 2.8 43.6 + - - +
249C ALA* 3.8 6.4 - - - +
250C ILE 3.2 0.2 - - - -
251C GLU* 1.3 78.1 - - - +
253C GLY* 1.3 59.5 + - - +
254C ASP* 3.3 6.4 + - + +
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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