Contacts of the helix formed by residues 225 - 241 (chain A) in PDB entry 2JDQ
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 ARG 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 4.1 26.9 + - + +
184A ASP* 2.8 44.5 + - - +
187A GLU* 2.8 27.3 + - - +
224A ASN* 1.3 79.4 + - - +
226A LEU* 1.3 66.2 + - - +
227A THR* 3.4 18.3 + - - +
228A MET* 3.4 17.6 + - + +
229A THR* 3.3 12.7 + - - -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASN 3.9 0.2 + - - -
225A ARG* 1.3 75.1 - - - +
227A THR* 1.3 58.5 + - + +
229A THR* 3.4 10.0 + - + -
230A ARG* 3.1 63.9 + - - +
265A VAL* 5.1 7.4 - - + -
267A ASP* 3.8 28.3 - - + +
270A VAL* 4.7 6.7 - - + -
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 2.8 20.7 + - - -
225A ARG* 3.4 23.3 + - + -
226A LEU* 1.3 74.5 - - + +
228A MET* 1.3 59.6 + - - +
230A ARG* 3.7 16.8 + - - +
231A ASN* 2.6 39.7 + - - -
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Residues in contact with MET 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU* 4.1 7.2 - - + +
186A GLN* 3.7 36.6 - - + +
187A GLU* 3.3 38.3 + - + +
190A VAL* 5.1 2.5 - - - -
219A LEU* 3.9 35.0 - - + -
224A ASN* 3.6 32.5 - - + +
225A ARG* 3.4 15.2 + - + +
227A THR* 1.3 79.3 + - - +
229A THR* 1.3 62.0 + - - +
231A ASN* 3.2 3.1 + - - +
232A ALA* 2.9 30.6 + - + +
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.9 10.6 - - + -
224A ASN* 4.3 13.3 + - - +
225A ARG 3.3 12.0 + - - -
226A LEU* 3.4 14.2 + - + -
228A MET* 1.3 77.4 - - - +
230A ARG* 1.3 52.0 + - - +
232A ALA* 3.5 5.5 + - - +
233A VAL* 2.7 39.8 + - - +
261A TRP* 6.4 0.2 - - + -
262A LEU* 4.3 15.9 - - + -
265A VAL* 5.6 4.9 - - + -
270A VAL* 3.9 26.0 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.1 42.4 + - - +
227A THR* 3.8 15.9 - - - +
229A THR* 1.3 74.4 - - - +
231A ASN* 1.3 59.5 + - - +
233A VAL* 4.0 2.0 - - - +
234A TRP* 3.0 30.7 + - - +
267A ASP* 2.7 35.3 + - - +
269A ASP* 3.4 30.6 + - + -
270A VAL* 3.5 22.0 - - + +
273A ASP* 4.3 4.8 - - - +
753E ARG* 5.9 0.4 - - - -
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Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.1 28.8 + - + +
190A VAL* 3.1 25.3 - - + +
191A TRP* 3.6 24.4 - - - +
227A THR* 2.6 27.7 + - - +
228A MET* 3.2 4.5 + - - +
230A ARG* 1.3 81.1 - - - +
232A ALA* 1.3 58.5 + - - +
234A TRP* 3.7 8.6 - - - +
235A ALA* 3.1 22.0 + - - +
753E ARG* 2.7 32.0 + - - +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 3.8 10.1 - - + +
216A LEU* 4.5 6.4 - - + +
219A LEU* 4.5 23.3 - - + -
220A PHE* 3.3 32.1 - - + -
228A MET* 2.9 18.5 + - + +
229A THR* 4.4 0.4 - - - -
231A ASN* 1.3 76.2 - - - +
233A VAL* 1.3 59.8 + - - +
235A ALA* 3.5 3.3 + - - +
236A LEU* 3.0 26.5 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.7 6.5 - - + -
229A THR 2.7 26.6 + - - +
230A ARG* 4.2 4.0 - - - +
232A ALA* 1.3 73.9 - - - +
234A TRP* 1.3 61.5 + - - +
236A LEU* 3.2 6.6 - - + +
237A SER* 2.9 28.6 + - - -
259A LEU* 4.4 8.7 - - + -
262A LEU* 3.8 27.6 - - + -
270A VAL* 3.8 24.7 - - + +
273A ASP* 4.0 9.0 - - + +
274A ALA* 3.8 31.4 - - + +
277A ALA* 5.6 0.2 - - + -
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Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 3.7 26.2 - + - -
194A GLY* 3.6 25.4 - - - -
195A ASN* 3.1 28.3 - - - -
230A ARG 3.0 20.0 + - - +
231A ASN* 3.7 11.4 - - - +
233A VAL* 1.3 77.3 - - - +
235A ALA* 1.3 72.4 + - + +
237A SER* 2.6 28.3 + - - -
238A ASN* 3.1 28.8 + - - +
273A ASP* 3.7 23.7 + - - +
750E ALA 3.8 17.1 + - - -
751E THR 3.8 7.2 - - - -
752E LYS* 4.2 0.4 - - - -
753E ARG* 3.7 43.8 - - + +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 3.9 25.4 - - + +
193A LEU 5.3 0.2 - - - -
194A GLY* 4.1 15.1 - - - +
197A ALA* 5.1 0.3 - - - +
212A ILE* 5.7 3.8 - - + -
216A LEU* 4.5 12.6 - - + -
231A ASN 3.1 18.4 + - - +
232A ALA 3.7 4.7 - - - +
234A TRP* 1.3 82.8 - - + +
236A LEU* 1.3 61.7 + - - +
238A ASN* 3.0 6.6 + - - +
239A LEU* 3.0 27.6 + - + +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.0 20.2 - - + -
216A LEU* 4.1 11.4 - - + +
217A LEU* 4.1 6.1 - - + -
220A PHE* 4.3 21.1 - - + -
232A ALA 3.0 13.4 + - - +
233A VAL* 3.2 12.3 - - + +
235A ALA* 1.3 75.6 - - - +
237A SER* 1.3 61.8 + - - +
239A LEU* 3.0 20.9 + - + +
240A CYS* 3.1 20.4 + - - -
252A VAL* 6.3 0.7 - - + -
255A CYS* 3.7 34.3 - - + -
258A VAL* 4.5 5.8 - - + -
259A LEU* 3.4 32.5 - - + -
277A ALA* 4.9 0.7 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL 2.9 13.3 + - - -
234A TRP* 2.6 30.2 + - - -
236A LEU* 1.3 74.3 - - - +
238A ASN* 1.3 65.0 + - - +
240A CYS 3.3 1.2 + - - -
241A ARG* 3.2 25.2 + - - +
273A ASP* 3.7 23.9 + - - -
276A TRP* 4.7 4.0 - - - -
277A ALA* 3.9 19.9 - - - +
280A TYR* 3.6 14.5 - - - -
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY* 3.0 28.3 + - - +
197A ALA* 4.2 14.1 - - + +
198A GLY* 3.8 8.8 - - - +
204A ARG* 3.7 12.6 - - - +
234A TRP* 3.1 26.3 + - - +
235A ALA* 3.0 11.7 + - - +
237A SER* 1.3 81.7 + - - +
239A LEU* 1.3 63.0 + - - +
241A ARG* 3.6 41.4 + - - +
751E THR* 3.0 26.7 + - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ALA* 3.9 20.4 - - + -
204A ARG* 3.3 27.5 - - - +
207A VAL* 4.1 18.8 - - + -
208A LEU* 4.2 22.1 - - + +
212A ILE* 4.0 21.1 - - + -
213A LEU* 4.3 11.7 - - + -
216A LEU* 3.5 31.9 - - + -
235A ALA* 3.0 16.8 + - + +
236A LEU* 3.0 11.4 + - + +
238A ASN* 1.3 78.3 - - - +
240A CYS* 1.3 59.0 + - - +
241A ARG 3.3 0.7 - - - -
247A PRO* 3.8 11.3 - - - +
252A VAL* 3.9 7.2 - - + +
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Residues in contact with CYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.1 19.7 + - - -
237A SER 3.3 7.8 + - - +
239A LEU* 1.3 75.0 - - - +
241A ARG* 1.3 61.1 + - - +
242A GLY 4.1 1.2 + - - +
247A PRO* 3.8 16.0 - - - +
252A VAL* 2.9 34.5 - - + -
255A CYS* 4.1 10.8 - - - -
277A ALA* 4.0 20.6 - - - +
280A TYR* 3.3 20.9 - - + +
281A LEU* 3.8 25.1 - - + +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLY* 6.3 0.7 - - - -
204A ARG* 2.8 30.0 + - - -
237A SER* 3.2 15.0 + - - +
238A ASN* 3.6 32.8 + - - +
239A LEU 3.3 1.0 - - - -
240A CYS* 1.3 79.2 - - - +
242A GLY* 1.3 65.4 + - - +
280A TYR* 3.6 37.0 + - + -
749E THR* 3.3 41.6 + - - +
750E ALA 3.9 14.3 + - - -
751E THR* 4.0 16.8 + - - +
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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