Contacts of the helix formed by residues 230 - 244 (chain D) in PDB entry 6Q2J
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 ASP 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D ARG* 5.5 1.7 + - - -
226D SER 3.9 9.0 - - - +
227D CYS 2.9 12.3 + - - +
228D GLN 3.2 0.6 - - - -
229D ASN* 1.3 80.9 - - - +
231D GLU* 1.3 63.2 + - - +
232D LEU* 3.6 10.6 + - - +
233D CYS* 3.5 20.4 + - + +
234D ARG* 2.8 28.1 + - - +
285D THR* 5.6 1.6 - - - +
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Residues in contact with GLU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D GLN 5.7 0.5 - - - +
229D ASN 5.9 1.6 - - - -
230D ASP* 1.3 74.8 + - - +
232D LEU* 1.3 61.2 + - - +
234D ARG* 3.2 38.4 + - - +
235D ARG* 3.0 37.8 + - + +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ARG* 3.4 43.3 - - - +
230D ASP* 3.5 9.4 + - - +
231D GLU* 1.3 75.3 - - - +
233D CYS* 1.3 59.9 - - - +
235D ARG* 3.4 20.8 + - - +
236D HIS* 2.5 64.0 + - + +
281D ASP 5.8 0.7 - - - +
285D THR* 4.0 11.2 - - + -
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Residues in contact with CYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D CYS* 2.0 58.9 - - - +
230D ASP* 3.5 13.0 + - + +
231D GLU 3.4 0.2 - - - -
232D LEU* 1.3 79.2 - - - +
234D ARG* 1.3 59.4 + - - +
236D HIS* 4.5 3.6 - - - +
237D TYR* 2.8 34.7 + - - +
285D THR* 3.5 39.7 - - + -
286D VAL* 4.6 2.0 - - - -
287D LEU* 3.7 9.0 - - - -
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Residues in contact with ARG 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D CYS* 3.7 6.7 + - - +
228D GLN* 4.3 24.8 + - + +
230D ASP 2.8 19.4 + - - +
231D GLU* 3.2 40.0 + - - +
233D CYS* 1.3 76.7 - - - +
235D ARG* 1.3 59.3 + - + +
237D TYR* 3.9 1.7 - - - -
238D ARG* 2.9 31.6 + - + +
254D GLU* 3.8 17.8 + - - +
76F TYR* 5.7 8.7 + - - -
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLU* 3.0 24.2 + - - +
232D LEU* 3.9 29.6 - - - +
234D ARG* 1.3 77.5 - - + +
236D HIS* 1.3 73.3 + - + +
238D ARG* 3.3 8.6 + - - +
239D THR* 3.0 32.0 + - - -
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Residues in contact with HIS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLN* 5.4 8.2 + - - -
232D LEU* 2.5 62.7 + - + +
233D CYS* 4.1 4.5 - - - +
235D ARG* 1.3 94.9 + - - +
237D TYR* 1.3 58.0 + - - +
239D THR* 3.4 9.1 + - - -
240D PHE 2.9 20.8 + - - -
278D ALA* 4.7 1.2 - - - +
281D ASP* 3.4 43.6 + - + +
282D ILE* 3.4 26.0 - - + +
285D THR* 5.6 2.0 - - + -
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Residues in contact with TYR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ILE* 4.3 14.1 - - + +
227D CYS* 3.8 12.8 - - + -
228D GLN* 3.9 27.8 - - + -
233D CYS 2.8 18.8 + - - +
234D ARG 4.2 1.8 - - - +
236D HIS* 1.3 74.1 - - - +
238D ARG* 1.3 60.4 + - - +
240D PHE* 4.1 20.4 - + - -
241D GLN* 2.9 64.9 + - + +
254D GLU* 3.5 16.2 - - + -
259D ILE* 4.8 2.2 - - + +
282D ILE* 4.1 2.8 - - - +
287D LEU* 4.0 18.4 - - + -
307D PHE* 3.8 25.3 - + - -
310D MET* 4.1 4.5 - - + +
311D LEU* 4.3 14.8 - - + -
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 2.9 21.6 + - + +
235D ARG* 3.5 8.7 - - - +
237D TYR* 1.3 77.9 - - - +
239D THR* 1.3 57.2 + - - +
241D GLN* 3.4 5.1 + - - +
242D SER* 3.0 44.2 + - - +
253D HIS 5.4 4.5 - - - +
254D GLU* 3.5 22.1 + - - +
76F TYR* 5.6 4.0 + - - -
116F PHE* 3.9 30.3 - - - -
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Residues in contact with THR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG 3.0 14.3 + - - -
236D HIS* 3.5 11.7 - - - -
237D TYR 3.3 0.2 - - - -
238D ARG* 1.3 78.0 + - - +
240D PHE* 1.3 55.5 + - - +
242D SER* 3.2 4.8 + - - -
243D LYS* 2.9 58.2 + - + +
278D ALA* 4.0 17.9 - - + -
281D ASP* 5.8 4.3 - - + +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D HIS 2.9 17.2 + - - +
237D TYR* 3.2 26.0 + + - +
239D THR* 1.3 76.5 - - - +
241D GLN* 1.3 63.9 + - - +
244D CYS* 3.4 48.2 + - - +
245D TRP* 4.3 14.1 + + - -
275D CYS* 4.7 1.1 - - - -
278D ALA* 3.7 7.8 - - + +
279D TYR* 3.8 48.0 - + + -
282D ILE* 4.0 20.9 - - + -
310D MET* 3.7 27.1 - - + -
311D LEU* 4.5 11.0 - - + -
316D CYS* 6.3 1.8 - - - -
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Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D TYR* 2.9 62.0 + - + +
238D ARG* 3.7 5.6 - - - +
240D PHE* 1.3 85.0 - - - +
242D SER* 1.3 58.9 + - - +
243D LYS 3.4 0.5 + - - -
245D TRP* 3.2 20.1 + - - +
248D VAL* 3.6 31.1 + - - +
249D THR* 2.4 25.7 + - - +
253D HIS 4.2 16.1 + - - +
254D GLU* 4.4 9.8 - - + +
259D ILE* 4.2 9.3 - - - +
310D MET* 3.7 17.6 - - - +
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ARG* 3.0 32.9 + - - +
239D THR* 3.2 5.3 + - - -
241D GLN* 1.3 77.5 - - - +
243D LYS* 1.3 74.3 + - - +
246D GLN* 3.6 18.2 + - - +
249D THR* 3.5 23.0 + - - +
253D HIS 5.6 0.9 + - - -
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D THR* 2.9 41.4 + - + +
242D SER* 1.3 93.7 - - - +
244D CYS* 1.3 62.5 - - - +
246D GLN* 3.5 20.3 + - - +
270D SER* 4.1 7.4 - - - -
272D SER* 4.6 4.5 + - - -
274D ASP* 3.7 54.9 - - + +
275D CYS* 4.0 6.4 - - - +
278D ALA* 4.4 2.2 - - + -
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Residues in contact with CYS 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D PHE* 3.4 40.0 + - + +
243D LYS* 1.3 78.3 - - - +
245D TRP* 1.3 80.3 + - + +
246D GLN 3.4 5.1 + - - -
268D THR 4.5 1.2 - - - +
269D CYS* 4.4 3.1 - - - -
270D SER* 3.4 30.3 + - - +
275D CYS* 2.0 57.2 - - - -
278D ALA* 4.8 0.4 - - - -
316D CYS* 5.5 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