Contacts of the strand formed by residues 229 - 238 (chain D) in PDB entry 1DGH
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 ALA 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D TYR 5.6 0.2 - - - -
221D LYS* 3.8 17.5 - - + -
222D LEU 3.1 13.5 - - - +
223D VAL* 4.2 3.1 - - + -
227D GLY 3.9 0.8 + - - -
228D GLU* 1.3 74.8 - - - +
230D VAL* 1.3 71.1 + - - +
286D PHE* 3.2 19.5 + - + -
421D HIS* 3.6 34.7 - - + +
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Residues in contact with VAL 230 (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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94D TYR* 4.0 30.5 - - + +
221D LYS* 3.3 6.6 - - - +
222D LEU* 2.9 43.6 + - + +
228D GLU* 5.9 0.7 - - + -
229D ALA* 1.3 79.9 - - - +
231D TYR* 1.3 65.4 + - - +
283D VAL* 4.1 22.7 - - + -
284D MET 4.0 6.1 - - - +
285D THR* 4.4 17.7 - - + -
286D PHE* 3.8 7.2 - - - +
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Residues in contact with TYR 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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219D THR* 3.7 19.5 - - + -
220D PHE 3.3 14.6 - - - -
221D LYS* 4.1 14.1 - - + -
230D VAL* 1.3 76.1 - - - +
232D CYS* 1.3 64.3 + - - +
283D VAL* 3.5 3.5 - - - +
284D MET* 2.8 38.8 + - + +
286D PHE* 3.7 38.1 - + + -
289D ALA* 3.9 25.1 - - + -
297D PHE* 3.6 32.4 - + - -
303D TRP* 3.7 8.7 - - + -
346D SER* 4.2 9.9 - - - -
347D PRO* 4.3 7.0 - - + +
423D ILE* 3.7 21.0 - - + +
425D TYR* 4.8 1.6 + - - -
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Residues in contact with CYS 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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218D HIS 3.9 0.2 - - - +
219D THR* 3.3 7.4 - - - -
220D PHE* 2.8 49.6 + - - +
222D LEU* 3.7 37.0 - - + -
231D TYR* 1.3 75.8 - - - +
233D LYS* 1.3 68.7 + - - +
234D PHE* 3.9 26.9 - - - -
281D ILE* 4.8 3.1 - - + -
282D GLN 2.9 15.9 - - - +
283D VAL* 4.8 2.7 - - + -
303D TRP* 3.6 4.4 - - - -
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Residues in contact with LYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D PRO 5.1 0.8 + - - -
217D SER* 2.7 27.4 + - - +
218D HIS* 3.6 14.5 - - - +
219D THR* 3.2 26.9 + - - +
232D CYS* 1.3 75.3 - - - +
234D PHE* 1.3 62.9 + - - +
235D HIS* 3.5 22.2 - - + +
281D ILE* 3.1 11.6 - - - +
282D GLN* 3.0 36.0 + - + +
296D PRO 4.4 3.4 + - - -
297D PHE 6.3 0.2 - - - -
298D ASP 5.3 3.2 + - - -
299D LEU* 5.5 1.8 - - - +
301D LYS 4.3 13.6 + - - -
302D VAL* 5.4 0.9 - - - +
303D TRP* 3.5 44.2 - - + +
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Residues in contact with PHE 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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100D PHE* 4.6 5.6 - + - -
143D TRP* 3.7 29.8 - + - -
145D LEU* 3.8 30.5 - - + -
215D TYR* 3.5 4.0 - - - +
216D GLY* 2.9 31.6 + - - +
217D SER 4.5 1.3 + - - +
218D HIS 5.0 1.2 + - - -
220D PHE* 3.6 44.6 - + + -
222D LEU* 4.2 16.2 - - + -
232D CYS* 3.9 14.6 - - - -
233D LYS* 1.3 74.2 - - - +
235D HIS* 1.3 65.9 + - - +
236D TYR* 4.6 1.6 - - + -
279D PHE* 3.6 24.5 - + + -
280D TYR 3.7 1.3 - - - -
281D ILE* 3.7 19.3 - - + -
343D ILE* 4.3 7.4 - - + -
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Residues in contact with HIS 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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151D PRO* 5.1 7.2 - - + -
214D GLY 3.7 4.5 - - - -
215D TYR* 3.3 31.8 - + + +
233D LYS* 3.5 21.0 - - + +
234D PHE* 1.3 80.1 + - - +
236D TYR* 1.3 62.6 + - - +
237D LYS* 4.1 5.5 - - + +
278D THR 3.7 0.6 - - - +
279D PHE* 3.4 3.1 - - - -
280D TYR* 2.6 54.6 + - + +
282D GLN* 2.7 34.4 + - + -
305D HIS* 4.1 15.5 + - - -
310D LEU* 3.8 21.1 - - + +
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Residues in contact with TYR 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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132D PHE* 2.8 57.5 + + - -
134D VAL* 4.0 12.5 - - + +
145D LEU* 4.0 22.2 + - + +
147D GLY* 3.7 15.2 + - - -
213D ASN* 4.7 0.7 - - - -
214D GLY* 2.8 70.8 + - - -
215D TYR 3.7 9.8 + - - -
216D GLY 4.3 0.7 - - - -
234D PHE 4.7 0.4 - - - -
235D HIS* 1.3 80.0 - - - +
237D LYS* 1.3 61.1 + - - +
277D TRP* 3.3 13.8 - + + -
278D THR 3.2 8.1 - - - +
279D PHE* 4.0 17.5 - + + -
316D LEU* 3.6 25.4 - - + -
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Residues in contact with LYS 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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213D ASN* 3.4 25.1 - - + +
215D TYR* 5.8 5.4 - - + -
235D HIS* 5.3 4.7 - - + +
236D TYR* 1.3 74.3 - - - +
238D THR* 1.3 66.0 + - - +
239D ASP* 3.5 2.7 - - - +
277D TRP* 3.1 4.0 - - - -
278D THR* 2.7 35.1 + - - +
280D TYR* 4.0 30.5 - - + +
305D HIS* 5.4 8.8 - - - -
310D LEU* 4.2 22.3 - - + +
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Residues in contact with THR 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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210D ARG 2.7 22.5 + - - -
212D MET 3.4 26.7 - - - +
213D ASN* 3.2 16.6 + - - +
237D LYS* 1.3 73.9 - - - +
239D ASP* 1.3 61.2 + - - +
240D GLN* 2.8 16.3 + - - +
241D GLY* 3.6 29.6 + - - +
242D ILE* 4.0 7.2 - - + +
277D TRP* 3.3 15.3 - - - -
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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