Contacts of the strand formed by residues 229 - 238 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B LYS* 4.0 9.6 - - + -
222B LEU 3.1 11.9 - - - +
223B VAL* 4.1 4.0 - - + -
227B GLY 4.0 0.6 + - - -
228B GLU* 1.3 76.7 - - - +
230B VAL* 1.3 70.3 + - - +
286B PHE* 3.5 26.2 + - + -
421B HIS* 3.6 33.3 - - + +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TYR* 4.1 26.0 - - + +
221B LYS* 3.5 4.9 - - - +
222B LEU* 2.8 49.1 + - + +
228B GLU* 5.8 1.3 - - + -
229B ALA* 1.3 79.1 - - - +
231B TYR* 1.3 65.5 + - - +
283B VAL* 4.0 25.8 - - + -
284B MET 3.8 9.4 - - - +
285B THR* 4.7 13.9 - - + -
286B PHE* 3.8 7.6 - - - -
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B THR* 3.7 20.4 - - + -
220B PHE 3.3 12.3 - - - -
221B LYS* 4.1 21.8 - - + -
230B VAL* 1.3 76.0 - - - +
232B CYS* 1.3 63.0 + - - +
283B VAL* 3.4 4.9 - - - +
284B MET* 2.7 38.4 + - + +
286B PHE* 3.6 33.2 - + - -
289B ALA* 4.1 21.1 - - + -
297B PHE* 3.5 33.6 - + - -
303B TRP* 3.7 10.3 - - + -
346B SER* 4.0 11.7 - - - -
347B PRO* 4.0 8.8 - - + +
423B ILE* 3.7 20.6 - - - +
425B TYR* 4.7 2.1 + - - -
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Residues in contact with CYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B THR* 3.3 8.5 - - - +
220B PHE* 2.8 42.8 + - - +
222B LEU* 3.4 45.3 - - + -
231B TYR* 1.3 76.7 - - - +
233B LYS* 1.3 64.9 + - - +
234B PHE* 3.7 26.7 - - - -
281B ILE* 4.7 3.1 - - + -
282B GLN 2.9 16.4 - - - +
283B VAL* 4.7 3.1 - - + -
303B TRP* 3.7 4.0 - - - -
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PRO 5.0 0.6 + - - -
217B SER* 2.7 25.6 + - - +
218B HIS* 3.4 18.2 - - - +
219B THR* 3.2 24.1 + - - +
232B CYS* 1.3 74.9 - - - +
234B PHE* 1.3 63.8 + - - +
235B HIS* 3.6 7.5 - - + +
281B ILE* 3.1 12.1 - - - +
282B GLN* 3.1 47.2 + - + +
296B PRO 4.5 2.4 + - - -
297B PHE 6.3 0.2 - - - -
298B ASP 5.3 3.8 + - - -
299B LEU* 5.8 1.8 - - - +
301B LYS 4.3 13.9 + - - -
302B VAL* 5.5 1.3 - - - +
303B TRP* 3.5 47.0 - - + +
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Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 4.7 6.3 - + - -
143B TRP* 3.8 29.6 - + - -
145B LEU* 3.7 29.2 - - + -
215B TYR* 3.4 4.4 - - - +
216B GLY* 2.9 32.8 + - - +
217B SER 4.4 1.1 + - - +
218B HIS 4.8 1.6 + - - -
220B PHE* 3.5 47.1 - + + -
222B LEU* 4.1 15.5 - - + -
232B CYS* 3.7 15.9 - - - -
233B LYS* 1.3 73.2 - - - +
235B HIS* 1.3 66.0 + - - +
236B TYR* 4.7 0.9 - - - -
279B PHE* 3.8 23.6 - + + -
280B TYR 3.9 0.9 - - - -
281B ILE* 3.9 17.9 - - + -
343B ILE* 4.5 5.6 - - + -
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Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PRO* 5.2 6.1 - - + -
214B GLY 3.7 5.4 - - - +
215B TYR* 3.4 32.8 - + + -
233B LYS* 3.6 19.1 - - + +
234B PHE* 1.3 78.6 - - - +
236B TYR* 1.3 62.6 + - - +
237B LYS* 4.0 9.7 - - + -
278B THR 4.2 0.2 - - - -
279B PHE* 3.4 4.0 - - - -
280B TYR* 2.7 53.7 + - + +
282B GLN* 2.7 38.0 + - + -
305B HIS* 4.1 17.1 + - - -
310B LEU* 3.6 19.3 - - + +
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 2.9 60.7 + + - -
134B VAL* 4.0 13.9 - - + +
145B LEU* 3.8 22.3 + - + +
147B GLY* 3.6 16.8 + - - -
214B GLY* 2.8 59.3 + - - -
215B TYR* 3.7 14.8 - - - -
216B GLY 4.3 1.1 - - - -
234B PHE 4.7 0.7 - - - -
235B HIS* 1.3 79.9 - - - +
237B LYS* 1.3 61.7 + - - +
277B TRP* 3.3 22.1 - - + -
278B THR 3.1 6.1 - - - +
279B PHE* 3.8 24.0 - + + -
316B LEU* 3.8 9.9 - - + -
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASN* 3.4 29.5 - - + +
215B TYR* 4.6 16.6 - - + -
235B HIS* 5.0 6.3 - - + -
236B TYR* 1.3 74.7 - - - +
238B THR* 1.3 65.5 + - - +
239B ASP* 3.4 1.7 + - - +
277B TRP* 3.1 5.2 - - - -
278B THR* 2.9 31.7 + - - +
280B TYR* 3.8 28.0 - - + -
305B HIS* 4.9 12.4 - - - -
310B LEU* 4.0 21.3 - - - +
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ARG 2.8 23.2 + - - -
212B MET 3.3 25.6 - - - +
213B ASN* 2.9 17.5 + - - +
237B LYS* 1.3 73.1 - - - +
239B ASP* 1.3 61.5 + - - +
240B GLN* 3.1 12.4 + - - -
241B GLY* 3.3 32.9 + - - +
242B ILE* 3.7 9.0 - - + +
277B TRP* 3.4 12.6 - - - -
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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