Contacts of the strand formed by residues 229 - 238 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C LYS* 3.9 13.5 - - + -
222C LEU 3.2 11.0 - - - +
223C VAL* 4.2 3.8 - - + -
227C GLY 3.8 0.6 + - - -
228C GLU* 1.3 77.0 - - - +
230C VAL* 1.3 70.0 + - - +
286C PHE* 3.6 18.8 + - + +
421C HIS* 3.6 39.8 - - + +
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Residues in contact with VAL 230 (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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94C TYR* 4.1 24.5 - - + +
221C LYS* 3.4 5.5 - - - +
222C LEU* 2.8 48.2 + - + +
228C GLU* 5.8 0.7 - - + -
229C ALA* 1.3 81.4 - - - +
231C TYR* 1.3 65.3 + - - +
283C VAL* 3.8 30.1 - - + -
284C MET 3.9 4.0 - - - +
285C THR* 4.4 19.5 - - + -
286C PHE* 4.0 6.3 - - - -
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Residues in contact with TYR 231 (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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219C THR* 3.7 15.5 - - + -
220C PHE 3.1 13.0 - - - +
221C LYS* 4.2 14.6 - - + -
230C VAL* 1.3 77.2 - - - +
232C CYS* 1.3 61.7 + - - +
283C VAL* 3.5 4.7 - - - +
284C MET* 2.8 40.8 + - + +
286C PHE* 3.5 44.5 - + - -
289C ALA* 4.2 18.8 - - + -
297C PHE* 3.5 39.1 - + - -
303C TRP* 3.9 9.2 - - + -
346C SER* 4.0 12.8 - - - -
347C PRO* 4.0 9.3 - - + +
423C ILE* 3.8 14.4 - - + +
425C TYR* 4.7 1.7 + - - -
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Residues in contact with CYS 232 (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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219C THR* 3.3 9.7 - - - +
220C PHE* 2.7 42.9 + - - +
222C LEU* 3.4 45.8 - - + -
230C VAL* 5.5 0.2 - - + -
231C TYR* 1.3 76.2 - - - +
233C LYS* 1.3 66.5 + - - +
234C PHE* 3.8 23.8 - - - -
281C ILE* 4.7 3.4 - - + -
282C GLN 3.0 15.7 - - - +
283C VAL* 4.8 1.8 - - + -
303C TRP* 3.8 4.0 - - - -
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Residues in contact with LYS 233 (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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151C PRO 5.1 0.4 + - - -
217C SER 2.8 26.1 + - - +
218C HIS* 3.3 16.3 - - - +
219C THR* 3.0 27.8 + - - +
232C CYS* 1.3 77.3 - - - +
234C PHE* 1.3 64.0 + - - +
235C HIS* 3.7 7.1 - - - +
281C ILE* 3.0 30.0 - - - +
282C GLN* 3.0 30.1 + - + +
296C PRO 4.4 2.0 + - - -
297C PHE* 6.0 0.4 - - - +
298C ASP 5.1 4.2 + - - -
299C LEU* 5.3 1.8 - - - +
301C LYS 4.3 14.7 + - - -
302C VAL* 5.5 1.1 - - - +
303C TRP* 3.5 45.6 - - + +
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Residues in contact with PHE 234 (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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100C PHE* 4.6 7.2 - + - -
143C TRP* 3.8 30.3 - + - -
145C LEU* 3.7 30.1 - - + -
215C TYR* 3.5 4.4 - - - +
216C GLY* 3.0 29.9 + - - +
217C SER 4.5 1.3 + - - +
218C HIS 5.0 1.0 + - - -
220C PHE* 3.5 42.4 - + + -
222C LEU* 4.3 13.0 - - + -
232C CYS* 3.8 15.7 - - - -
233C LYS* 1.3 73.9 - - - +
235C HIS* 1.3 67.5 + - - +
236C TYR* 4.6 1.1 - - + -
279C PHE* 3.7 19.5 - + + -
280C TYR 3.6 1.3 - - - -
281C ILE* 3.7 24.9 - - + -
343C ILE* 4.5 7.2 - - + -
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Residues in contact with HIS 235 (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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151C PRO* 5.3 2.0 - - + -
214C GLY 3.7 4.7 - - - -
215C TYR* 3.6 26.0 - + + -
233C LYS* 3.7 16.8 - - + +
234C PHE* 1.3 81.2 + - - +
236C TYR* 1.3 64.6 + - - +
237C LYS* 4.1 8.3 - - + -
278C THR 3.7 0.6 - - - +
279C PHE* 3.5 2.1 - - - -
280C TYR* 2.7 47.1 + - + +
282C GLN* 2.8 31.4 + - + -
305C HIS* 4.2 4.2 + - - -
310C LEU* 3.6 33.4 - - + +
3001C NDP 3.4 25.1 - - - -
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Residues in contact with TYR 236 (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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132C PHE* 3.0 58.4 + + - -
134C VAL* 4.1 7.6 - - + +
145C LEU* 3.6 32.1 + - + +
147C GLY* 3.7 15.8 + - - -
213C ASN* 3.5 0.2 - - - -
214C GLY* 2.8 70.9 + - - -
215C TYR* 3.9 8.7 + - - -
216C GLY 4.3 1.1 - - - -
234C PHE 4.7 0.9 - - - -
235C HIS* 1.3 80.3 - - - +
237C LYS* 1.3 62.7 + - - +
277C TRP* 3.3 15.0 - + + -
278C THR 3.3 5.4 - - - +
279C PHE* 3.6 18.6 - + + -
316C LEU* 3.7 21.1 - - + -
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Residues in contact with LYS 237 (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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213C ASN* 3.4 26.5 - - + +
215C TYR* 4.8 7.4 - - + +
235C HIS* 5.0 13.7 - - + -
236C TYR* 1.3 74.0 - - - +
238C THR* 1.3 64.3 + - - +
239C ASP* 3.4 2.1 + - - +
277C TRP* 3.0 5.4 - - - -
278C THR* 2.8 37.2 + - - +
280C TYR* 3.6 26.2 - - + +
305C HIS* 5.4 3.5 - - - -
310C LEU* 4.1 22.0 - - - +
3001C NDP 3.1 35.5 + - - -
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Residues in contact with THR 238 (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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210C ARG 2.6 24.4 + - - -
211C HIS 4.0 0.4 - - - -
212C MET 3.4 28.5 - - - +
213C ASN* 3.1 17.2 + - - +
237C LYS* 1.3 73.1 - - - +
239C ASP* 1.3 61.8 + - - +
240C GLN* 3.0 13.2 + - - -
241C GLY* 3.3 30.7 + - - -
242C ILE* 3.9 6.7 - - + +
276C SER 3.9 0.2 - - - -
277C TRP* 3.4 13.4 - - - -
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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