Contacts of the strand formed by residues 276 - 284 (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 SER 276 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C ASP* 2.6 61.1 + - - +
240C GLN* 3.0 12.9 + - - -
274C TYR 4.6 4.1 + - - -
275C PRO* 1.3 76.0 - - - +
277C TRP* 1.3 61.8 + - - +
315C LYS* 5.0 4.5 - - - -
316C LEU 3.1 12.8 - - - -
317C VAL* 4.2 13.9 - - - -
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Residues in contact with TRP 277 (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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113C PHE* 3.8 16.6 - + - -
132C PHE* 3.4 27.5 - + - -
209C HIS 3.6 21.1 - - - -
210C ARG* 4.0 13.2 - - + -
212C MET 2.9 19.8 + - - -
236C TYR* 3.3 36.8 - - + -
237C LYS 3.0 4.9 - - - +
238C THR* 3.4 19.6 - - - -
239C ASP* 3.9 3.8 - - - -
240C GLN* 4.3 0.7 - - - -
275C PRO* 3.7 39.0 - - + -
276C SER* 1.3 93.3 - - - +
278C THR* 1.3 62.1 + - - +
279C PHE 3.6 0.3 + - - -
315C LYS* 3.4 6.2 - - - +
316C LEU* 2.9 47.2 + - + +
318C LEU* 3.8 17.5 - - + -
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Residues in contact with THR 278 (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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88C THR* 6.0 1.1 - - - +
236C TYR* 3.3 2.9 - - - -
237C LYS* 2.8 35.0 + - - -
239C ASP* 2.7 23.3 + - - -
277C TRP* 1.3 70.6 - - - +
279C PHE* 1.3 63.7 + - - +
280C TYR* 3.4 40.1 - - + +
312C PRO* 5.4 4.7 - - + -
314C GLY 3.7 9.2 - - - +
315C LYS* 3.0 22.3 + - - -
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Residues in contact with PHE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 4.0 15.3 - + + -
100C PHE* 4.7 8.3 - + - -
134C VAL* 6.2 0.2 - - + -
136C PHE* 4.6 8.1 - + - -
143C TRP* 4.3 11.7 - + - -
145C LEU* 3.8 17.5 - - + -
234C PHE* 3.7 35.9 - + + -
235C HIS 3.5 1.6 - - - -
236C TYR* 3.6 36.1 - + + -
277C TRP 3.6 2.1 + - - +
278C THR* 1.3 72.8 - - - +
280C TYR* 1.3 59.0 + - - +
281C ILE* 4.7 3.4 - - + -
312C PRO* 3.6 2.3 - - - +
313C VAL* 2.7 47.8 + - + +
314C GLY 2.7 27.8 + - - +
315C LYS* 4.3 2.0 - - - +
316C LEU* 4.0 17.3 - - + -
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Residues in contact with TYR 280 (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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234C PHE* 3.6 1.9 - - - -
235C HIS* 2.7 40.8 + - + +
237C LYS* 3.6 27.1 - - + +
278C THR* 3.4 40.4 - - + +
279C PHE* 1.3 77.7 - - - +
281C ILE* 1.3 72.5 + - - +
310C LEU* 3.7 36.3 - - + -
311C ILE 3.1 9.4 - - - +
312C PRO* 3.5 37.9 - - + -
313C VAL* 4.0 1.6 - - - -
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Residues in contact with ILE 281 (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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91C ILE* 4.1 34.5 - - + -
94C TYR* 4.2 10.1 - - + -
100C PHE* 5.9 0.2 - - + -
222C LEU* 4.2 12.3 - - + -
232C CYS* 4.7 2.5 - - + -
233C LYS 3.0 9.2 - - - +
234C PHE* 3.7 30.1 - - + -
235C HIS* 4.8 1.6 - - - -
279C PHE* 4.7 2.0 - - + -
280C TYR* 1.3 82.3 - - - +
282C GLN* 1.3 65.3 + - - +
283C VAL* 3.8 22.0 - - + -
310C LEU 3.8 0.9 - - - -
311C ILE* 2.9 46.8 + - + +
313C VAL* 3.8 12.6 - - + -
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Residues in contact with GLN 282 (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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232C CYS* 3.0 29.3 - - - +
233C LYS* 3.0 25.2 + - + +
235C HIS* 2.8 35.3 + - - +
281C ILE* 1.3 75.0 - - - +
283C VAL* 1.3 60.4 + - - +
303C TRP* 2.9 48.1 + - + +
305C HIS* 3.7 7.2 - - - -
308C TYR* 2.7 30.9 - - + +
309C PRO 4.1 5.6 - - - +
310C LEU* 3.9 13.7 - - + -
311C ILE* 5.0 0.2 - - - -
3001C NDP 4.4 2.2 + - - -
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Residues in contact with VAL 283 (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* 4.0 27.4 - - + +
222C LEU* 5.3 0.2 - - + -
230C VAL* 3.8 33.4 - - + -
231C TYR 3.5 3.1 - - - +
232C CYS* 4.8 2.5 - - + -
281C ILE* 3.8 25.1 - - + -
282C GLN* 1.3 79.6 - - - +
284C MET* 1.3 65.5 + - - +
285C THR* 4.2 5.2 - - + +
288C GLN* 3.9 3.7 - - - +
303C TRP* 4.1 1.6 - - - -
308C TYR* 3.2 20.9 - - - +
309C PRO 5.0 1.0 + - - -
311C ILE* 3.9 20.6 - - + +
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Residues in contact with MET 284 (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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231C TYR* 2.8 36.3 + - + +
283C VAL* 1.3 76.7 - - - +
285C THR* 1.3 72.2 + - - +
288C GLN* 3.4 18.2 - - + -
289C ALA* 3.7 24.5 - - + -
292C PHE* 3.6 24.0 - - + -
296C PRO* 3.8 15.5 - - - -
303C TRP* 3.5 45.7 - - + +
308C TYR* 3.5 25.4 - - + +
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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