Contacts of the strand formed by residues 276 - 284 (chain A) in PDB entry 1DGB
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ASP* 2.8 45.0 + - - +
240A GLN* 2.9 14.5 + - - +
274A TYR 4.7 3.4 + - - -
275A PRO* 1.3 77.3 - - - +
277A TRP* 1.3 69.4 + - - +
315A LYS* 4.4 6.9 + - - -
316A LEU 2.9 14.6 - - - -
317A VAL* 4.1 15.3 - - - -
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.0 15.7 - + - -
132A PHE* 3.4 29.8 - + - -
209A HIS 3.5 23.6 - - - -
210A ARG* 4.0 7.2 - - + -
212A MET 2.9 19.8 + - - -
236A TYR* 3.3 30.7 - - + -
237A LYS 3.2 4.7 - - - +
238A THR* 3.2 28.2 - - - +
239A ASP* 3.4 5.2 - - - -
240A GLN* 4.0 7.2 - - - -
265A LEU* 6.1 0.2 - - + -
275A PRO* 3.6 39.3 - - + -
276A SER* 1.3 95.8 - - - +
278A THR* 1.3 60.8 + - - +
279A PHE 3.7 0.2 + - - -
315A LYS* 3.3 6.6 - - - +
316A LEU* 2.7 47.1 + - + +
318A LEU* 3.9 13.9 - - + -
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 6.1 0.4 - - - +
236A TYR* 3.1 3.6 - - - -
237A LYS* 2.9 30.7 + - - -
239A ASP* 2.5 27.1 + - - -
277A TRP* 1.3 71.4 - - - +
279A PHE* 1.3 64.2 + - - +
280A TYR* 3.5 41.5 + - + +
312A PRO* 5.5 4.3 - - + -
314A GLY 3.7 9.0 - - - +
315A LYS* 3.5 15.3 + - + -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.0 15.9 - + + -
100A PHE* 4.8 11.4 - + - -
134A VAL* 6.3 0.2 - - + -
136A PHE* 4.6 8.5 - + - -
143A TRP* 4.3 8.3 - + - -
145A LEU* 3.9 16.8 - - + -
234A PHE* 3.5 41.3 - + + -
235A HIS 3.6 2.0 - - - -
236A TYR* 3.7 29.2 - + - +
277A TRP 3.7 1.2 + - - -
278A THR* 1.3 71.0 - - - +
280A TYR* 1.3 60.2 + - - +
281A ILE* 4.4 2.2 - - + -
312A PRO* 3.7 2.1 - - - +
313A VAL* 2.8 46.3 + - + +
314A GLY 2.7 28.7 + - - +
315A LYS* 4.4 1.1 - - - +
316A LEU* 4.1 22.0 - - + -
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE* 3.7 1.6 - - - -
235A HIS* 2.7 40.7 + - + +
237A LYS* 3.6 30.7 - - + -
278A THR* 3.5 37.6 + - + +
279A PHE* 1.3 78.0 - - - +
281A ILE* 1.3 72.0 + - - +
310A LEU* 3.9 34.1 - - + -
311A ILE 3.1 8.3 - - - +
312A PRO* 3.5 37.2 - - + -
313A VAL* 4.3 0.7 - - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 4.2 22.0 - - + -
94A TYR* 4.2 16.8 - - + -
222A LEU* 4.3 12.6 - - + -
232A CYS* 4.8 3.4 - - + -
233A LYS 3.1 9.0 - - - +
234A PHE* 3.5 31.6 - - + -
235A HIS* 4.8 1.6 - - - -
279A PHE* 4.4 2.0 - - + -
280A TYR* 1.3 82.4 - - - +
282A GLN* 1.3 64.7 + - - +
283A VAL* 3.8 22.0 - - + -
310A LEU* 4.7 0.4 - - - -
311A ILE* 2.7 54.0 + - + +
313A VAL* 3.9 13.2 - - + -
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A CYS* 3.1 29.1 - - - +
233A LYS* 3.2 22.6 + - + +
235A HIS* 2.6 33.2 + - - +
281A ILE* 1.3 73.7 - - - +
283A VAL* 1.3 61.7 + - - +
303A TRP* 2.9 50.8 + - + +
305A HIS* 3.9 12.1 - - - -
308A TYR* 2.9 28.6 + - + +
309A PRO 3.8 7.6 - - - +
310A LEU* 3.8 13.5 - - + -
311A ILE* 4.9 0.2 - - - -
1300A NDP 4.1 2.0 + - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 4.2 26.7 - - + +
222A LEU* 5.3 0.2 - - + -
230A VAL* 3.8 24.5 - - + -
231A TYR 3.4 10.8 - - - +
232A CYS* 4.7 2.9 - - + -
281A ILE* 3.8 19.3 + - + -
282A GLN* 1.3 81.2 - - - +
284A MET* 1.3 67.4 + - - +
285A THR* 4.8 5.2 - - + +
288A GLN* 3.9 3.6 - - - +
303A TRP* 4.0 1.8 - - - -
308A TYR* 3.3 22.3 - - - +
309A PRO* 4.7 1.4 + - - +
311A ILE* 3.8 24.9 - - + +
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 3.8 0.9 - - - +
231A TYR* 2.8 35.7 + - + +
283A VAL* 1.3 79.0 - - - +
285A THR* 1.3 67.4 + - - +
288A GLN* 3.1 24.0 - - + -
289A ALA* 3.6 24.9 - - + -
292A PHE* 3.7 17.9 - - + -
296A PRO* 3.8 14.8 - - - -
303A TRP* 3.5 46.7 - - + +
308A TYR* 3.6 28.3 - - + +
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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