Contacts of the strand formed by residues 276 - 284 (chain B) in PDB entry 1DGF
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B ASP* 2.6 50.8 + - - +
240B GLN* 2.9 17.2 + - - +
274B TYR 3.7 4.1 + - - -
275B PRO* 1.3 74.9 - - - +
277B TRP* 1.3 68.6 + - - +
315B LYS* 4.5 6.4 + - - -
316B LEU 3.0 13.9 - - - -
317B VAL* 4.0 16.2 - - - -
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Residues in contact with TRP 277 (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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113B PHE* 3.7 17.0 - + - -
132B PHE* 3.4 28.9 - + - -
209B HIS 3.5 22.7 - - - -
210B ARG* 3.9 11.4 - - + -
212B MET 2.9 20.7 + - - -
236B TYR* 3.4 29.6 - - + -
237B LYS 3.1 5.6 - - - +
238B THR* 3.3 27.5 - - - -
239B ASP* 3.7 4.9 - - - -
240B GLN* 4.2 2.5 - - - -
275B PRO* 3.7 37.5 - - + -
276B SER* 1.3 92.9 - - - +
278B THR* 1.3 61.3 + - - +
315B LYS* 3.3 6.4 - - - +
316B LEU* 2.8 47.1 + - + +
318B LEU* 3.8 18.8 - - + -
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Residues in contact with THR 278 (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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88B THR* 6.1 0.2 - - - +
236B TYR* 3.2 2.3 - - - -
237B LYS* 2.8 33.3 + - - -
239B ASP* 2.7 22.0 + - - -
277B TRP* 1.3 69.9 - - - +
279B PHE* 1.3 62.2 + - - +
280B TYR* 3.2 43.8 - - + +
312B PRO* 5.3 5.4 - - + -
314B GLY 3.7 9.9 - - - +
315B LYS* 3.4 20.8 + - + -
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Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.0 13.0 - + + -
100B PHE* 4.6 9.9 - + - -
136B PHE* 4.3 12.6 - + - -
143B TRP* 4.1 12.6 - + - -
145B LEU* 3.8 24.7 - - + -
234B PHE* 3.6 36.3 - + + -
235B HIS 3.4 3.8 - - - -
236B TYR* 3.8 28.3 - + + +
277B TRP 3.7 1.4 + - - -
278B THR* 1.3 72.2 - - - +
280B TYR* 1.3 66.2 + - - +
281B ILE* 4.5 4.0 - - + -
312B PRO* 3.8 1.2 - - - +
313B VAL* 2.8 38.0 + - + -
314B GLY 2.8 27.6 + - - +
315B LYS* 4.3 2.2 - - - +
316B LEU* 4.2 16.2 - - + -
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Residues in contact with TYR 280 (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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234B PHE* 3.7 1.2 - - - -
235B HIS* 2.7 36.5 + - + +
237B LYS* 3.8 32.3 - - + +
278B THR* 3.2 43.0 - - + +
279B PHE* 1.3 77.4 - - - +
281B ILE* 1.3 70.3 + - - +
310B LEU* 3.8 37.0 - - + -
311B ILE 3.2 7.6 - - - +
312B PRO* 3.6 35.2 - - + -
313B VAL* 4.3 1.6 - - - -
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Residues in contact with ILE 281 (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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91B ILE* 4.1 20.2 - - + -
94B TYR* 4.1 15.5 - - + -
222B LEU* 4.1 17.3 - - + -
232B CYS* 4.7 4.3 - - + -
233B LYS 3.1 9.4 - - - +
234B PHE* 3.7 30.7 - - + -
235B HIS* 4.9 0.2 - - - -
279B PHE* 4.5 2.5 - - + -
280B TYR* 1.3 82.0 - - - +
282B GLN* 1.3 63.1 - - - +
283B VAL* 3.7 22.9 - - + -
310B LEU* 3.7 2.3 - - - -
311B ILE* 2.7 47.4 + - + +
313B VAL* 3.8 13.5 - - + -
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Residues in contact with GLN 282 (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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232B CYS* 3.1 29.1 - - - +
233B LYS* 3.0 21.7 + - + +
235B HIS* 2.8 28.3 + - - +
281B ILE* 1.3 75.3 - - - +
283B VAL* 1.3 61.4 + - - +
303B TRP* 2.9 48.4 + - + +
305B HIS* 4.1 7.9 - - - +
308B TYR* 2.7 36.2 + - + +
309B PRO 4.0 5.4 - - - +
310B LEU* 3.6 20.6 - - + +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.9 31.9 - - + +
230B VAL* 3.9 25.8 - - + -
231B TYR 3.4 4.3 - - - +
232B CYS* 4.9 1.8 - - + -
281B ILE* 3.7 25.1 - - + -
282B GLN* 1.3 79.4 - - - +
284B MET* 1.3 65.3 + - - +
285B THR* 4.3 6.3 - - + +
288B GLN* 4.0 3.1 - - - +
303B TRP* 4.1 1.8 - - - -
308B TYR* 3.3 20.4 - - - +
309B PRO 4.8 1.4 + - - -
311B ILE* 3.9 21.4 - - + +
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Residues in contact with MET 284 (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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230B VAL 3.8 0.3 - - - -
231B TYR* 2.8 37.6 + - + +
283B VAL* 1.3 77.8 - - - +
285B THR* 1.3 71.8 + - - +
288B GLN* 3.4 15.5 - - + -
289B ALA* 3.6 25.6 - - + -
292B PHE* 3.8 20.6 - - + -
296B PRO* 3.8 14.6 - - + -
303B TRP* 3.5 49.1 - - + +
308B TYR* 3.5 28.9 - - + +
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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