Contacts of the strand formed by residues 229 - 237 (chain B) in PDB entry 6DO5
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 ARG 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B ALA 3.8 0.2 - - - +
225B THR* 3.5 4.9 - - - +
226B VAL 3.1 36.1 + - - +
227B GLY 3.2 1.4 + - - -
228B ASN* 1.3 92.4 + - - +
230B GLY* 1.3 59.9 + - - +
231B PHE* 3.7 22.2 + - + -
247B TYR* 3.4 55.3 + - + -
248B LEU 3.8 1.8 - - - -
249B ASN* 4.9 6.2 - - - +
250B LEU* 4.1 3.1 - - - -
258B LEU* 6.0 1.2 - - - +
302B ILE* 4.6 17.5 - - - +
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Residues in contact with GLY 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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151B TRP* 3.1 42.1 - - - -
229B ARG* 1.3 72.4 - - - +
231B PHE* 1.3 57.6 + - - -
247B TYR* 3.0 3.8 - - - -
248B LEU 2.6 43.5 + - - -
250B LEU* 3.8 5.6 - - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TRP* 2.8 20.2 + - - -
222B ALA 4.4 0.2 - - - -
223B CYS* 3.1 2.1 - - - -
224B ALA 2.7 37.7 + - - +
226B VAL* 4.1 11.4 - - + -
229B ARG* 3.8 36.8 - - + -
230B GLY* 1.3 72.6 - - - -
232B VAL* 1.3 61.8 + - - +
245B LEU* 4.8 6.3 - - + -
246B HIS 3.5 4.0 - - - -
247B TYR* 3.5 17.5 - + + -
258B LEU* 3.7 28.3 - - + -
273B LEU* 4.6 4.5 - - + -
281B LEU* 3.7 26.7 - - + -
300B TYR* 4.5 3.6 - + - -
302B ILE* 3.5 45.8 - - + -
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Residues in contact with VAL 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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151B TRP* 4.3 5.8 - - + -
160B PHE* 4.2 10.5 - - + -
215B PRO* 4.0 26.5 - - + -
218B ARG* 4.4 8.1 - - - +
221B HIS* 3.7 36.8 - - + -
222B ALA 3.3 7.0 - - - +
223B CYS* 4.2 6.5 - - - -
231B PHE* 1.3 75.6 - - - +
233B PHE* 1.3 64.3 + - - +
244B ASP 3.9 0.7 - - - +
245B LEU* 3.5 6.0 - - - +
246B HIS* 3.0 42.8 + - + +
255B TRP* 4.1 13.0 - - + -
273B LEU* 4.8 0.2 - - - -
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Residues in contact with PHE 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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222B ALA 3.0 14.8 + - - -
232B VAL* 1.3 76.3 - - - +
234B GLY* 1.3 66.4 + - - +
243B ASN* 3.0 41.1 - - + -
244B ASP 3.2 16.2 - - - -
245B LEU* 3.6 18.6 - - + -
265B PRO* 4.1 16.2 - - + -
266B VAL 4.7 0.9 - - - -
268B ARG* 4.1 26.9 - - + -
271B HIS* 2.6 44.1 + + - +
273B LEU* 3.9 15.5 - - + +
283B LEU* 4.1 14.1 - - + -
307B TRP* 3.6 33.7 - + + -
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Residues in contact with GLY 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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218B ARG* 3.0 23.4 + - - +
221B HIS* 3.4 8.7 - - - +
233B PHE* 1.3 81.8 - - - +
235B GLY* 1.3 61.0 + - - -
242B MET* 3.0 29.4 - - - -
243B ASN 4.3 0.2 - - - -
244B ASP* 3.1 16.9 + - - -
268B ARG 3.9 2.0 - - - -
271B HIS* 3.9 3.4 - - - -
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Residues in contact with GLY 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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218B ARG* 4.8 1.1 - - - -
219B ALA 3.5 9.9 - - - -
220B ALA 3.6 15.5 - - - -
221B HIS* 3.7 5.4 - - - -
234B GLY* 1.3 73.7 - - - -
236B ARG* 1.3 60.7 + - - -
241B ARG* 3.3 0.9 - - - -
242B MET* 2.8 34.3 + - - +
268B ARG 2.9 12.1 + - - -
269B SER* 3.9 5.4 - - - -
271B HIS* 3.7 3.0 - - - -
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Residues in contact with ARG 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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178B ASP* 4.5 8.5 + - - -
180B THR* 5.3 6.3 + - - +
191B TRP* 3.6 21.4 - - - +
218B ARG* 3.3 5.2 - - - +
219B ALA 2.7 36.3 + - - +
235B GLY* 1.3 73.8 - - - -
237B TYR* 1.3 64.5 + - - +
238B ARG 2.4 32.5 + - - -
239B ASP* 4.4 7.9 + - - +
240B ALA 3.6 14.3 + - - +
241B ARG* 3.7 27.4 - - + +
269B SER* 3.9 2.0 - - - -
670D GLY* 3.4 31.8 - - - +
671D GLY* 2.9 37.2 + - - +
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Residues in contact with TYR 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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176B GLU* 3.7 29.4 - - + +
191B TRP* 4.0 13.5 - + - -
216B SER* 3.6 21.0 - - - -
217B PRO* 3.0 37.1 - - + +
235B GLY 4.0 0.4 + - - -
236B ARG* 1.3 78.3 - - - +
238B ARG* 1.3 123.0 + - + +
239B ASP 3.1 2.3 + - - -
240B ALA* 3.0 21.8 + - - +
242B MET* 3.7 18.6 - - + +
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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