Contacts of the strand formed by residues 240 - 245 (chain B) in PDB entry 6DDE
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B PHE* 3.2 10.7 - - - -
235B PHE* 2.6 48.3 + - + +
238B GLY 3.8 0.8 - - - -
239B ASN* 1.3 80.0 - - - +
241B PHE* 1.3 58.8 + - - +
252B LEU* 4.0 15.0 - - + -
253B PHE 3.3 15.3 - - - +
254B ASP* 4.4 6.7 - - - +
255B LEU* 4.2 4.1 - - - +
37C LEU* 4.5 13.5 - - + -
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Residues in contact with PHE 241 (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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200B VAL* 4.1 14.8 - - + -
208B ALA* 3.6 17.0 - - + -
222B PHE* 3.4 29.2 - + + -
232B ILE* 3.6 18.6 - - + -
233B CYS 3.2 16.6 - - - +
234B PHE* 3.5 20.0 - + + -
235B PHE 4.2 0.9 - - - +
240B ALA* 1.3 75.2 - - - +
242B ALA* 1.3 59.7 + - - +
243B THR* 3.6 12.2 + - + -
252B LEU* 3.6 5.2 - - - -
253B PHE* 2.9 63.6 + + + +
255B LEU* 3.6 31.6 - - + -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA 3.4 5.9 - - - +
232B ILE* 3.4 2.9 - - - +
233B CYS* 2.9 29.3 + - - -
241B PHE* 1.3 73.0 - - - +
243B THR* 1.3 61.8 + - - +
244B GLY 4.1 0.2 - - - -
250B CYS 5.1 2.2 - - - +
251B ARG 3.7 6.3 - - - +
252B LEU* 3.8 6.2 - - + +
276B VAL* 3.8 14.6 - - + +
278B PHE* 3.6 29.1 - - + -
285B LEU* 3.6 18.6 - - + -
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Residues in contact with THR 243 (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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208B ALA* 4.2 3.8 - - + -
225B HIS* 2.7 26.6 + - - -
229B ILE* 4.6 4.0 - - + -
231B ALA 3.3 4.0 - - - -
232B ILE* 3.7 17.5 - - + -
241B PHE* 3.6 31.6 - - + -
242B ALA* 1.3 73.2 - - - +
244B GLY* 1.3 59.9 + - - +
249B THR 3.3 2.9 - - - +
250B CYS* 3.0 5.0 - - - -
251B ARG* 2.9 38.7 + - - +
253B PHE* 3.6 16.6 - - + -
276B VAL* 4.9 0.2 - - - -
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Residues in contact with GLY 244 (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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229B ILE* 3.2 8.0 - - - +
230B ASN 2.9 22.9 + - - -
231B ALA 2.9 13.1 + - - -
243B THR* 1.3 74.9 - - - +
245B SER* 1.3 59.6 + - - -
249B THR 3.9 0.2 - - - -
250B CYS* 3.7 22.4 - - - -
273B ILE* 3.4 15.5 - - - -
276B VAL* 4.0 6.0 - - - +
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Residues in contact with SER 245 (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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225B HIS* 3.3 28.6 + - - -
227B SER 4.7 2.2 - - - -
228B ASP 3.3 14.6 - - - -
229B ILE* 3.7 5.6 - - - +
244B GLY* 1.3 74.3 - - - -
246B ASP* 1.3 62.4 + - - +
247B ASP* 3.2 22.6 + - - +
248B ALA* 3.6 6.4 + - - -
249B THR* 3.1 20.1 + - - -
273B ILE* 3.3 26.6 + - - +
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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