Contacts of the strand formed by residues 231 - 237 (chain B) in PDB entry 6CDS
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 GLU 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B ALA* 5.3 5.7 - - - +
224B ILE 3.4 14.9 + - - +
225B ARG* 3.5 27.5 + - - +
229B GLY 3.5 7.3 + - - +
230B THR* 1.3 77.1 - - - +
232B LEU* 1.3 67.0 + - - +
246B PRO* 3.1 27.3 - - + +
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Residues in contact with LEU 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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223B ALA* 3.8 4.7 - - - +
224B ILE* 2.9 43.3 + - + +
226B ASN* 4.3 26.0 - - + +
230B THR* 3.5 15.9 + - + +
231B GLU* 1.3 84.3 - - - +
233B LEU* 1.3 65.8 + - - +
243B ILE* 3.8 22.2 - - + -
244B TYR 3.7 16.2 - - - +
245B ASP* 4.7 2.7 - - - -
246B PRO* 3.6 12.7 - - + +
283B PHE* 4.2 16.4 - - + -
285B PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 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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221B TYR* 4.4 9.9 - - + -
222B PHE 3.2 17.7 - - - +
223B ALA* 4.0 12.3 - - + +
224B ILE* 3.8 3.4 - - - -
232B LEU* 1.3 79.8 - - - +
234B LEU* 1.3 60.1 + - - +
243B ILE* 3.7 5.5 - - - +
244B TYR* 3.0 47.3 + - + +
246B PRO* 3.9 28.3 - - + +
249B ARG* 3.7 49.6 - - + +
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Residues in contact with LEU 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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220B ASN 3.5 1.4 - - - +
221B TYR* 3.2 5.2 - - - +
222B PHE* 2.8 39.5 + - + +
224B ILE* 3.6 21.6 - - + +
233B LEU* 1.3 72.8 - - - +
235B GLY* 1.3 58.7 - - - +
236B VAL* 3.7 26.0 - - + -
241B LEU* 4.3 20.2 - - + -
242B HIS 3.5 6.3 - - - +
243B ILE* 3.5 24.7 - - + -
244B TYR* 4.5 1.6 - - - -
273B ILE* 4.7 1.1 - - + -
285B PHE* 3.6 35.2 - - + -
296B ILE* 3.9 18.6 - - + -
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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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219B VAL* 3.6 20.0 - - - -
220B ASN 3.3 6.1 - - - -
234B LEU* 1.3 72.5 - - - +
236B VAL* 1.3 62.5 + - - +
237B ASP 4.1 0.4 - - - -
241B LEU* 3.4 6.8 - - - +
242B HIS* 2.7 42.9 + - - -
244B TYR* 3.9 9.7 - - - -
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Residues in contact with VAL 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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219B VAL* 4.7 0.2 - - - -
220B ASN* 2.9 44.7 + - + +
222B PHE* 3.9 17.5 - - + -
234B LEU* 3.7 18.2 - - + -
235B GLY* 1.3 74.6 - - - -
237B ASP* 1.3 61.4 + - - +
240B GLY 3.9 2.5 - - - -
241B LEU* 3.7 19.3 - - + -
258B TRP* 4.1 15.9 - - + -
296B ILE* 4.7 4.3 - - + +
299B LEU* 3.8 36.6 - - + +
300B CYS* 4.2 5.8 - - - +
303B ASN* 4.2 4.3 - - - +
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Residues in contact with ASP 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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217B TYR 5.0 0.6 - - - +
218B GLY 3.3 24.9 - - - +
219B VAL* 3.8 15.9 - - + +
220B ASN* 4.8 0.9 - - - +
236B VAL* 1.3 74.2 - - - +
238B ALA* 1.3 59.0 + - - +
239B LEU* 3.0 19.8 + - - +
240B GLY 3.0 7.5 + - - +
242B HIS* 3.0 33.5 + - - -
258B TRP* 2.9 25.5 + - - -
303B ASN* 3.7 12.3 - - - +
641B PO4 4.0 15.6 + - - -
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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