Contacts of the strand formed by residues 245 - 248 (chain C) in PDB entry 3DBI
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 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C LEU* 3.8 26.5 - - + -
181C HIS* 3.6 19.7 - - + +
183C GLU 3.6 1.2 + - - -
184C ILE* 3.5 17.0 - - + -
185C ALA 2.8 24.8 + - - -
243C PHE* 3.5 11.1 - - - +
244C SER* 1.3 82.6 + - - +
246C LEU* 1.3 59.3 + - - +
272C VAL* 4.2 0.2 - - - -
273C SER* 3.2 8.5 - - - +
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 5.8 0.9 - - - +
185C ALA* 3.4 12.3 - - + +
187C LEU* 3.9 25.4 - - + -
233C VAL* 3.8 20.2 - - + -
236C LEU* 3.8 28.7 - - + -
243C PHE* 4.2 7.6 - - + -
245C ALA* 1.3 76.2 - - - +
247C VAL* 1.3 65.5 + - - +
248C ALA* 3.8 16.4 - - + +
257C ALA* 4.0 14.6 - - + -
261C LEU* 5.1 1.8 - - + -
272C VAL* 4.1 9.9 - - + -
273C SER 2.8 13.2 + - - +
274C VAL* 3.4 13.5 - - + -
275C ILE* 3.1 25.3 + - - +
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Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C VAL* 4.3 14.4 - - + -
176C LEU* 3.7 30.3 - - + -
184C ILE* 3.9 15.0 - - + -
185C ALA 2.8 12.3 + - - +
186C PHE* 3.4 23.2 - - + -
187C LEU 2.8 26.2 + - - +
203C TYR* 5.1 0.2 - - + -
246C LEU* 1.3 77.6 - - - +
248C ALA* 1.3 61.7 + - - +
275C ILE* 3.8 16.2 - - + -
277C PHE* 3.8 30.1 - - + -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 4.0 10.8 - - + -
246C LEU* 3.8 12.7 - - + +
247C VAL* 1.3 76.1 - - - +
249C SER* 1.3 64.8 + - - +
250C ASN 3.2 5.8 + - - +
253C MSE 4.0 9.2 - - + -
254C ALA* 3.5 39.0 - - + +
275C ILE 3.0 12.7 + - - +
276C GLY* 3.6 3.1 - - - -
277C PHE* 3.3 16.6 - - - -
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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