Contacts of the strand formed by residues 239 - 244 (chain C) in PDB entry 1BZI
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 TRP 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B MET* 4.7 7.2 - - - -
197C PHE* 3.2 35.7 - - + -
198C ARG* 3.3 43.0 - - - +
199C GLY* 3.1 42.2 + - - +
207C LEU* 5.0 5.6 - - + -
240C ALA* 1.3 67.7 + - - +
241C ARG* 3.9 34.3 - - - +
263C GLU* 3.2 28.5 - - - -
266C LEU* 3.7 13.2 - - + -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LYS* 3.6 9.9 - - + +
229B MET* 2.9 22.3 - - - +
230B MET* 2.8 31.8 + - + +
196C TYR* 3.1 27.6 - - - +
197C PHE 3.4 7.6 - - - -
198C ARG* 5.1 0.2 - - + -
239C TRP* 1.3 75.8 - - - +
241C ARG* 1.3 69.5 + - - +
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LYS 4.1 0.4 + - - -
229B MET* 3.8 13.6 - - - +
230B MET* 3.2 30.5 + - - +
197C PHE* 3.1 38.8 + - - +
207C LEU* 4.1 19.7 - - + +
229C MET* 3.6 35.4 - - + +
230C MET 5.1 5.5 + - - +
239C TRP* 3.9 26.1 - - + +
240C ALA* 1.3 102.8 + - - +
242C SER* 1.3 64.0 + - - +
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Residues in contact with SER 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY* 4.0 8.8 - - - -
228B LYS 3.1 29.6 + - - -
229B MET* 5.0 6.0 - - - +
243B SER* 6.1 5.4 - - - -
194C LYS* 5.9 4.7 - - - -
195C VAL 3.9 7.9 - - - -
196C TYR* 3.4 16.2 - - - +
197C PHE* 6.1 0.4 - - - -
207C LEU* 6.0 1.2 - - - +
229C MET* 5.8 4.3 - - - +
241C ARG* 1.3 74.0 - - - +
243C SER* 1.3 63.9 + - - +
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Residues in contact with SER 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B TYR 5.0 0.9 - - - -
194C LYS* 3.5 9.4 - - - +
195C VAL* 3.3 47.7 + - - +
197C PHE* 4.8 2.8 - - - -
207C LEU* 5.2 11.6 - - - +
209C HIS* 4.4 7.2 - - - +
227C GLY* 5.8 9.4 - - - -
229C MET* 6.4 0.4 - - - -
242C SER* 1.3 78.0 - - - +
244C TYR* 1.3 61.6 + - - +
245C LEU* 4.4 5.8 - - - +
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Residues in contact with TYR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 4.7 1.9 - + - -
244B TYR* 3.0 57.6 + + + +
245B LEU* 4.0 2.2 - - - -
246B GLY* 2.9 46.5 + - - -
190C PHE* 4.3 7.4 - + - -
192C TYR* 2.9 28.3 - - + +
193C SER 3.0 31.9 - - - -
194C LYS* 3.5 14.4 - - + -
243C SER* 1.3 74.5 - - - +
245C LEU* 1.3 74.9 + - - +
246C GLY* 4.0 14.4 - - - -
275C PHE* 3.9 3.1 - + - -
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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