Contacts of the strand formed by residues 235 - 241 (chain L) in PDB entry 1DZG
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 235 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226I LYS* 6.1 0.6 - - - +
232L GLU 2.8 29.5 + - - -
233L ASN* 3.5 21.1 + - - +
234L THR* 1.3 76.8 - - - +
236L LYS* 1.3 69.2 + - - +
237L GLU* 3.5 2.8 + - + +
250L SER* 4.6 1.8 - - - -
251L MET* 2.9 38.2 + - + +
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Residues in contact with LYS 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I LYS* 5.0 11.4 + - - +
235L ARG* 1.3 76.7 - - - +
237L GLU* 1.3 60.0 + - - +
248L SER* 3.6 25.0 + - - +
249L ALA 3.4 7.0 - - - +
250L SER* 3.2 24.0 + - - +
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Residues in contact with GLU 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I LYS* 6.5 1.3 - - + -
315I MET* 3.9 14.2 - - + +
392I GLY 5.6 0.2 - - - -
393I ARG* 3.2 60.7 + - - +
394I SER 4.2 0.2 + - - -
395I LEU* 4.0 7.2 - - + +
235L ARG* 3.5 4.5 + - + +
236L LYS* 1.3 75.6 - - - +
238L LEU* 1.3 71.9 + - - +
239L PHE* 5.5 0.9 - - - -
248L SER* 4.6 2.5 - - - -
249L ALA* 2.7 41.6 + - + +
251L MET* 3.6 24.7 - - + +
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Residues in contact with LEU 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394I SER 3.1 13.2 - - - +
395I LEU* 4.1 7.5 - - - +
237L GLU* 1.3 85.4 - - - +
239L PHE* 1.3 61.8 + - - +
240L TYR* 3.2 39.7 - - + +
246L SER* 4.2 13.7 - - - +
247L CYS 3.5 12.1 - - - +
248L SER* 4.4 3.1 - - - +
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Residues in contact with PHE 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392I GLY* 3.9 24.7 - - - -
393I ARG* 4.0 1.3 - - - -
394I SER* 3.5 28.5 - - - +
237L GLU* 3.7 1.3 + - + -
238L LEU* 1.3 74.3 - - - +
240L TYR* 1.3 67.2 + - - +
241L LYS 4.1 0.6 + - - -
246L SER* 3.2 5.5 - - - -
247L CYS* 2.6 51.9 + - - +
249L ALA* 4.0 10.5 - - + -
404L ALA* 3.4 29.8 - - + -
405L ASN 3.3 33.2 - - - -
406L ARG 4.7 1.1 - - - -
427L ALA 3.7 8.1 - - - -
428L ASN* 4.7 0.7 - - - -
429L PRO* 3.9 21.1 - - + -
430L CYS* 4.0 11.7 - - - -
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Residues in contact with TYR 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394I SER* 2.6 42.6 + - - +
395I LEU* 4.4 6.7 - - + +
396I ASN* 3.4 55.5 - - + +
397I PRO* 4.8 5.2 - - + -
238L LEU* 3.2 41.9 - - + +
239L PHE* 1.3 80.6 - - - +
241L LYS* 1.3 65.4 + - - +
244L GLY 5.7 2.7 - - - -
245L GLU 3.4 14.4 - - - +
246L SER* 4.2 9.6 - - - -
405L ASN* 3.4 12.3 + - - +
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Residues in contact with LYS 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L PHE* 4.5 0.7 - - + -
240L TYR* 1.3 77.2 - - - +
242L ALA* 1.3 65.5 + - - +
243L ASP* 3.8 9.9 - - + +
244L GLY* 3.0 15.8 + - - -
245L GLU* 2.9 42.3 + - - +
246L SER 4.2 12.6 - - - -
247L CYS* 4.0 28.0 - - - -
402L PHE* 3.2 44.6 - - + -
403L LYS 3.8 4.3 - - - +
404L ALA* 3.6 30.1 - - + +
405L ASN* 3.5 1.6 + - - -
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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