Contacts of the strand formed by residues 216 - 220 (chain L) in PDB entry 3STJ
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 GLY 216 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176L ILE 3.6 0.2 - - - +
177L GLN* 3.2 8.8 - - - +
178L THR* 2.9 43.1 + - - +
180L ALA 5.3 1.9 + - - -
182L ILE* 4.3 13.0 - - - -
204L ALA 3.7 6.1 - - - -
205L ILE* 4.1 9.2 - - - -
215L ILE* 1.3 74.2 - - - +
217L PHE* 1.3 64.9 + - - -
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Residues in contact with PHE 217 (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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150K LEU* 4.3 7.9 - - + -
164L ARG* 4.4 5.6 - - + -
167L LEU* 3.7 30.5 - - + -
169L LEU* 4.2 10.3 - - + -
175L PHE* 3.7 31.2 - - + -
176L ILE 3.2 5.4 - - - -
177L GLN* 3.5 30.3 - - + -
178L THR* 5.7 0.2 - - - -
182L ILE* 4.9 3.7 - - - +
202L ASN* 3.9 3.9 + - - +
203L THR 2.9 22.7 + - - -
204L ALA* 2.7 34.5 + - + +
205L ILE* 4.2 0.4 - - - -
206L LEU* 3.7 32.1 - - + -
215L ILE* 3.6 24.5 - - + -
216L GLY* 1.3 77.0 - - - -
218L ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 218 (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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175L PHE* 3.3 10.2 - - - -
176L ILE* 2.9 37.3 + - + +
178L THR* 5.6 1.6 - - + -
191L LEU* 4.1 26.9 - - + -
200L GLY* 4.3 2.5 - - - -
201L ILE 3.1 24.9 - - - +
202L ASN* 4.2 7.0 - - - +
217L PHE* 1.3 74.4 - - - +
219L ILE* 1.4 63.9 + - - +
220L PRO 3.4 0.5 - - - -
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Residues in contact with ILE 219 (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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80L ASN* 3.9 2.5 - - - +
111L SER 3.2 26.9 - - - +
112L ASP 3.7 16.8 - - - +
113L ILE* 3.5 31.2 - - + -
172L LEU 6.0 0.9 - - - +
175L PHE* 3.9 15.7 - - + -
200L GLY* 3.1 1.6 - - - -
201L ILE* 2.8 36.5 + - + +
203L THR* 3.1 25.0 + - + +
218L ALA* 1.4 70.1 - - - +
220L PRO* 1.3 80.6 - - + +
223L MET* 4.0 19.7 - - + -
224L ALA* 4.2 2.3 - - + +
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Residues in contact with PRO 220 (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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132L SER* 3.5 22.2 - - - +
174L ASN* 3.1 44.0 - - - +
176L ILE* 3.6 21.5 - - + +
218L ALA 3.4 5.3 - - - +
219L ILE* 1.3 89.6 - - + +
221L SER* 1.4 54.7 + - - +
222L ASN* 3.3 0.7 - - + +
223L MET* 3.1 20.5 + - + +
224L ALA* 2.9 30.5 + - - +
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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