Contacts of the strand formed by residues 196 - 201 (chain B) in PDB entry 1D0N
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 ASN 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A SER 5.8 3.8 + - - +
148A GLY* 6.1 2.2 - - - -
191B LEU 4.1 0.7 - - - +
193B LEU* 3.1 33.7 + - + +
194B GLY 3.6 0.9 + - - +
195B ASN* 1.3 91.6 + - - +
197B ILE* 1.3 62.4 + - - +
198B TYR* 3.6 33.9 + - + +
230B GLN* 3.2 28.0 - - - +
232B SER* 5.5 0.9 + - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 3.4 31.4 - - + -
191B LEU 3.7 4.3 - - - +
192B ASP* 3.8 15.3 - - - +
194B GLY 4.3 2.9 - - - +
196B ASN* 1.3 78.1 - - - +
198B TYR* 1.3 62.3 + - - +
217B SER* 4.2 17.9 - - - +
220B ILE* 3.8 26.9 - - + -
221B ARG* 3.9 28.9 - - + +
225B ARG* 4.2 7.4 - - - +
229B ALA* 4.2 8.3 - - + -
230B GLN 2.5 14.1 + - - +
231B VAL* 3.0 8.8 - - + +
232B SER* 2.9 26.9 + - - +
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Residues in contact with TYR 198 (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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146A ALA 4.8 2.8 + - - -
189B PHE 3.7 0.2 - - - +
190B ILE* 3.4 4.7 - - - -
191B LEU* 2.8 59.2 + - + +
193B LEU* 3.9 25.6 - - + -
196B ASN* 3.6 39.4 + - + +
197B ILE* 1.3 72.6 - - - +
199B GLN* 1.3 61.1 + - - +
200B TRP* 3.7 2.5 + - - +
232B SER* 3.7 13.5 - - - -
234B PHE* 3.5 30.5 - + + -
240B PRO* 3.9 19.1 - - + -
242B ALA* 3.4 23.2 - - + +
243B MET* 4.8 11.4 - - + +
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Residues in contact with GLN 199 (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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188B CYS* 5.0 0.7 - - + -
189B PHE 3.6 7.4 - - - +
190B ILE* 4.4 6.7 - - + +
197B ILE 4.0 1.0 + - - -
198B TYR* 1.3 70.5 - - - +
200B TRP* 1.3 59.6 + - - +
201B CYS* 3.8 17.7 - - - -
210B ARG* 3.6 11.7 + - - +
213B ALA* 3.4 13.8 - - + +
214B THR* 3.2 38.3 + - - +
217B SER* 2.7 35.0 + - - +
231B VAL* 5.2 1.8 - - + -
232B SER 2.8 16.6 + - - +
233B VAL* 3.5 22.6 - - + +
234B PHE* 2.9 31.8 + - - +
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Residues in contact with TRP 200 (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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180B TRP* 4.5 4.2 - + - -
183B PHE* 3.5 27.4 - + + -
184B ASN 3.4 18.6 - - - -
187B ASP 4.0 0.2 - - - -
188B CYS* 3.1 2.4 - - - +
189B PHE* 2.6 53.9 + + - +
198B TYR 3.7 1.5 + - - +
199B GLN* 1.3 73.9 - - - +
201B CYS* 1.3 63.0 + - - +
202B GLY* 3.4 23.3 - - - -
234B PHE* 3.5 11.9 - - + -
235B GLU 4.5 4.7 - - - -
236B GLU* 3.4 35.5 - - + +
239B GLU* 3.1 27.7 + - + -
243B MET* 3.4 37.0 - - + +
250B LYS* 4.8 0.2 - - + -
253B LEU* 3.4 33.0 - - + -
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Residues in contact with CYS 201 (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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187B ASP 3.9 0.7 - - - -
188B CYS* 2.0 47.6 - - - -
199B GLN* 3.8 20.6 - - - -
200B TRP* 1.3 78.4 - - - +
202B GLY* 1.3 66.8 + - - +
205B SER* 3.7 11.4 - - - +
210B ARG* 3.6 21.3 - - + +
233B VAL* 5.4 4.0 - - + -
234B PHE 3.2 12.3 + - - +
235B GLU* 3.6 8.4 - - + +
236B GLU 3.1 20.1 + - - -
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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