Contacts of the strand formed by residues 193 - 198 (chain B) in PDB entry 5WRS
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 THR 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PHE 4.7 1.8 - - - +
192B PRO* 1.3 81.0 - - - +
194B ILE* 1.3 65.2 + - - +
195B SER 4.5 6.3 - - - -
226B LEU* 4.2 21.3 - - + -
227B ARG 3.3 11.9 - - - +
228B PHE* 4.1 20.2 - - + -
284B ARG* 4.9 4.7 - - - +
291B GLU* 2.9 51.9 + - + +
295B VAL* 3.8 12.3 - - - +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 3.7 30.7 - - + -
137B HIS* 5.3 3.6 - - - -
153B LEU* 3.6 33.0 - - + -
192B PRO* 5.2 1.1 - - + -
193B THR* 1.3 80.3 - - - +
195B SER* 1.3 63.9 + - - +
227B ARG* 2.8 23.0 + - + +
228B PHE 3.4 21.1 - - - +
229B SER* 3.9 22.0 - - - -
231B PHE* 5.0 0.4 - - + -
295B VAL* 3.5 20.5 - - - +
297B LYS* 4.5 3.1 + - - -
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 4.0 25.7 + - - -
136B ARG* 5.7 1.0 + - - -
193B THR* 3.9 2.1 - - - -
194B ILE* 1.3 81.6 + - - +
196B ALA* 1.3 69.5 + - - +
197B ASP* 5.6 1.4 - - - +
226B LEU* 3.8 1.9 - - - +
227B ARG* 3.0 38.9 + - - +
295B VAL* 3.5 16.7 + - - +
297B LYS* 4.2 13.5 + - - +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER* 1.3 81.2 + - - +
197B ASP* 1.3 65.0 + - - +
224B LEU* 5.3 1.8 - - + -
225B VAL 3.6 6.5 - - - -
226B LEU* 3.8 21.5 - - + -
292B ILE* 4.0 20.9 - - + +
295B VAL* 4.0 19.6 + - + -
296B THR* 2.8 26.9 + - - -
297B LYS 4.1 2.8 + - - -
301B LEU* 4.4 2.7 - - + -
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER* 5.6 1.3 - - - +
196B ALA* 1.3 76.2 - - - +
198B TYR* 1.3 80.1 + - - +
203B LYS* 2.9 28.0 + - - -
224B LEU* 3.7 12.8 - - - +
225B VAL* 3.1 34.3 + - + +
296B THR* 4.6 0.2 - - - -
298B ASN* 3.1 36.3 + - - +
301B LEU* 4.2 7.1 - - - +
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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
----------------------------------------------------------
197B ASP* 1.3 94.4 + - - +
199B SER* 1.3 70.7 + - - +
200B GLN* 4.2 2.8 - - - +
202B GLU* 4.4 18.6 - - + -
203B LYS* 3.6 26.2 + - + +
206B LEU* 4.4 25.3 - - + +
222B LEU* 5.9 4.0 - - - -
223B LYS 5.3 0.2 - - - -
224B LEU* 3.9 21.5 - - + -
225B VAL* 3.3 9.6 - - - +
298B ASN* 4.0 11.0 - - - -
300B ILE* 4.2 12.5 + - + +
301B LEU* 3.7 46.8 + - + +
304B VAL* 3.8 17.5 - - - +
315B PHE* 5.7 3.9 - + - -
316B PHE 4.7 2.8 + - - -
317B ALA* 5.9 4.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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