Contacts of the strand formed by residues 196 - 201 (chain B) in PDB entry 6FY5
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 LYS 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B SER* 3.6 22.6 + - - -
189B LYS 3.5 9.0 - - - +
190B SER* 4.0 20.4 - - - +
194B GLY 3.8 2.2 + - - +
195B GLN* 1.3 74.0 - - - +
197B LEU* 1.4 60.7 + - - +
198B SER* 3.7 18.2 + - - +
347B LYS 2.9 8.9 + - - +
348B ASN* 3.3 22.2 - - - +
349B VAL* 2.9 31.4 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 3.1 4.7 - - - -
189B LYS* 2.9 38.0 + - + +
191B LEU* 4.3 26.9 - - + -
196B LYS* 1.4 72.2 - - - +
198B SER* 1.3 60.7 + - - +
331B LEU* 3.9 27.1 - - + -
334B ILE* 3.6 31.0 - - + -
335B SER* 5.2 3.6 - - - -
338B PHE* 4.6 2.9 - - + -
349B VAL* 3.5 21.3 - - + -
351B PHE* 4.1 9.0 - - + -
366B MET* 3.7 15.5 - - + +
369B LEU* 3.9 19.7 - - + -
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 4.3 13.4 - - - +
187B SER 3.5 7.0 - - - -
188B SER* 3.4 13.4 - - - -
196B LYS* 3.7 16.5 - - - +
197B LEU* 1.3 75.7 + - - +
199B LEU* 1.3 63.1 + - - +
200B THR* 3.6 1.6 + - - -
348B ASN* 4.9 1.2 + - - -
349B VAL 2.9 10.5 + - - -
350B TYR* 3.3 31.5 - - - -
351B PHE* 2.9 27.1 + - - -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.7 4.0 - - - +
186B LEU* 2.8 37.6 + - + -
187B SER* 2.8 26.5 + - - +
198B SER* 1.3 71.3 - - - +
200B THR* 1.3 55.1 + - - +
351B PHE* 3.5 28.3 - - + -
353B LEU* 4.0 11.2 - - + -
359B ILE* 4.5 4.5 - - + +
362B TYR* 3.9 18.6 - - + -
363B VAL* 3.4 38.8 - - + +
366B MET* 3.5 34.1 - - - -
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Residues in contact with THR 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 GLY 5.9 0.7 - - - +
183B PHE* 3.7 33.9 - - + -
184B THR 3.4 16.2 - - - +
185B ILE* 3.6 13.7 - - + +
186B LEU* 3.8 4.0 - - - -
198B SER 3.6 2.6 + - - -
199B LEU* 1.3 74.9 - - - +
201B GLN* 1.3 62.0 + - - +
202B SER* 3.5 5.3 + - - -
210B MET* 5.7 1.3 - - + -
350B TYR* 3.4 30.7 - - + +
351B PHE 2.9 8.9 + - - +
352B LEU* 4.3 7.2 - - + -
353B LEU* 3.0 29.8 + - - +
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Residues in contact with GLN 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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182B GLY 4.4 2.1 - - - +
183B PHE* 3.5 10.0 - - - -
184B THR* 2.9 40.9 + - - +
186B LEU* 3.6 22.5 - - + +
200B THR* 1.3 69.1 - - - +
202B SER* 1.3 67.9 + - - +
203B ASP 4.3 0.3 + - - -
353B LEU 3.6 7.7 + - - -
354B PHE* 3.0 29.4 + - - +
359B ILE* 3.4 20.6 - - - +
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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