Contacts of the strand formed by residues 208 - 212 (chain B) in PDB entry 3SN6
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 ALA 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER 3.0 15.0 - - - +
207B SER* 1.3 73.6 - - - +
209B LYS* 1.3 61.2 + - - +
221B THR* 3.7 1.6 - - - +
222B PHE* 2.9 39.3 + - + +
229B ILE* 3.6 14.2 - - + +
232B ILE* 3.7 23.3 - - + -
241B PHE* 3.9 17.5 - - + -
243B THR* 4.3 1.1 - - + -
253B PHE* 5.6 1.6 - - + -
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY* 3.4 27.8 - - - -
183B HIS* 3.6 23.0 - - + +
200B VAL* 3.0 6.4 - - - +
201B SER 2.9 30.8 + - - -
205B ASP* 5.1 2.9 - - - -
207B SER* 5.1 1.8 - - - +
208B ALA* 1.3 76.2 - - - +
210B LEU* 1.3 60.7 + - - +
211B TRP* 3.4 42.2 - - + +
218B CYS* 3.6 17.7 - - - +
220B GLN 3.6 1.6 - - - -
221B THR* 2.6 41.8 + - + +
222B PHE* 5.1 0.9 - - - -
18G GLN* 4.9 8.5 - - - +
22G GLU* 4.8 1.4 + - - -
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Residues in contact with LEU 210 (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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198B LEU* 3.9 32.1 - - + -
199B PHE 3.8 1.8 - - - -
200B VAL* 3.3 26.7 - - + +
208B ALA 4.3 0.2 + - - -
209B LYS* 1.3 74.1 - - - +
211B TRP* 1.3 66.8 + - - +
218B CYS* 3.6 2.3 - - - -
219B ARG* 2.9 45.4 + - + +
220B GLN* 2.9 36.1 + - + +
222B PHE* 3.9 12.1 - - + -
234B PHE* 4.1 0.9 - - + -
255B LEU* 3.7 31.9 - - + -
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Residues in contact with TRP 211 (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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166B CYS* 5.1 3.2 - - + -
180B PHE* 3.5 36.5 - + + +
181B THR 2.7 46.4 - - - -
183B HIS* 3.8 14.1 - + - -
198B LEU* 2.7 31.1 - - - +
199B PHE* 2.9 45.3 + + + +
201B SER* 3.2 22.2 + - - -
209B LYS* 3.4 40.1 - - + +
210B LEU* 1.3 76.0 - - - +
212B ASP* 1.3 53.7 + - - +
216B GLY 4.8 0.7 - - - -
217B MET* 3.7 10.1 - - - -
218B CYS* 3.3 39.0 - - + -
219B ARG* 5.2 2.7 - - - -
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Residues in contact with ASP 212 (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 PHE* 3.1 10.7 - - - -
197B ARG* 3.1 15.7 - - - +
198B LEU* 3.9 5.6 - - + -
199B PHE* 5.2 0.2 - - - -
211B TRP* 1.3 75.9 - - - +
213B VAL* 1.3 76.3 + - - +
214B ARG* 3.0 16.2 + - - +
215B GLU* 2.9 28.3 + - + +
216B GLY 2.9 24.6 + - - -
217B MET 3.4 9.3 + - - +
219B ARG* 2.8 42.5 + - - +
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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
------------------------------------------------------------
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