Contacts of the strand formed by residues 189 - 197 (chain B) in PDB entry 6VSB
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 LEU 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG* 3.6 26.9 - - - +
91B TYR* 5.8 0.7 - - - +
93B ALA* 4.4 7.6 - - + -
94B SER* 3.3 32.8 - - - +
95B THR* 3.7 15.3 - - + +
188B ASN* 1.3 67.7 - - - +
190B ARG* 1.3 62.9 + - - +
191B GLU* 3.8 14.1 + - + +
206B LYS 5.3 0.2 - - - -
208B THR* 2.4 61.3 + - + +
209B PRO 3.7 7.1 - - - +
217B PRO* 3.9 22.4 - - + -
266B TYR* 5.6 6.3 - - + -
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Residues in contact with ARG 190 (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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92B PHE* 5.2 1.9 - - + -
93B ALA* 3.2 4.2 - - - +
94B SER* 2.6 48.0 + - - +
95B THR 6.0 0.2 - - - -
96B GLU 5.2 7.6 + - - -
97B LYS* 5.7 5.2 - - - +
98B SER 6.1 0.2 - - - +
176B LEU* 3.1 39.6 + - - +
188B ASN* 3.9 21.9 - - - +
189B LEU* 1.3 77.8 - - - +
191B GLU* 1.3 60.2 - - - +
192B PHE* 4.9 17.9 - - + -
206B LYS 4.2 9.0 - - - +
207B HIS* 3.2 33.6 - - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 2.7 59.1 + - - +
91B TYR* 3.7 14.4 + - + +
92B PHE 3.5 5.6 - - - +
93B ALA* 4.3 0.9 - - + -
189B LEU* 3.8 17.4 + - + +
190B ARG* 1.3 80.0 - - - +
192B PHE* 1.3 74.3 + - - +
205B SER* 3.3 1.2 - - - -
206B LYS* 3.2 31.3 + - + +
208B THR* 4.4 12.2 + - - +
221B SER* 5.4 1.7 - - - -
223B LEU* 3.3 30.4 - - + +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.7 1.7 - - - -
92B PHE* 2.7 55.3 + + + +
93B ALA* 4.8 0.2 - - - +
104B TRP* 3.3 41.1 - + - -
121B ASN* 5.7 1.1 - - - -
175B PHE* 4.3 28.7 - + + -
190B ARG* 4.9 15.5 - - + -
191B GLU* 1.3 95.6 - - - +
193B VAL* 1.3 63.9 + - - +
194B PHE* 3.5 24.5 - + + -
203B ILE* 5.8 1.3 - - + -
204B TYR 3.2 5.6 - - - +
205B SER* 3.0 32.1 - - - -
206B LYS 4.5 4.5 - - - -
223B LEU* 3.9 2.2 - - - -
226B LEU* 5.3 0.9 - - + -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 4.9 4.3 - - - +
37B TYR* 4.4 18.4 - - + -
56B LEU* 6.5 0.2 - - + -
90B VAL 3.7 3.4 - - - +
91B TYR* 3.7 21.5 - - + -
192B PHE* 1.3 80.1 - - - +
194B PHE* 1.3 69.1 + - - +
195B LYS* 4.2 2.0 + - + +
203B ILE* 3.6 1.4 - - - -
204B TYR* 2.7 66.4 + - + +
223B LEU* 3.7 16.1 - - + +
270B LEU* 4.0 27.1 - - + -
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Residues in contact with PHE 194 (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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86B PHE* 3.6 6.8 - - + -
89B GLY* 3.1 3.5 - - - -
90B VAL* 2.9 45.0 + - + +
92B PHE* 4.4 12.8 - + + -
104B TRP* 4.1 32.3 - + - -
106B PHE* 3.3 41.5 - + + -
119B ILE* 6.3 2.5 - - + -
192B PHE* 3.5 40.4 - + + -
193B VAL* 1.3 78.8 - - - +
195B LYS* 1.3 60.7 + - - +
201B PHE* 4.3 7.0 - + + -
202B LYS 3.9 3.1 - - - -
203B ILE* 3.8 32.3 - - + -
238B PHE* 5.5 2.2 - + - -
270B LEU* 4.3 0.5 - - - +
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Residues in contact with LYS 195 (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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37B TYR* 5.7 3.6 - - - +
54B LEU* 5.4 8.7 - - + -
86B PHE* 4.9 0.4 - - - -
89B GLY* 4.1 5.4 - - - -
193B VAL* 4.1 6.6 + - + -
194B PHE* 1.3 75.9 - - - +
196B ASN* 1.3 62.7 + - - +
197B ILE* 4.1 3.7 + - + +
200B TYR 4.1 0.2 - - - +
201B PHE* 3.8 7.9 - - - -
202B LYS* 3.1 38.8 + - + +
204B TYR* 5.2 10.3 - - + -
270B LEU* 4.4 15.5 - - + -
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Residues in contact with ASN 196 (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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54B LEU* 4.8 11.8 - - - +
86B PHE* 4.5 20.1 - - + -
88B ASP* 6.0 3.4 - - - -
89B GLY* 4.8 3.7 - - - +
195B LYS* 1.3 74.6 - - - +
197B ILE* 1.3 63.8 + - - +
199B GLY 6.1 0.9 - - - +
200B TYR 4.1 2.7 - - - -
201B PHE* 4.7 10.1 - - + +
233B ILE 5.6 5.6 - - - +
235B ILE* 5.7 6.3 - - + +
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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
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54B LEU* 6.5 0.2 - - + -
195B LYS* 5.3 3.4 - - + +
196B ASN* 1.3 76.8 - - - +
198B ASP* 1.3 61.3 + - + +
199B GLY 3.1 2.9 - - - +
200B TYR* 2.7 47.4 + - + +
202B LYS* 5.9 9.2 - - + -
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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