Contacts of the strand formed by residues 185 - 193 (chain B) in PDB entry 3VRY
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 TYR 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.3 30.0 - - + +
150B PHE* 3.7 26.0 - + - -
175B ILE* 4.1 11.4 - - + -
176B ARG 3.4 10.1 - - - +
177B ASP* 4.0 11.4 - - - -
178B SER* 4.1 3.3 - - - -
183B GLY 4.4 15.1 + - - -
184B SER* 1.3 83.5 - - - +
186B SER* 1.3 68.0 + - - +
204B LYS* 4.2 1.4 - - - +
205B ILE* 3.1 36.7 + - + +
207B THR* 5.0 3.1 - - + -
213B PHE* 4.2 25.4 - + - -
224B LEU* 4.1 17.9 - - + -
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Residues in contact with SER 186 (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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174B MET 3.6 1.2 - - - +
175B ILE* 3.2 4.5 - - - -
176B ARG* 2.8 59.4 + - - +
178B SER* 3.7 3.3 + - - -
185B TYR* 1.3 79.5 + - - +
187B LEU* 1.3 61.2 + - - +
203B TYR 3.3 12.8 + - - -
204B LYS* 3.9 4.9 - - - +
205B ILE* 4.1 5.6 - - - -
527B PTR 2.6 34.7 + - - -
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Residues in contact with LEU 187 (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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173B PHE* 4.1 20.0 - - + -
174B MET 3.4 13.5 - - - +
175B ILE* 4.0 17.3 - - + +
186B SER* 1.3 74.1 - - - +
188B SER* 1.3 61.8 + - - +
189B VAL* 3.8 17.0 - - + -
201B LYS 3.8 0.3 - - - +
202B HIS* 3.1 5.7 - - - +
203B TYR* 2.8 48.3 + - + +
205B ILE* 4.1 7.3 - - + +
215B ILE* 3.5 31.6 - - + -
227B LEU* 4.9 7.6 - - + -
228B VAL* 5.8 0.4 - - + -
238B LEU* 3.9 23.3 - - + -
242B LEU* 4.5 9.0 - - + -
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Residues in contact with SER 188 (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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159B ALA* 4.5 1.6 - - - -
163B LEU* 3.8 20.6 - - - +
173B PHE* 3.0 8.8 - - - +
174B MET* 2.8 45.6 + - - -
176B ARG* 2.8 21.0 + - - -
187B LEU* 1.3 73.3 - - - +
189B VAL* 1.3 62.1 + - - +
201B LYS 3.3 4.0 - - - -
202B HIS* 2.6 30.9 + - - -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.7 0.7 - - - -
171B GLY* 4.1 14.8 - - - +
172B SER 3.5 7.2 - - - +
173B PHE* 4.2 0.7 - - + -
187B LEU* 3.8 27.6 - - + -
188B SER* 1.3 80.9 - - - +
190B ARG* 1.3 75.0 + - - +
191B ASP* 3.4 2.6 + - - +
200B VAL* 3.1 9.3 - - - +
201B LYS 2.8 39.3 + - - +
203B TYR* 4.4 11.2 - - + -
238B LEU* 4.8 3.1 - - + -
239B CYS* 4.3 10.8 - - - -
240B GLN* 4.2 16.4 - - + +
242B LEU* 4.0 18.6 - - + -
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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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163B LEU* 3.3 31.8 + - + +
164B LEU* 3.5 29.8 + - - +
165B ALA 4.7 2.2 + - - -
168B ASN* 3.1 39.0 + - - +
169B MET* 3.1 37.4 - - - +
170B LEU* 3.6 6.3 - - + +
171B GLY* 2.8 27.5 + - - -
172B SER* 2.8 20.8 + - - +
189B VAL* 1.3 74.9 - - - +
191B ASP* 1.3 60.6 + - - +
198B ASP* 3.2 32.4 + - - +
199B THR 3.5 6.3 - - - -
200B VAL* 4.7 2.0 - - - +
240B GLN* 3.9 2.3 - - - +
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Residues in contact with ASP 191 (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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170B LEU* 3.6 5.7 - - - +
189B VAL 3.4 0.6 + - - +
190B ARG* 1.3 76.6 - - - +
192B TYR* 1.3 89.0 + - - +
193B ASP* 5.5 1.9 - - - +
198B ASP* 3.5 6.6 - - - +
199B THR* 2.8 41.6 + - - +
201B LYS* 2.8 37.3 + - + -
239B CYS* 3.4 41.6 - - - +
240B GLN* 3.5 6.0 - - - +
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Residues in contact with TYR 192 (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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170B LEU* 3.5 23.0 - - + +
191B ASP* 1.3 93.5 + - - +
193B ASP* 1.3 92.8 + - - +
194B PRO* 3.9 16.8 + - + +
197B GLY* 3.9 7.0 - - - -
198B ASP* 3.7 40.2 - - - -
240B GLN* 4.5 1.0 + - - +
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Residues in contact with ASP 193 (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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195A ARG* 5.1 7.6 + - - -
191B ASP* 5.5 1.8 - - - +
192B TYR* 1.3 82.9 - - - +
194B PRO* 1.3 76.8 - - - +
195B ARG* 3.2 16.3 + - - +
196B GLN* 3.1 39.9 + - + +
197B GLY* 2.7 41.6 + - - +
199B THR* 5.2 4.7 - - + +
201B LYS* 6.3 1.1 - - - +
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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