Contacts of the strand formed by residues 197 - 207 (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 GLY 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B TYR* 3.9 16.8 - - - -
193B ASP* 2.7 38.2 + - - +
194B PRO 4.4 2.1 + - - -
195B ARG 3.8 0.6 - - - -
196B GLN* 1.3 74.2 - - - +
198B ASP* 1.3 67.1 + - - -
199B THR* 3.4 7.1 + - - +
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Residues in contact with ASP 198 (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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164B LEU* 3.8 26.0 - - + +
170B LEU* 6.1 0.3 - - - +
190B ARG* 3.2 27.6 + - - +
191B ASP 3.5 7.0 - - - +
192B TYR* 3.7 22.1 - - - +
196B GLN 4.2 3.3 - - - +
197B GLY* 1.3 72.0 - - - -
199B THR* 1.3 66.0 + - - +
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Residues in contact with THR 199 (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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164B LEU* 4.5 7.4 - - - -
190B ARG* 3.5 9.2 - - - -
191B ASP* 2.8 52.4 + - - +
192B TYR* 4.4 1.6 + - - -
193B ASP* 5.2 3.0 - - + +
196B GLN* 4.1 31.4 - - + +
197B GLY 3.8 8.7 + - - +
198B ASP* 1.3 80.1 - - - +
200B VAL* 1.3 67.9 + - - +
201B LYS* 4.1 10.4 - - - -
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Residues in contact with VAL 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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160B GLU* 3.7 37.7 - - + +
163B LEU* 3.8 30.1 - - + -
164B LEU* 4.0 20.1 - - + +
188B SER* 4.1 0.2 - - - -
189B VAL 3.1 11.7 - - - +
190B ARG* 5.0 1.1 - - - -
199B THR* 1.3 83.6 - - - +
201B LYS* 1.3 82.1 + - - +
202B HIS* 3.7 25.6 + - + -
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Residues in contact with LYS 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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187B LEU 3.8 0.2 - - - +
188B SER* 3.3 4.3 - - - -
189B VAL 2.8 31.6 + - - +
191B ASP* 2.8 28.5 + - + +
193B ASP* 6.3 1.0 - - - +
196B GLN* 6.1 1.6 - - - -
199B THR* 4.1 14.8 - - - -
200B VAL* 1.3 81.6 - - - +
202B HIS* 1.3 66.6 + - - +
203B TYR* 3.9 19.7 - - + -
239B CYS* 3.7 27.2 - - + +
525B SER 5.9 0.2 - - - +
526B GLN 5.7 0.2 - - - -
528B GLU* 3.1 33.2 + - + +
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Residues in contact with HIS 202 (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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156B ARG* 3.5 35.9 - - + +
159B ALA* 4.4 1.8 - - + -
160B GLU* 3.4 26.3 + - + +
176B ARG* 3.1 10.1 + - - +
187B LEU 3.1 4.7 - - - +
188B SER* 2.6 28.3 + - - -
200B VAL* 3.7 21.8 - - + +
201B LYS* 1.3 78.8 - - - +
203B TYR* 1.3 67.2 + - - +
526B GLN 3.7 19.2 + - - +
527B PTR 3.4 25.5 - - + -
528B GLU* 2.9 29.3 + - - +
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Residues in contact with TYR 203 (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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186B SER* 3.3 5.5 - - - -
187B LEU* 2.8 51.9 + - + +
189B VAL* 4.4 11.7 - - + -
201B LYS* 3.9 19.3 - - + -
202B HIS* 1.3 76.0 - - - +
204B LYS* 1.3 62.8 + - - +
215B ILE* 4.0 23.1 - - + -
237B GLY 4.9 1.7 + - - -
238B LEU* 3.6 33.0 - - + -
239B CYS* 3.0 37.5 + - - +
527B PTR 4.0 4.7 - - - -
528B GLU* 3.4 36.2 - - + +
530B ILE* 3.8 24.0 - - + -
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Residues in contact with LYS 204 (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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489A GLU* 3.9 36.6 - - + +
493A ASN* 4.2 3.7 - - - +
178B SER* 4.7 1.1 - - - +
180B THR* 2.6 30.7 + - - -
181B THR* 3.9 13.3 + - - +
185B TYR 4.2 1.1 - - - +
186B SER* 3.9 5.8 - - - +
203B TYR* 1.3 72.4 - - - +
205B ILE* 1.3 63.6 + - - +
206B ARG* 3.8 28.1 + - - +
214B TYR 4.0 0.2 - - - +
215B ILE* 3.8 22.5 - - - +
527B PTR 2.9 60.6 + - + +
528B GLU 4.8 4.7 + - - +
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Residues in contact with ILE 205 (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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175B ILE* 4.1 26.5 - - + -
184B SER* 4.3 8.7 - - - -
185B TYR* 3.1 36.5 + - + +
186B SER 4.1 16.4 - - - -
187B LEU* 4.1 12.6 - - + +
204B LYS* 1.3 74.9 - - - +
206B ARG* 1.3 65.4 + - - +
207B THR* 3.8 3.5 + - - +
213B PHE* 3.7 37.0 - - + -
214B TYR 3.5 7.9 - - - +
215B ILE* 3.8 15.5 - - + -
224B LEU* 4.2 9.4 - - + -
227B LEU* 4.0 13.9 - - + -
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Residues in contact with ARG 206 (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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483A ARG* 2.8 32.8 - - - +
489A GLU* 2.6 46.8 + - - +
181B THR* 5.5 3.6 + - - +
184B SER* 5.9 0.7 - - - -
204B LYS* 3.9 24.9 + - - +
205B ILE* 1.3 73.8 - - - +
207B THR* 1.3 63.0 + - - +
213B PHE* 3.3 5.0 - - - -
214B TYR* 2.9 76.3 + - + +
215B ILE 5.1 4.0 + - - +
529B GLU* 6.1 4.2 - - - +
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Residues in contact with THR 207 (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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183B GLY 5.1 3.8 - - - +
184B SER* 4.4 17.5 + - - +
185B TYR* 5.0 7.4 - - + -
205B ILE 4.5 6.3 - - - +
206B ARG* 1.3 77.5 - - - +
208B LEU* 1.3 73.1 + - - +
211B GLY* 5.2 2.5 - - - -
212B GLY 3.3 7.6 - - - -
213B PHE* 3.4 31.9 - - + -
214B TYR* 4.1 5.7 + - - -
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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