Contacts of the strand formed by residues 257 - 264 (chain A) in PDB entry 5VGR
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 PHE 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A THR* 3.8 27.4 - - + -
170A GLN* 5.0 2.5 - - + -
186A LEU* 4.7 4.9 - - + -
189A PHE* 4.4 14.6 - + - -
203A LYS* 3.8 4.9 + - - +
205A PHE* 3.5 27.8 - + + -
206A GLN 3.4 10.5 - - - +
207A THR 4.0 4.3 - - - -
208A LEU* 3.6 55.0 - - + -
253A ILE* 3.2 15.6 + - + -
254A HIS* 3.5 21.1 + - - +
256A CYS* 1.3 92.7 - - + +
258A SER* 1.3 63.4 + - - +
259A ASP* 3.6 11.9 - - - +
260A VAL* 3.8 10.1 - - + +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LYS* 3.7 25.6 + - - +
205A PHE 3.1 17.8 + - - -
206A GLN* 3.0 18.8 + - - +
257A PHE* 1.3 73.5 - - - +
259A ASP* 1.3 72.1 + - - +
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Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLN 3.1 5.9 + - - +
207A THR* 3.3 24.9 + - + +
208A LEU 2.9 25.7 + - - -
257A PHE* 3.6 3.3 - - - +
258A SER* 1.3 90.7 + - - +
260A VAL* 1.3 63.4 + - - +
261A THR* 4.8 9.4 - - + +
307A MET* 5.3 5.0 - - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.3 8.1 - - + +
210A PHE* 3.8 28.5 - - + -
229A MET* 3.3 14.4 - - - +
232A LEU* 3.6 14.4 - - + +
236A LEU* 4.5 4.5 - - + -
253A ILE* 4.1 24.5 - - + +
254A HIS* 3.8 32.9 + - + +
257A PHE* 3.8 20.6 - - + +
259A ASP* 1.3 78.5 - - - +
261A THR* 1.3 63.0 + - - +
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Residues in contact with THR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A THR* 4.2 7.5 - - + +
208A LEU 2.9 8.7 + - - -
209A MET* 3.3 28.6 - - - +
210A PHE* 2.8 29.7 + - - -
225A LEU* 4.5 7.9 - - + -
229A MET* 3.4 20.2 - - + -
232A LEU* 4.0 3.1 - - - -
259A ASP* 4.8 10.8 - - + +
260A VAL* 1.3 82.2 - - - +
262A CYS* 1.3 64.1 + - - +
299A TYR* 4.2 14.9 + - - +
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Residues in contact with CYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ILE* 4.2 8.3 - - - -
209A MET* 4.5 2.0 - - - -
210A PHE* 3.2 22.9 - - + +
212A VAL* 3.9 11.7 - - - -
225A LEU* 3.6 19.6 - - - +
228A GLY* 3.4 36.5 - - - +
229A MET* 3.2 4.8 - - - +
231A PHE* 4.5 2.0 - - - -
232A LEU* 3.7 14.1 - - + -
261A THR* 1.3 80.2 + - - +
263A PHE* 1.3 63.0 + - - +
264A LEU* 3.7 23.1 - - - -
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Residues in contact with PHE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A MET* 4.3 15.9 - - + +
210A PHE 2.8 6.6 + - - +
211A LEU* 3.6 23.6 - - + +
212A VAL* 3.0 24.9 + - - +
224A GLY* 3.5 25.1 - - - -
225A LEU* 3.7 25.1 - - + -
262A CYS* 1.3 75.0 - - - +
264A LEU* 1.3 75.7 + - - +
265A LEU* 3.9 14.8 - - + -
292A GLN* 3.6 17.5 - - - -
295A ALA* 4.4 8.7 - - + -
296A LEU* 3.5 44.9 - - + -
299A TYR* 5.2 8.1 - + + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.8 19.5 - - + -
215A TRP* 3.5 46.2 - - + +
221A TYR* 3.6 16.6 - - + -
222A SER 3.5 19.5 - - - +
223A TYR* 3.4 8.4 - - - +
224A GLY* 2.7 35.7 + - - +
227A GLY 3.7 6.3 - - - +
228A GLY* 3.6 11.7 - - - +
231A PHE* 4.2 12.1 - - + -
262A CYS* 3.7 24.7 - - - -
263A PHE* 1.3 74.8 - - - +
265A LEU* 1.3 59.9 + - - +
266A PRO* 4.0 0.2 - - - +
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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